From aa72aab9d2a892a4d6baf5b2308cadbae0af49a5 Mon Sep 17 00:00:00 2001
From: PauAndrio <andriopau@gmail.com>
Date: Fri, 15 Nov 2024 12:15:46 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
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MIME-Version: 1.0
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---
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     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -270,13 +270,13 @@ <h2>
     <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -386,7 +386,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_canonicalag_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_canonicalag_py.html b/coverage/z_159731231e5c9c9d_canonicalag_py.html
index 4be832e5..790fbdff 100644
--- a/coverage/z_159731231e5c9c9d_canonicalag_py.html
+++ b/coverage/z_159731231e5c9c9d_canonicalag_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -204,7 +204,7 @@ <h2>
     <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -278,13 +278,13 @@ <h2>
     <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -401,7 +401,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d_puckering_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_puckering_py.html b/coverage/z_159731231e5c9c9d_puckering_py.html
index c8958e9f..15247095 100644
--- a/coverage/z_159731231e5c9c9d_puckering_py.html
+++ b/coverage/z_159731231e5c9c9d_puckering_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -196,7 +196,7 @@ <h2>
     <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -263,13 +263,13 @@ <h2>
     <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="key">def</span> <span class="nam">get_xlabels</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">strand1</span><span class="op">,</span> <span class="nam">strand2</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># get list of tetramers, except first and last two bases</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsW[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsW</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">labelsW</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">labelsW</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="nam">list</span><span class="op">(</span><span class="nam">strand2</span><span class="op">)</span><span class="op">[</span><span class="op">:</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[0]}5'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="str">f"{labelsC[-1]}3'"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i}-{j}"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">}</span><span class="fst">5'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">labelsC</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">3'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">}</span><span class="fst">-</span><span class="op">{</span><span class="nam">j</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span><span class="op">,</span> <span class="nam">j</span> <span class="key">in</span> <span class="nam">zip</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">,</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">labelsC</span><span class="op">)</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="op">-</span><span class="num">1</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">labelsC</span> <span class="op">=</span> <span class="op">[</span><span class="nam">labelsC</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -370,7 +370,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91___init___py.html b/coverage/z_3afbcd666ed82c91___init___py.html
index d88324a0..d3e1d708 100644
--- a/coverage/z_3afbcd666ed82c91___init___py.html
+++ b/coverage/z_3afbcd666ed82c91___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -95,7 +95,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_averages_py.html b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
index bd28982a..a87e09fc 100644
--- a/coverage/z_3afbcd666ed82c91_dna_averages_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -226,7 +226,7 @@ <h2>
     <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -242,12 +242,12 @@ <h2>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{sequence[i:i+1+self.baselen]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">-</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="key">while</span> <span class="nam">any</span><span class="op">(</span><span class="nam">pd</span><span class="op">.</span><span class="nam">Index</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">.</span><span class="nam">duplicated</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -269,19 +269,19 @@ <h2>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">means</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair "</span> <span class="str">f"{'Step' if self.baselen==1 else ''}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair "</span> <span class="fst">f"</span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="str">"Base Pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="str">f"{'Step' if self.baselen==1 else ''} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="str">f"Helical Parameter: {self.helpar_name.capitalize()}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="fst">f"</span><span class="fst">Helical Parameter: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                <span class="str">f"Base Pair {'Step' if self.baselen==1 else ''}"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                <span class="fst">f"</span><span class="fst">Base Pair </span><span class="op">{</span><span class="str">'Step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst">"</span><span class="op">:</span> <span class="nam">xlabels</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                <span class="str">"mean"</span><span class="op">:</span> <span class="nam">means</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                <span class="str">"std"</span><span class="op">:</span> <span class="nam">stds</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
@@ -369,7 +369,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_bimodality_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
index 2cd4366d..02ffab01 100644
--- a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -208,7 +208,7 @@ <h2>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># get  unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_angular</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -300,8 +300,8 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">vlines</span><span class="op">(</span><span class="nam">info</span><span class="op">[</span><span class="str">'mean2'</span><span class="op">]</span><span class="op">,</span> <span class="num">0</span><span class="op">,</span> <span class="nam">ylim</span><span class="op">,</span> <span class="nam">colors</span><span class="op">=</span><span class="str">"r"</span><span class="op">,</span> <span class="nam">linestyles</span><span class="op">=</span><span class="str">"dashed"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">legend</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="str">f"Distribution of {self.helpar_name} states"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">xlabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">title</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Distribution of </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst"> states</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">output_jpg_path</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -426,7 +426,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
index 8895b8c9..c017bfff 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -185,7 +185,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># get base length from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -229,7 +229,7 @@ <h2>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 1}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -237,7 +237,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">elif</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span> <span class="key">and</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">hp_basepairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">cols</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">0</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence)}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -254,7 +254,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">            <span class="com"># create indices list</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">indices</span> <span class="op">=</span> <span class="nam">cols</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="com"># create subunits list from cols</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i-1:i+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">-</span><span class="num">1</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="com"># clean subunits (leave only basepairs)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">            <span class="nam">pattern</span> <span class="op">=</span> <span class="nam">re</span><span class="op">.</span><span class="nam">compile</span><span class="op">(</span><span class="str">r"\d+_[A-Za-z]{2}"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="com"># get removed items</span>&nbsp;</span><span class="r"></span></p>
@@ -277,7 +277,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="com"># trick for getting the index column from the .ser file</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">            <span class="nam">indices</span><span class="op">.</span><span class="nam">insert</span><span class="op">(</span><span class="num">0</span><span class="op">,</span> <span class="num">0</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">            <span class="com"># create subunits list from cols</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1+self.baselen]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">            <span class="nam">subunits</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">+</span><span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">cols</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">        <span class="com"># read input .ser file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">        <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">read_series</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
@@ -293,64 +293,64 @@ <h2>
     <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="com"># unstack columns to prevent errors from repeated base pairs</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="nam">column_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="op">[</span><span class="nam">col</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">unstack</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">dropna</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">reset_index</span><span class="op">(</span><span class="nam">drop</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">name</span> <span class="op">=</span> <span class="nam">col</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Computing base number {col}..."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Computing base number </span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">...</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">            <span class="com"># column series</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="str">f"series_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">            <span class="nam">series_colfn</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">series_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">            <span class="nam">column_data</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">reduced_data</span> <span class="op">=</span> <span class="nam">column_data</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="op">:</span><span class="op">:</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stride</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">plot</span><span class="op">(</span><span class="nam">reduced_data</span><span class="op">.</span><span class="nam">index</span><span class="op">,</span> <span class="nam">reduced_data</span><span class="op">.</span><span class="nam">to_numpy</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Time (Snapshots)"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="str">f"Helical Parameter vs Time: {self.helpar_name.capitalize()} "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">                <span class="fst">f"</span><span class="fst">Helical Parameter vs Time: </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">                <span class="str">"(base pair "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="str">f"{'step' if self.baselen==1 else ''} {col})"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="str">'step'</span> <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">baselen</span><span class="op">==</span><span class="num">1</span> <span class="key">else</span> <span class="str">''</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t237" href="#t237">237</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t238" href="#t238">238</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t239" href="#t239">239</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t240" href="#t240">240</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t241" href="#t241">241</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{series_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">series_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">            <span class="com"># columns histogram</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="str">f"hist_{self.helpar_name}_{col}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">            <span class="nam">hist_colfn</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">hist_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">col</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">            <span class="nam">fig</span><span class="op">,</span> <span class="nam">axs</span> <span class="op">=</span> <span class="nam">plt</span><span class="op">.</span><span class="nam">subplots</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="num">1</span><span class="op">,</span> <span class="nam">dpi</span><span class="op">=</span><span class="num">300</span><span class="op">,</span> <span class="nam">tight_layout</span><span class="op">=</span><span class="key">True</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">            <span class="nam">ybins</span><span class="op">,</span> <span class="nam">x</span><span class="op">,</span> <span class="nam">_</span> <span class="op">=</span> <span class="nam">axs</span><span class="op">.</span><span class="nam">hist</span><span class="op">(</span><span class="nam">column_data</span><span class="op">,</span> <span class="nam">bins</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">bins</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">            <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">:</span> <span class="nam">x</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="str">"density"</span><span class="op">:</span> <span class="nam">ybins</span><span class="op">}</span><span class="op">)</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">                <span class="nam">index</span><span class="op">=</span><span class="key">False</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">            <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.csv"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">"Density"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">            <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">            <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">                <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">            <span class="com"># save plot</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">            <span class="nam">zf</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="str">f"{hist_colfn}.jpg"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">                <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">                <span class="nam">arcname</span><span class="op">=</span><span class="fst">f"</span><span class="op">{</span><span class="nam">hist_colfn</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">            <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">            <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="nam">zf</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -424,7 +424,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91_dna_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
index 0c3418c5..c43ea1e7 100644
--- a/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
+++ b/coverage/z_3afbcd666ed82c91_dna_timeseries_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -187,26 +187,26 @@ <h2>
     <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># Check that the type is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="op">[</span><span class="str">"series"</span><span class="op">,</span> <span class="str">"hist"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Type {self.type} not valid. Valid types are: series, hist."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Type </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst"> not valid. Valid types are: series, hist.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># Check that the parameter is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Parameter {self.parameter} not valid. Valid parameters are: {constants.helical_parameters}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Parameter </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span><span class="op">}</span><span class="fst"> not valid. Valid parameters are: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="com"># Check that the sequence is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">pattern</span> <span class="op">=</span> <span class="str">r'^[ACGT]+$'</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">pattern</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Sequence {self.sequence} not valid. Only 'A', 'C', 'G' or 'T' bases allowed."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Sequence </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst"> not valid. Only 'A', 'C', 'G' or 'T' bases allowed.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># Check that the index is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">index</span> <span class="op">&lt;</span> <span class="num">1</span> <span class="key">or</span> <span class="nam">self</span><span class="op">.</span><span class="nam">index</span> <span class="op">>=</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">1</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Index {self.index} not valid. It should be between 0 and {len(self.sequence) - 2}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Index </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">}</span><span class="fst"> not valid. It should be between 0 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -214,39 +214,39 @@ <h2>
     <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">bp</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">-</span><span class="num">1</span><span class="op">]</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># Get the filename</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="str">f"{self.type}_{self.parameter}_{self.index}_{bp}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">csv_file</span> <span class="op">=</span> <span class="str">f"{filename}.csv"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">jpg_file</span> <span class="op">=</span> <span class="str">f"{filename}.jpg"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">parameter</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">index</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">bp</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">csv_file</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst">.csv</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="nam">jpg_file</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst">.jpg</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># Unzip the file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_zip_file"</span><span class="op">]</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="com"># Check if the csv file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="key">if</span> <span class="nam">csv_file</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{csv_file} exists, copying into {self.stage_io_dict["out"]["output_path_csv"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">csv_file</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_csv"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">csv_file</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_csv"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {csv_file} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">csv_file</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="com"># Check if the jpg file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="key">if</span> <span class="nam">jpg_file</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{jpg_file} exists, copying into {self.stage_io_dict["out"]["output_path_jpg"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">jpg_file</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_jpg"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">jpg_file</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path_jpg"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {jpg_file} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">jpg_file</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="com"># Write the list of files</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="key">for</span> <span class="nam">name</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f"{name}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">name</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
@@ -322,7 +322,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc___init___py.html b/coverage/z_64e03be4370b7ecc___init___py.html
index aeca703c..540944d2 100644
--- a/coverage/z_64e03be4370b7ecc___init___py.html
+++ b/coverage/z_64e03be4370b7ecc___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -98,7 +98,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intrabpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
index a1937704..adfdff4a 100644
--- a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -242,15 +242,15 @@ <h2>
     <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">propel</span> <span class="op">=</span> <span class="nam">propel</span><span class="op">[</span><span class="nam">propel</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">opening</span> <span class="op">=</span> <span class="nam">opening</span><span class="op">[</span><span class="nam">opening</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">shear</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
@@ -288,7 +288,7 @@ <h2>
     <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">/</span><span class="op">{</span><span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -464,7 +464,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intrahpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
index cf2a21c0..67d0d30a 100644
--- a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -295,7 +295,7 @@ <h2>
     <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_matrix</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -305,7 +305,7 @@ <h2>
     <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.base}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="fst">f"</span><span class="fst">for Base Pair Step \'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">base</span><span class="op">}</span><span class="fst">\'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -432,7 +432,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc_intraseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
index 89bb487b..292003f8 100644
--- a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
+++ b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -201,7 +201,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -225,9 +225,9 @@ <h2>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+1]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
@@ -245,7 +245,7 @@ <h2>
     <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_data</span><span class="op">[</span><span class="nam">corr_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -255,7 +255,7 @@ <h2>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="fst">f"</span><span class="fst">for Helical Parameter '</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -350,7 +350,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4___init___py.html b/coverage/z_74fa14c6d0e940a4___init___py.html
index c6c8efd4..b074a390 100644
--- a/coverage/z_74fa14c6d0e940a4___init___py.html
+++ b/coverage/z_74fa14c6d0e940a4___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -95,7 +95,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
index 9cb6cbeb..778e49b0 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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         <aside class="hidden">
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@@ -205,8 +205,8 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">                <span class="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"Strand  1"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">" "</span><span class="op">)</span><span class="op">[</span><span class="op">-</span><span class="num">1</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="str">f"using sequence {self.sequence} "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                        <span class="str">f"from {self.stage_io_dict['in']['input_lis_file']}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                        <span class="fst">f"</span><span class="fst">using sequence </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst"> </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                        <span class="fst">f"</span><span class="fst">from </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_lis_file'</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                        <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># define temporary file name</span>&nbsp;</span><span class="r"></span></p>
@@ -218,29 +218,29 @@ <h2>
     <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">            <span class="str">"  lis=canal_output,"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  seq=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">bases</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Adding null values string specification to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  nastr={self.nastr},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  nastr=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">nastr</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="str">f"  cormin={self.cormin},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="str">f"  lev1={self.lev1},lev2={self.lev2},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">f"  histo={self.histo},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">f"  series={self.series},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">f"  corr={self.corr},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  cormin=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">cormin</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  lev1=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">lev1</span><span class="op">}</span><span class="fst">,lev2=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">lev2</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  histo=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">histo</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  series=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">series</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  corr=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">corr</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"{tmp_cda_path} {self.sequence}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">tmp_cda_path</span><span class="op">}</span><span class="fst"> </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">"!"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -329,7 +329,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
index 96df74a3..998837ea 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -217,7 +217,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">ion_type_options</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="op">(</span><span class="str">"Invalid value for property type! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                              <span class="str">f"Option include: {ion_type_options}"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                              <span class="fst">f"</span><span class="fst">Option include: </span><span class="op">{</span><span class="nam">ion_type_options</span><span class="op">}</span><span class="fst">"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># define temporary file names</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="nam">input_cdi_file</span> <span class="op">=</span> <span class="nam">Path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_cdi_path'</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</span>&nbsp;</span><span class="r"></span></p>
@@ -230,29 +230,29 @@ <h2>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="str">"  lis=canion_output,"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="str">f"  dat={input_cdi_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="str">f"  axfrm={input_afr_file[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="str">f"  solute={input_avg_struc[:-4]},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="str">f"  type={self.type},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="str">f"  dlow={self.dlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="str">f"  dhig={self.dhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="str">f"  rlow={self.rlow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="str">f"  rhig={self.rhig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="str">f"  alow={self.alow},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="str">f"  ahig={self.ahig},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="str">f"  itst={self.itst},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="str">f"  itnd={self.itnd},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="str">f"  itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="str">f"  rmsf={self.rmsf},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="str">f"  circ={self.circ},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dat=</span><span class="op">{</span><span class="nam">input_cdi_file</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  axfrm=</span><span class="op">{</span><span class="nam">input_afr_file</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  solute=</span><span class="op">{</span><span class="nam">input_avg_struc</span><span class="op">[</span><span class="op">:</span><span class="op">-</span><span class="num">4</span><span class="op">]</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  type=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dlow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">dlow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  dhig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">dhig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rlow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rlow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rhig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rhig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  alow=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">alow</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  ahig=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">ahig</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  rmsf=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">rmsf</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  circ=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">circ</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">bases</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending sequence of bases to be searched to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">f"  seq={self.bases},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="fst">f"</span><span class="fst">  seq=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">bases</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"&amp;end"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"!"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -341,7 +341,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_biobb_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
index b1c18b93..a29dc6aa 100644
--- a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
+++ b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_74fa14c6d0e940a4_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -216,7 +216,7 @@ <h2>
     <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">range1_end</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">":"</span><span class="op">)</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">s2start</span> <span class="op">=</span> <span class="nam">range1_end</span> <span class="op">+</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">s2end</span> <span class="op">=</span> <span class="num">2</span> <span class="op">*</span> <span class="nam">range1_end</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="str">f"{s2end}:{s2start}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span> <span class="op">=</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">s2end</span><span class="op">}</span><span class="fst">:</span><span class="op">{</span><span class="nam">s2start</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># check standard library files location if not provided</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="key">is</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
@@ -228,14 +228,14 @@ <h2>
     <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                    <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">list</span><span class="op">(</span><span class="nam">curves_aux_path</span><span class="op">.</span><span class="nam">glob</span><span class="op">(</span><span class="str">"standard_*.lib"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">!=</span> <span class="num">3</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                        <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                            <span class="str">"One or all standard library files "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                            <span class="str">f"missing from {curves_aux_path}! "</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                            <span class="fst">f"</span><span class="fst">missing from </span><span class="op">{</span><span class="nam">curves_aux_path</span><span class="op">}</span><span class="fst">! </span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">                            <span class="str">"Check files standard_b.lib, "</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                            <span class="str">"standard_s.lib and standard_i.lib exist."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                    <span class="nam">self</span><span class="op">.</span><span class="nam">stdlib_path</span> <span class="op">=</span> <span class="nam">curves_aux_path</span> <span class="op">/</span> <span class="str">"standard"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                    <span class="key">raise</span> <span class="nam">FileNotFoundError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                        <span class="str">".curvesplus directory not found in "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                        <span class="str">f"{os.getenv('CONDA_PREFIX')} !"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                        <span class="fst">f"</span><span class="op">{</span><span class="nam">os</span><span class="op">.</span><span class="nam">getenv</span><span class="op">(</span><span class="str">'CONDA_PREFIX'</span><span class="op">)</span><span class="op">}</span><span class="fst"> !</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">                        <span class="str">"Please indicate where standard_*.lib files are "</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                        <span class="str">"located with the stdlib_path property."</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="com"># copy standard library files to temporary folder</span>&nbsp;</span><span class="r"></span></p>
@@ -267,30 +267,30 @@ <h2>
     <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="str">f"{self.binary_path} &lt;&lt;! "</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">}</span><span class="fst"> &lt;&lt;! </span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">            <span class="str">"&amp;inp"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="str">f"  file={tmp_struc_input},"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  file=</span><span class="op">{</span><span class="nam">tmp_struc_input</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'in'</span><span class="op">]</span><span class="op">[</span><span class="str">'input_top_path'</span><span class="op">]</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">            <span class="com"># add topology file if needed</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Appending provided topology to command'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">            <span class="nam">instructions</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                <span class="str">f"  ftop={tmp_top_input},"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">                <span class="fst">f"</span><span class="fst">  ftop=</span><span class="op">{</span><span class="nam">tmp_top_input</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">        <span class="com"># create intructions</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">        <span class="nam">instructions</span> <span class="op">=</span> <span class="nam">instructions</span> <span class="op">+</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">            <span class="str">"  lis='curves_output',"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="str">f"  lib={relative_lib_path},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="str">f"  ions={self.ions},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="str">f"  test={self.test},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="str">f"  line={self.line},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="str">f"  fit={self.fit},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="str">f"  axfrm={self.axfrm},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="str">f"  itst={self.itst},itnd={self.itnd},itdel={self.itdel},"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  lib=</span><span class="op">{</span><span class="nam">relative_lib_path</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  ions=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">ions</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  test=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">test</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  line=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">line</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  fit=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">fit</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  axfrm=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">axfrm</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="fst">f"</span><span class="fst">  itst=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itst</span><span class="op">}</span><span class="fst">,itnd=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itnd</span><span class="op">}</span><span class="fst">,itdel=</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">itdel</span><span class="op">}</span><span class="fst">,</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="str">"&amp;end"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="str">"2 1 -1 0 0"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="str">f"{self.s1range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="str">f"{self.s2range}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">s1range</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">            <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">s2range</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">            <span class="str">"!"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">"\n"</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">instructions</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
@@ -393,7 +393,7 @@ <h2>
             <a class="nav" href="z_74fa14c6d0e940a4_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
index 887a829f..7cb89076 100644
--- a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
+++ b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -197,7 +197,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="com"># Check that the type is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">type</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">extensions</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Type {self.type} not valid. Valid types are: {', '.join(extensions.keys())}."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Type </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">}</span><span class="fst"> not valid. Valid types are: </span><span class="op">{</span><span class="str">', '</span><span class="op">.</span><span class="nam">join</span><span class="op">(</span><span class="nam">extensions</span><span class="op">.</span><span class="nam">keys</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">}</span><span class="fst">.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">                   <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">            <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -207,7 +207,7 @@ <h2>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="com"># Check that the correlation is valid</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">pattern</span> <span class="op">=</span> <span class="str">r'\d+_\d+'</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="nam">re</span><span class="op">.</span><span class="nam">match</span><span class="op">(</span><span class="nam">pattern</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Correlation {self.correlation} not valid. It should match the pattern &lt;number_number>."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Correlation </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span><span class="op">}</span><span class="fst"> not valid. It should match the pattern &lt;number_number>.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">sufix</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">correlation</span>&nbsp;</span><span class="r"></span></p>
@@ -219,32 +219,32 @@ <h2>
     <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">                                        <span class="str">"opening"</span><span class="op">,</span> <span class="str">"phaseC"</span><span class="op">,</span> <span class="str">"phaseW"</span><span class="op">,</span> <span class="str">"propel"</span><span class="op">,</span> <span class="str">"reg"</span><span class="op">,</span> <span class="str">"rise"</span><span class="op">,</span> <span class="str">"roll"</span><span class="op">,</span> <span class="str">"shear"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">                                        <span class="str">"shift"</span><span class="op">,</span> <span class="str">"slide"</span><span class="op">,</span> <span class="str">"stagger"</span><span class="op">,</span> <span class="str">"stretch"</span><span class="op">,</span> <span class="str">"tbend"</span><span class="op">,</span> <span class="str">"tilt"</span><span class="op">,</span> <span class="str">"tip"</span><span class="op">,</span> <span class="str">"twist"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">                                        <span class="str">"xdisp"</span><span class="op">,</span> <span class="str">"ydisp"</span><span class="op">,</span> <span class="str">"zetaC"</span><span class="op">,</span> <span class="str">"zetaW"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"Parameter {self.helpar_name} not valid. Valid parameters are: alphaC, alphaW, ampC, ampW, ax-bend, betaC, betaW, buckle, chiC, chiW, curv, deltaC, deltaW, epsilC, epsilW, gammaC, gammaW, h-ris, h-twi, inclin, majd, majw, mind, minw, opening, phaseC, phaseW, propel, reg, rise, roll, shear, shift, slide, stagger, stretch, tbend, tilt, tip, twist, xdisp, ydisp, zetaC, zetaW."</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Parameter </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst"> not valid. Valid parameters are: alphaC, alphaW, ampC, ampW, ax-bend, betaC, betaW, buckle, chiC, chiW, curv, deltaC, deltaW, epsilC, epsilW, gammaC, gammaW, h-ris, h-twi, inclin, majd, majw, mind, minw, opening, phaseC, phaseW, propel, reg, rise, roll, shear, shift, slide, stagger, stretch, tbend, tilt, tip, twist, xdisp, ydisp, zetaC, zetaW.</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="nam">sufix</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># Generate the filename</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="str">f"canal_output_{sufix}.{extensions[self.type]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="nam">filename</span> <span class="op">=</span> <span class="fst">f"</span><span class="fst">canal_output_</span><span class="op">{</span><span class="nam">sufix</span><span class="op">}</span><span class="fst">.</span><span class="op">{</span><span class="nam">extensions</span><span class="op">[</span><span class="nam">self</span><span class="op">.</span><span class="nam">type</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="com"># Unzip the file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="key">with</span> <span class="nam">zipfile</span><span class="op">.</span><span class="nam">ZipFile</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_zip_file"</span><span class="op">]</span><span class="op">,</span> <span class="str">'r'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">zip_ref</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="com"># Check if the file exists in the zip file</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">            <span class="key">if</span> <span class="nam">filename</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">                <span class="com"># Extract the file</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f'{filename} exists, copying into {self.stage_io_dict["out"]["output_path"]}.'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f'</span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst"> exists, copying into </span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">}</span><span class="fst">.</span><span class="fst">'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">                       <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">                <span class="key">with</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">open</span><span class="op">(</span><span class="nam">filename</span><span class="op">)</span> <span class="key">as</span> <span class="nam">source</span><span class="op">,</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"wb"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">target</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">                    <span class="nam">shutil</span><span class="op">.</span><span class="nam">copyfileobj</span><span class="op">(</span><span class="nam">source</span><span class="op">,</span> <span class="nam">target</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">f"File {filename} not found in the zip file."</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="fst">f"</span><span class="fst">File </span><span class="op">{</span><span class="nam">filename</span><span class="op">}</span><span class="fst"> not found in the zip file.</span><span class="fst">"</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">global_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                <span class="nam">exit</span><span class="op">(</span><span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="com"># Write the list of files</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_list_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span> <span class="key">as</span> <span class="nam">f</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="key">for</span> <span class="nam">name</span> <span class="key">in</span> <span class="nam">zip_ref</span><span class="op">.</span><span class="nam">namelist</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">f"{name}\n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">                        <span class="nam">f</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">name</span><span class="op">}</span><span class="fst">\n</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="com"># self.run_biobb()</span>&nbsp;</span><span class="r"></span></p>
@@ -315,7 +315,7 @@ <h2>
             <a class="nav" href="z_3afbcd666ed82c91___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_76997f7c8cf1ed45___init___py.html b/coverage/z_76997f7c8cf1ed45___init___py.html
index ee138c26..f578b756 100644
--- a/coverage/z_76997f7c8cf1ed45___init___py.html
+++ b/coverage/z_76997f7c8cf1ed45___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -99,7 +99,7 @@ <h2>
             <a class="nav" href="z_159731231e5c9c9d___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
index 741daa9f..bb41cdb1 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -111,7 +111,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
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 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
index e838c72d..5a082aba 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canal_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -113,7 +113,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canion_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
index f901db39..188e27b8 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_canion_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -111,7 +111,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_curves_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
index 237d1f3c..1b9dce5a 100644
--- a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
+++ b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -113,7 +113,7 @@ <h2>
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_833b0317e3c43dca___init___py.html b/coverage/z_833b0317e3c43dca___init___py.html
index ed2e63cb..3671ebdb 100644
--- a/coverage/z_833b0317e3c43dca___init___py.html
+++ b/coverage/z_833b0317e3c43dca___init___py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_833b0317e3c43dca_common_py.html b/coverage/z_833b0317e3c43dca_common_py.html
index 08fe98b3..19e67f5d 100644
--- a/coverage/z_833b0317e3c43dca_common_py.html
+++ b/coverage/z_833b0317e3c43dca_common_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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@@ -119,7 +119,7 @@ <h2>
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+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_833b0317e3c43dca_constants_py.html b/coverage/z_833b0317e3c43dca_constants_py.html
index 7ac07e90..72982e32 100644
--- a/coverage/z_833b0317e3c43dca_constants_py.html
+++ b/coverage/z_833b0317e3c43dca_constants_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_loader_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
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+            created at 2024-11-15 12:15 +0000
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index 79307e36..d5eb737e 100644
--- a/coverage/z_833b0317e3c43dca_loader_py.html
+++ b/coverage/z_833b0317e3c43dca_loader_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_833b0317e3c43dca_transform_py.html b/coverage/z_833b0317e3c43dca_transform_py.html
index 812c3e68..e88ddd7f 100644
--- a/coverage/z_833b0317e3c43dca_transform_py.html
+++ b/coverage/z_833b0317e3c43dca_transform_py.html
@@ -65,7 +65,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,7 +102,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_8a2a7f872cf1434f___init___py.html b/coverage/z_8a2a7f872cf1434f___init___py.html
index a82e8294..ba7a99ad 100644
--- a/coverage/z_8a2a7f872cf1434f___init___py.html
+++ b/coverage/z_8a2a7f872cf1434f___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -97,7 +97,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interbpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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diff --git a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
index 0ca5da7c..dc7a068e 100644
--- a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -242,15 +242,15 @@ <h2>
     <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">roll</span> <span class="op">=</span> <span class="nam">roll</span><span class="op">[</span><span class="nam">roll</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">            <span class="nam">twist</span> <span class="op">=</span> <span class="nam">twist</span><span class="op">[</span><span class="nam">twist</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">2</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">3</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="num">1</span><span class="op">,</span> <span class="nam">len</span><span class="op">(</span><span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span> <span class="op">+</span> <span class="num">1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">            <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{self.sequence[i:i+3]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">            <span class="nam">corr_index</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">3</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="com"># rename duplicated subunits</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">shift</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
@@ -288,7 +288,7 @@ <h2>
     <p class="run"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">                <span class="nam">method</span> <span class="op">=</span> <span class="str">"pearson"</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">            <span class="nam">corr_data</span> <span class="op">=</span> <span class="nam">ser1</span><span class="op">.</span><span class="nam">corrwith</span><span class="op">(</span><span class="nam">ser2_shifted</span><span class="op">,</span> <span class="nam">method</span><span class="op">=</span><span class="nam">method</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">            <span class="nam">corr_data</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="str">f"{ser1.name}/{ser2.name}"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">            <span class="nam">results</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">ser1</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">/</span><span class="op">{</span><span class="nam">ser2</span><span class="op">.</span><span class="nam">name</span><span class="op">}</span><span class="fst">"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">corr_data</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">result_df</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">.</span><span class="nam">from_dict</span><span class="op">(</span><span class="nam">results</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">        <span class="nam">result_df</span><span class="op">.</span><span class="nam">index</span> <span class="op">=</span> <span class="nam">corr_index</span>  <span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -468,7 +468,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interhpcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
index a5e6149a..a81c8b26 100644
--- a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -293,7 +293,7 @@ <h2>
     <p class="run"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">                    <span class="nam">j</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                    <span class="nam">i</span><span class="op">+</span><span class="num">.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="str">f"{corr_matrix[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_matrix</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -303,7 +303,7 @@ <h2>
     <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">corr_matrix</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="str">"Helical Parameter Correlation "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="str">f"for Base Pair Step \'{self.basepair}\'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">            <span class="fst">f"</span><span class="fst">for Base Pair Step \'</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">basepair</span><span class="op">}</span><span class="fst">\'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">'out'</span><span class="op">]</span><span class="op">[</span><span class="str">'output_jpg_path'</span><span class="op">]</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -430,7 +430,7 @@ <h2>
             <a class="nav" href="z_8a2a7f872cf1434f_interseqcorr_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
index e91134b4..bcee0a3a 100644
--- a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
+++ b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -205,7 +205,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -229,9 +229,9 @@ <h2>
     <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from strands</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{i+1}_{self.sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">labels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">i</span><span class="op">+</span><span class="num">1</span><span class="op">}</span><span class="fst">_</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span> <span class="op">=</span> <span class="nam">labels</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># make matrix</span>&nbsp;</span><span class="r"></span></p>
@@ -249,7 +249,7 @@ <h2>
     <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                    <span class="str">f"{corr_data[corr_data.columns[j]].iloc[i]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">corr_data</span><span class="op">[</span><span class="nam">corr_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">iloc</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -259,7 +259,7 @@ <h2>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">corr_data</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">labels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="str">f"for Helical Parameter '{self.helpar_name}'"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="str">"Base Pair Correlation "</span> <span class="fst">f"</span><span class="fst">for Helical Parameter '</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -354,7 +354,7 @@ <h2>
             <a class="nav" href="z_64e03be4370b7ecc___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_957b841f7413f0a1___init___py.html b/coverage/z_957b841f7413f0a1___init___py.html
index 7a6dfc08..59b84792 100644
--- a/coverage/z_957b841f7413f0a1___init___py.html
+++ b/coverage/z_957b841f7413f0a1___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -89,7 +89,7 @@ <h2>
             <a class="nav" href="z_020f76a90aa51c7b_test_bipopulations_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_97f47455ed834d2d_test_correlation_py.html b/coverage/z_97f47455ed834d2d_test_correlation_py.html
index 443d0222..1ea875fc 100644
--- a/coverage/z_97f47455ed834d2d_test_correlation_py.html
+++ b/coverage/z_97f47455ed834d2d_test_correlation_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
             <a class="nav" href="z_8030ef0ea5bfd6aa_test_canal_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
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 </footer>
diff --git a/coverage/z_9de9475b0a6fab52___init___py.html b/coverage/z_9de9475b0a6fab52___init___py.html
index 105106cc..eb5c0753 100644
--- a/coverage/z_9de9475b0a6fab52___init___py.html
+++ b/coverage/z_9de9475b0a6fab52___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -93,7 +93,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52_average_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
index 4538e77b..eacc031d 100644
--- a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -209,7 +209,7 @@ <h2>
     <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">                    <span class="str">"Helical parameter name is invalid! "</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="str">f"Options: {constants.helical_parameters}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">Options: </span><span class="op">{</span><span class="nam">constants</span><span class="op">.</span><span class="nam">helical_parameters</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="com"># get base length and unit from helical parameter name</span>&nbsp;</span><span class="r"></span></p>
@@ -224,7 +224,7 @@ <h2>
     <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="key">if</span> <span class="op">(</span><span class="nam">max</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">)</span> <span class="key">or</span> <span class="op">(</span><span class="nam">min</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                    <span class="str">f"seqpos values must be between 1 and {len(self.sequence) - 2}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                    <span class="fst">f"</span><span class="fst">seqpos values must be between 1 and </span><span class="op">{</span><span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">)</span> <span class="op">-</span> <span class="num">2</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">                <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="key">if</span> <span class="key">not</span> <span class="op">(</span><span class="nam">isinstance</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">,</span> <span class="nam">list</span><span class="op">)</span> <span class="key">and</span> <span class="nam">len</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">)</span> <span class="op">></span> <span class="num">1</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="key">raise</span> <span class="nam">ValueError</span><span class="op">(</span><span class="str">"seqpos must be a list of at least two integers"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -239,10 +239,10 @@ <h2>
     <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">            <span class="nam">ser_data</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">[</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">-</span><span class="num">1</span><span class="op">]</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="com"># discard first and last base(pairs) from sequence</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span><span class="op">[</span><span class="num">1</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">ser_data</span><span class="op">.</span><span class="nam">columns</span><span class="op">)</span><span class="op">)</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
     <p class="mis show_mis"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="nam">sequence</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">sequence</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="str">f"{sequence[i:i+2]}"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">xlabels</span> <span class="op">=</span> <span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">sequence</span><span class="op">[</span><span class="nam">i</span><span class="op">:</span><span class="nam">i</span><span class="op">+</span><span class="num">2</span><span class="op">]</span><span class="op">}</span><span class="fst">"</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">seqpos</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># calculate average stiffness</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">cov</span> <span class="op">=</span> <span class="nam">ser_data</span><span class="op">.</span><span class="nam">cov</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -255,15 +255,15 @@ <h2>
     <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticks</span><span class="op">(</span><span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">xlabels</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xlabel</span><span class="op">(</span><span class="str">"Sequence Base Pair"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="str">f"{self.helpar_name.capitalize()} ({self.hp_unit})"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_ylabel</span><span class="op">(</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst"> (</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">hp_unit</span><span class="op">}</span><span class="fst">)</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span> <span class="str">f"{self.helpar_name.capitalize()}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">            <span class="str">"Base Pair Helical Parameter Stiffness: "</span> <span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">.</span><span class="nam">capitalize</span><span class="op">(</span><span class="op">)</span><span class="op">}</span><span class="fst">"</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="com"># save table</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">dataset</span> <span class="op">=</span> <span class="nam">pd</span><span class="op">.</span><span class="nam">DataFrame</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="str">f"{self.helpar_name}_stiffness"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">            <span class="nam">data</span><span class="op">=</span><span class="nam">avg_stiffness</span><span class="op">,</span> <span class="nam">index</span><span class="op">=</span><span class="nam">xlabels</span><span class="op">,</span> <span class="nam">columns</span><span class="op">=</span><span class="op">[</span><span class="fst">f"</span><span class="op">{</span><span class="nam">self</span><span class="op">.</span><span class="nam">helpar_name</span><span class="op">}</span><span class="fst">_stiffness</span><span class="fst">"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="nam">dataset</span><span class="op">.</span><span class="nam">to_csv</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_csv_path"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
@@ -348,7 +348,7 @@ <h2>
             <a class="nav" href="z_9de9475b0a6fab52_basepair_stiffness_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
index 0f73f4fa..2ea58382 100644
--- a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
+++ b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -240,7 +240,7 @@ <h2>
     <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">                <span class="nam">axs</span><span class="op">.</span><span class="nam">text</span><span class="op">(</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">                    <span class="nam">j</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">                    <span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="str">f"{stiff_df[coordinates[j]].loc[coordinates[i]]:.2f}"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">                    <span class="fst">f"</span><span class="op">{</span><span class="nam">stiff_df</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">j</span><span class="op">]</span><span class="op">]</span><span class="op">.</span><span class="nam">loc</span><span class="op">[</span><span class="nam">coordinates</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span><span class="op">]</span><span class="op">:</span><span class="fst">.2f</span><span class="op">}</span><span class="fst">"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">                    <span class="nam">ha</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">                    <span class="nam">va</span><span class="op">=</span><span class="str">"center"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">                    <span class="nam">color</span><span class="op">=</span><span class="str">"w"</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
@@ -257,7 +257,7 @@ <h2>
     <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_xticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">columns</span><span class="op">,</span> <span class="nam">rotation</span><span class="op">=</span><span class="num">90</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticks</span><span class="op">(</span><span class="op">[</span><span class="nam">i</span> <span class="op">+</span> <span class="num">0.5</span> <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">)</span><span class="op">)</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_yticklabels</span><span class="op">(</span><span class="nam">stiff_df</span><span class="op">.</span><span class="nam">index</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="str">f"Stiffness Constants for Base Pair Step '{basepairname}'"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">axs</span><span class="op">.</span><span class="nam">set_title</span><span class="op">(</span><span class="fst">f"</span><span class="fst">Stiffness Constants for Base Pair Step '</span><span class="op">{</span><span class="nam">basepairname</span><span class="op">}</span><span class="fst">'</span><span class="fst">"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">tight_layout</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">fig</span><span class="op">.</span><span class="nam">savefig</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_jpg_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">format</span><span class="op">=</span><span class="str">"jpg"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">plt</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
@@ -381,7 +381,7 @@ <h2>
             <a class="nav" href="z_957b841f7413f0a1___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
index a171046a..a3edfea1 100644
--- a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
+++ b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -130,7 +130,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca___init___py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 12:10 +0000
+            created at 2024-11-15 12:15 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/biobb_dna.dna.dna_averages.report.html b/flake8/biobb_dna.dna.dna_averages.report.html
new file mode 100644
index 00000000..49419b66
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_averages.report.html
@@ -0,0 +1,83 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/dna/dna_averages.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.dna.dna_averages.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_averages.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="E225">
+               <span class="count sev-2">
+                  3
+               </span>
+               <strong>E225:</strong> missing whitespace around operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l190">
+                  <tt><i>190</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Sequence Base Pair &quot;</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l194">
+                  <tt><i>194</i>             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+               </a>
+            </li><li>
+               
+               <a href="biobb_dna.dna.dna_averages.source.html#l202">
+                  <tt><i>202</i>                 <span class="sa">f</span><span class="s2">&quot;Base Pair </span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">:</span> <span class="n">xlabels</span><span class="p">,</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.dna.dna_averages.source.html b/flake8/biobb_dna.dna.dna_averages.source.html
new file mode 100644
index 00000000..db5d0a64
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_averages.source.html
@@ -0,0 +1,890 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/dna/dna_averages.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.dna.dna_averages.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_averages.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the HelParAverages class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span> <span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> &nbsp;</tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span></tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">from</span> <span class="nn">biobb_common.configuration</span> <span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">from</span> <span class="nn">biobb_common.generic.biobb_object</span> <span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span> <span class="nn">biobb_common.tools.file_utils</span> <span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> &nbsp;</tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils</span> <span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.common</span> <span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.loader</span> <span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> &nbsp;</tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> &nbsp;</tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> <span class="k">class</span> <span class="nc">HelParAverages</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> <span class="sd">    | biobb_dna HelParAverages</span></tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="sd">    | Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="sd">    | Calculate average values for each base pair and save them in a .csv file.</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> &nbsp;</tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> <span class="sd">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> <span class="sd">        output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.csv&gt;`_. Accepted formats: csv (edam:format_3752).</span></tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">        output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/shift_avg.jpg&gt;`_. Accepted formats: jpg (edam:format_3579).</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *seqpos* option).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">            * **helpar_name** (*str*) - (Optional) helical parameter name.</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> &nbsp;</tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> <span class="sd">            from biobb_dna.dna.dna_averages import dna_averages</span></tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> &nbsp;</tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> <span class="sd">            prop = {</span></tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> <span class="sd">                &#39;helpar_name&#39;: &#39;twist&#39;,</span></tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">                &#39;seqpos&#39;: [1,2],</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> <span class="sd">                &#39;sequence&#39;: &#39;GCAT&#39;</span></tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            }</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> <span class="sd">            dna_averages(</span></tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">                input_ser_path=&#39;/path/to/twist.ser&#39;,</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                output_csv_path=&#39;/path/to/table/output.csv&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">                output_jpg_path=&#39;/path/to/table/output.jpg&#39;,</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> &nbsp;</tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> &nbsp;</tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> &nbsp;</tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i>     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i>         <span class="bp">self</span><span class="p">,</span></tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i>         <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i>         <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i>         <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>         <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i> &nbsp;</tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i> &nbsp;</tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>                 <span class="s2">&quot;input_ser_path&quot;</span><span class="p">:</span> <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>                 <span class="s2">&quot;output_csv_path&quot;</span><span class="p">:</span> <span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>                 <span class="s2">&quot;output_jpg_path&quot;</span><span class="p">:</span> <span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i> &nbsp;</tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="c1"># Properties specific for BB</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stride</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;stride&quot;</span><span class="p">,</span> <span class="mi">1000</span><span class="p">)</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>         <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;helpar_name&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i> &nbsp;</tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i> &nbsp;</tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i>     <span class="k">def</span> <span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParAverages &lt;dna.averages.HelParAverages&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i> &nbsp;</tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i> &nbsp;</tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i> &nbsp;</tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>         <span class="c1"># get helical parameter from filename if not specified</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i>             <span class="k">for</span> <span class="n">hp</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>                 <span class="n">ser_name</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">])</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i>                 <span class="k">if</span> <span class="n">hp</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">ser_name</span><span class="p">:</span></tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>                     <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">hp</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i>                     <span class="s2">&quot;Helical parameter name can&#39;t be inferred from file, &quot;</span></tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>                     <span class="s2">&quot;so it must be specified!&quot;</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>                     <span class="s2">&quot;Helical parameter name is invalid! &quot;</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>                     <span class="sa">f</span><span class="s2">&quot;Options: </span><span class="si">{</span><span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i> &nbsp;</tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i>         <span class="c1"># get base length and unit from helical parameter name</span></tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">1</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i>         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_singlebases</span><span class="p">:</span></tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Degrees&quot;</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Angstroms&quot;</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i> &nbsp;</tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="c1"># check seqpos</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">2</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>             <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="kc">None</span>  <span class="c1"># type: ignore</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i> &nbsp;</tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="c1"># read input .ser file</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>         <span class="n">ser_data</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>         <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>             <span class="n">ser_data</span> <span class="o">=</span> <span class="n">ser_data</span><span class="p">[</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]]</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="c1"># discard first and last base(pairs) from sequence</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i>             <span class="n">xlabels</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>                 <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span> <span class="o">-</span> <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>             <span class="n">xlabels</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i> &nbsp;</tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>         <span class="c1"># rename duplicated subunits</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>         <span class="k">while</span> <span class="nb">any</span><span class="p">(</span><span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="o">.</span><span class="n">duplicated</span><span class="p">()):</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i>             <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>                 <span class="n">name</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">duplicated</span> <span class="k">else</span> <span class="n">name</span> <span class="o">+</span> <span class="s2">&quot;_dup&quot;</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>                 <span class="k">for</span> <span class="n">duplicated</span><span class="p">,</span> <span class="n">name</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>                     <span class="n">pd</span><span class="o">.</span><span class="n">Index</span><span class="p">(</span><span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="o">.</span><span class="n">duplicated</span><span class="p">(),</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i> &nbsp;</tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>         <span class="c1"># write output files for all selected bases</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i>         <span class="n">means</span> <span class="o">=</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:</span> <span class="nb">len</span><span class="p">(</span><span class="n">xlabels</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>         <span class="n">stds</span> <span class="o">=</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">iloc</span><span class="p">[:</span> <span class="nb">len</span><span class="p">(</span><span class="n">xlabels</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i> &nbsp;</tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>         <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>         <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>         <span class="n">axs</span><span class="o">.</span><span class="n">errorbar</span><span class="p">(</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>             <span class="n">means</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">means</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span> <span class="n">yerr</span><span class="o">=</span><span class="n">stds</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span> <span class="n">marker</span><span class="o">=</span><span class="s2">&quot;o&quot;</span><span class="p">,</span> <span class="n">capsize</span><span class="o">=</span><span class="mi">5</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xticks</span><span class="p">(</span><span class="n">means</span><span class="o">.</span><span class="n">index</span><span class="p">)</span></tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xticklabels</span><span class="p">(</span><span class="n">xlabels</span><span class="p">,</span> <span class="n">rotation</span><span class="o">=</span><span class="mi">90</span><span class="p">)</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>190</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Sequence Base Pair &quot;</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>         <span class="n">axs</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="s2">&quot;Base Pair &quot;</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>194</i>             <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="sa">f</span><span class="s2">&quot;Helical Parameter: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>         <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_jpg_path&quot;</span><span class="p">],</span> <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i> &nbsp;</tt>
+            </div>
+            <div id="l199"
+               class="code sev- "><tt><i>199</i>         <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>         <span class="n">dataset</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>             <span class="p">{</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>202</i>                 <span class="sa">f</span><span class="s2">&quot;Base Pair </span><span class="si">{</span><span class="s1">&#39;Step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">:</span> <span class="n">xlabels</span><span class="p">,</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>                 <span class="s2">&quot;mean&quot;</span><span class="p">:</span> <span class="n">means</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i>                 <span class="s2">&quot;std&quot;</span><span class="p">:</span> <span class="n">stds</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">(),</span></tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>             <span class="p">}</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i>         <span class="n">dataset</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_csv_path&quot;</span><span class="p">],</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i> &nbsp;</tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>         <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i> &nbsp;</tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i> &nbsp;</tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">)])</span></tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i> &nbsp;</tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i> &nbsp;</tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i> &nbsp;</tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i> &nbsp;</tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i> <span class="k">def</span> <span class="nf">dna_averages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>     <span class="n">input_ser_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i>     <span class="n">output_csv_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i>     <span class="n">output_jpg_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParAverages &lt;dna.dna_averages.HelParAverages&gt;` class and</span></tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i> <span class="sd">    execute the :meth:`launch() &lt;dna.dna_averages.HelParAverages.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i> &nbsp;</tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>     <span class="k">return</span> <span class="n">HelParAverages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l235"
+               class="code sev- "><tt><i>235</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i> &nbsp;</tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i> &nbsp;</tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i> <span class="k">def</span> <span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Load helical parameter file and calculate average values for each base pair.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i> &nbsp;</tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>         <span class="s2">&quot;--input_ser_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Helical parameter input ser file path. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i>         <span class="s2">&quot;--output_csv_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output csv file. Accepted formats: csv.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>         <span class="s2">&quot;--output_jpg_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output jpg file. Accepted formats: jpg.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i> &nbsp;</tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i> &nbsp;</tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>     <span class="n">dna_averages</span><span class="p">(</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>         <span class="n">output_csv_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_csv_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>         <span class="n">output_jpg_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_jpg_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i> &nbsp;</tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i> &nbsp;</tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.dna.dna_timeseries.report.html b/flake8/biobb_dna.dna.dna_timeseries.report.html
new file mode 100644
index 00000000..9c998414
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_timeseries.report.html
@@ -0,0 +1,73 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>flake8 violations: biobb_dna/dna/dna_timeseries.py</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+<script>
+function bindHandler(link) {
+   var code = link.getAttribute('data-code');
+   var key = location.pathname + '#' + code;
+
+   var ul = link.parentNode.querySelector('.details');
+   if (sessionStorage[key] != 'open') {
+      ul.style.display = 'none';
+   }
+   link.addEventListener('click', function (event) {
+      if (!ul.style.display || ul.style.display == 'none') {
+         ul.style.display = 'block';
+         sessionStorage[key] = 'open';
+      } else {
+         ul.style.display = 'none';
+         sessionStorage[key] = 'closed';
+      }
+   });
+}
+
+window.addEventListener('DOMContentLoaded', function () {
+   var links = document.querySelectorAll('#index > li > a');
+   for (var i = 0; i < links.length; i++) {
+      bindHandler(links[i]);
+   }
+});
+</script>
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <p id="srclink">
+            <a title="View full annotated source"
+               href="biobb_dna.dna.dna_timeseries.source.html">
+               <img src="file.svg" alt="&#x2261;">
+            </a></p>
+         <h1>
+            <a href="index.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_timeseries.py
+            </a>
+         </h1>
+
+         <ul id="index">
+         
+         <li>
+            <a data-code="E225">
+               <span class="count sev-2">
+                  1
+               </span>
+               <strong>E225:</strong> missing whitespace around operator
+               
+            </a>
+            <ul class="details">
+            <li>
+               
+               <a href="biobb_dna.dna.dna_timeseries.source.html#l235">
+                  <tt><i>235</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">)&quot;</span></tt>
+               </a>
+            </li>
+            </ul>
+         </li>
+         
+         </ul>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/biobb_dna.dna.dna_timeseries.source.html b/flake8/biobb_dna.dna.dna_timeseries.source.html
new file mode 100644
index 00000000..2d47b578
--- /dev/null
+++ b/flake8/biobb_dna.dna.dna_timeseries.source.html
@@ -0,0 +1,1037 @@
+<!DOCTYPE html>
+<html>
+   <head>
+      <title>biobb_dna/dna/dna_timeseries.py - flake8 annotated source</title>
+      <meta http-equiv="Content-Type" value="text/html; charset=UTF-8">
+      <link rel="stylesheet" href="styles.css">
+   </head>
+   <body>
+      <div id="masthead" class="sev-2"></div>
+      <div id="page">
+         <h1>
+            <a href="biobb_dna.dna.dna_timeseries.report.html">
+               <img src="back.svg" alt="&#x2B05;">
+               biobb_dna/dna/dna_timeseries.py source
+            </a>
+         </h1>
+
+         <div id="doc">
+            <div id="l1"
+               class="code sev- "><tt><i>1</i> <span class="ch">#!/usr/bin/env python3</span></tt>
+            </div>
+            <div id="l2"
+               class="code sev- "><tt><i>2</i> &nbsp;</tt>
+            </div>
+            <div id="l3"
+               class="code sev- "><tt><i>3</i> <span class="sd">&quot;&quot;&quot;Module containing the HelParTimeSeries class and the command line interface.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l4"
+               class="code sev- "><tt><i>4</i> &nbsp;</tt>
+            </div>
+            <div id="l5"
+               class="code sev- "><tt><i>5</i> <span class="kn">import</span> <span class="nn">argparse</span></tt>
+            </div>
+            <div id="l6"
+               class="code sev- "><tt><i>6</i> <span class="kn">import</span> <span class="nn">re</span></tt>
+            </div>
+            <div id="l7"
+               class="code sev- "><tt><i>7</i> <span class="kn">import</span> <span class="nn">zipfile</span></tt>
+            </div>
+            <div id="l8"
+               class="code sev- "><tt><i>8</i> <span class="kn">from</span> <span class="nn">pathlib</span> <span class="kn">import</span> <span class="n">Path</span></tt>
+            </div>
+            <div id="l9"
+               class="code sev- "><tt><i>9</i> <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Optional</span></tt>
+            </div>
+            <div id="l10"
+               class="code sev- "><tt><i>10</i> &nbsp;</tt>
+            </div>
+            <div id="l11"
+               class="code sev- "><tt><i>11</i> <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span></tt>
+            </div>
+            <div id="l12"
+               class="code sev- "><tt><i>12</i> <span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span></tt>
+            </div>
+            <div id="l13"
+               class="code sev- "><tt><i>13</i> <span class="kn">from</span> <span class="nn">biobb_common.configuration</span> <span class="kn">import</span> <span class="n">settings</span></tt>
+            </div>
+            <div id="l14"
+               class="code sev- "><tt><i>14</i> <span class="kn">from</span> <span class="nn">biobb_common.generic.biobb_object</span> <span class="kn">import</span> <span class="n">BiobbObject</span></tt>
+            </div>
+            <div id="l15"
+               class="code sev- "><tt><i>15</i> <span class="kn">from</span> <span class="nn">biobb_common.tools</span> <span class="kn">import</span> <span class="n">file_utils</span> <span class="k">as</span> <span class="n">fu</span></tt>
+            </div>
+            <div id="l16"
+               class="code sev- "><tt><i>16</i> <span class="kn">from</span> <span class="nn">biobb_common.tools.file_utils</span> <span class="kn">import</span> <span class="n">launchlogger</span></tt>
+            </div>
+            <div id="l17"
+               class="code sev- "><tt><i>17</i> &nbsp;</tt>
+            </div>
+            <div id="l18"
+               class="code sev- "><tt><i>18</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils</span> <span class="kn">import</span> <span class="n">constants</span></tt>
+            </div>
+            <div id="l19"
+               class="code sev- "><tt><i>19</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.common</span> <span class="kn">import</span> <span class="n">_from_string_to_list</span></tt>
+            </div>
+            <div id="l20"
+               class="code sev- "><tt><i>20</i> <span class="kn">from</span> <span class="nn">biobb_dna.utils.loader</span> <span class="kn">import</span> <span class="n">read_series</span></tt>
+            </div>
+            <div id="l21"
+               class="code sev- "><tt><i>21</i> &nbsp;</tt>
+            </div>
+            <div id="l22"
+               class="code sev- "><tt><i>22</i> &nbsp;</tt>
+            </div>
+            <div id="l23"
+               class="code sev- "><tt><i>23</i> <span class="k">class</span> <span class="nc">HelParTimeSeries</span><span class="p">(</span><span class="n">BiobbObject</span><span class="p">):</span></tt>
+            </div>
+            <div id="l24"
+               class="code sev- "><tt><i>24</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l25"
+               class="code sev- "><tt><i>25</i> <span class="sd">    | biobb_dna HelParTimeSeries</span></tt>
+            </div>
+            <div id="l26"
+               class="code sev- "><tt><i>26</i> <span class="sd">    | Created time series and histogram plots for each base pair from a helical parameter series file.</span></tt>
+            </div>
+            <div id="l27"
+               class="code sev- "><tt><i>27</i> <span class="sd">    | The helical parameter series file is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair.</span></tt>
+            </div>
+            <div id="l28"
+               class="code sev- "><tt><i>28</i> &nbsp;</tt>
+            </div>
+            <div id="l29"
+               class="code sev- "><tt><i>29</i> <span class="sd">    Args:</span></tt>
+            </div>
+            <div id="l30"
+               class="code sev- "><tt><i>30</i> <span class="sd">        input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/dna/canal_output_shift.ser&gt;`_. Accepted formats: ser (edam:format_2330).</span></tt>
+            </div>
+            <div id="l31"
+               class="code sev- "><tt><i>31</i> <span class="sd">        output_zip_path (str): Path to output .zip files where data is saved. File type: output. `Sample file &lt;https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/timeseries_output.zip&gt;`_. Accepted formats: zip (edam:format_3987).</span></tt>
+            </div>
+            <div id="l32"
+               class="code sev- "><tt><i>32</i> <span class="sd">        properties (dict):</span></tt>
+            </div>
+            <div id="l33"
+               class="code sev- "><tt><i>33</i> <span class="sd">            * **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).</span></tt>
+            </div>
+            <div id="l34"
+               class="code sev- "><tt><i>34</i> <span class="sd">            * **bins** (*int*) - (None) Bins for histogram. Parameter has same options as matplotlib.pyplot.hist.</span></tt>
+            </div>
+            <div id="l35"
+               class="code sev- "><tt><i>35</i> <span class="sd">            * **helpar_name** (*str*) - (None) Helical parameter name. It must match the name of the helical parameter in the .ser input file. Values: majd, majw, mind, minw, inclin, tip, xdisp, ydisp, shear, stretch, stagger, buckle, propel, opening, rise, roll, twist, shift, slide, tilt, alphaC, alphaW, betaC, betaW, gammaC, gammaW, deltaC, deltaW, epsilC, epsilW, zetaC, zetaW, chiC, chiW, phaseC, phaseW.</span></tt>
+            </div>
+            <div id="l36"
+               class="code sev- "><tt><i>36</i> <span class="sd">            * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.</span></tt>
+            </div>
+            <div id="l37"
+               class="code sev- "><tt><i>37</i> <span class="sd">            * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 1) to analyze.  If not specified it will analyse the complete sequence.</span></tt>
+            </div>
+            <div id="l38"
+               class="code sev- "><tt><i>38</i> <span class="sd">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span></tt>
+            </div>
+            <div id="l39"
+               class="code sev- "><tt><i>39</i> <span class="sd">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span></tt>
+            </div>
+            <div id="l40"
+               class="code sev- "><tt><i>40</i> <span class="sd">            * **sandbox_path** (*str*) - (&quot;./&quot;) [WF property] Parent path to the sandbox directory.</span></tt>
+            </div>
+            <div id="l41"
+               class="code sev- "><tt><i>41</i> &nbsp;</tt>
+            </div>
+            <div id="l42"
+               class="code sev- "><tt><i>42</i> <span class="sd">    Examples:</span></tt>
+            </div>
+            <div id="l43"
+               class="code sev- "><tt><i>43</i> <span class="sd">        This is a use example of how to use the building block from Python::</span></tt>
+            </div>
+            <div id="l44"
+               class="code sev- "><tt><i>44</i> &nbsp;</tt>
+            </div>
+            <div id="l45"
+               class="code sev- "><tt><i>45</i> <span class="sd">            from biobb_dna.dna.dna_timeseries import dna_timeseries</span></tt>
+            </div>
+            <div id="l46"
+               class="code sev- "><tt><i>46</i> &nbsp;</tt>
+            </div>
+            <div id="l47"
+               class="code sev- "><tt><i>47</i> <span class="sd">            prop = {</span></tt>
+            </div>
+            <div id="l48"
+               class="code sev- "><tt><i>48</i> <span class="sd">                &#39;helpar_name&#39;: &#39;twist&#39;,</span></tt>
+            </div>
+            <div id="l49"
+               class="code sev- "><tt><i>49</i> <span class="sd">                &#39;seqpos&#39;: [1,2,3,4,5],</span></tt>
+            </div>
+            <div id="l50"
+               class="code sev- "><tt><i>50</i> <span class="sd">                &#39;sequence&#39;: &#39;GCAACGTGCTATGGAAGC&#39;,</span></tt>
+            </div>
+            <div id="l51"
+               class="code sev- "><tt><i>51</i> <span class="sd">            }</span></tt>
+            </div>
+            <div id="l52"
+               class="code sev- "><tt><i>52</i> <span class="sd">            dna_timeseries(</span></tt>
+            </div>
+            <div id="l53"
+               class="code sev- "><tt><i>53</i> <span class="sd">                input_ser_path=&#39;/path/to/twist.ser&#39;,</span></tt>
+            </div>
+            <div id="l54"
+               class="code sev- "><tt><i>54</i> <span class="sd">                output_zip_path=&#39;/path/to/output/file.zip&#39;</span></tt>
+            </div>
+            <div id="l55"
+               class="code sev- "><tt><i>55</i> <span class="sd">                properties=prop)</span></tt>
+            </div>
+            <div id="l56"
+               class="code sev- "><tt><i>56</i> <span class="sd">    Info:</span></tt>
+            </div>
+            <div id="l57"
+               class="code sev- "><tt><i>57</i> <span class="sd">        * wrapped_software:</span></tt>
+            </div>
+            <div id="l58"
+               class="code sev- "><tt><i>58</i> <span class="sd">            * name: In house</span></tt>
+            </div>
+            <div id="l59"
+               class="code sev- "><tt><i>59</i> <span class="sd">            * license: Apache-2.0</span></tt>
+            </div>
+            <div id="l60"
+               class="code sev- "><tt><i>60</i> <span class="sd">        * ontology:</span></tt>
+            </div>
+            <div id="l61"
+               class="code sev- "><tt><i>61</i> <span class="sd">            * name: EDAM</span></tt>
+            </div>
+            <div id="l62"
+               class="code sev- "><tt><i>62</i> <span class="sd">            * schema: http://edamontology.org/EDAM.owl</span></tt>
+            </div>
+            <div id="l63"
+               class="code sev- "><tt><i>63</i> &nbsp;</tt>
+            </div>
+            <div id="l64"
+               class="code sev- "><tt><i>64</i> <span class="sd">    &quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l65"
+               class="code sev- "><tt><i>65</i> &nbsp;</tt>
+            </div>
+            <div id="l66"
+               class="code sev- "><tt><i>66</i>     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span></tt>
+            </div>
+            <div id="l67"
+               class="code sev- "><tt><i>67</i>         <span class="bp">self</span><span class="p">,</span> <span class="n">input_ser_path</span><span class="p">,</span> <span class="n">output_zip_path</span><span class="p">,</span> <span class="n">properties</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span></tt>
+            </div>
+            <div id="l68"
+               class="code sev- "><tt><i>68</i>     <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l69"
+               class="code sev- "><tt><i>69</i>         <span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span> <span class="ow">or</span> <span class="p">{}</span></tt>
+            </div>
+            <div id="l70"
+               class="code sev- "><tt><i>70</i> &nbsp;</tt>
+            </div>
+            <div id="l71"
+               class="code sev- "><tt><i>71</i>         <span class="c1"># Call parent class constructor</span></tt>
+            </div>
+            <div id="l72"
+               class="code sev- "><tt><i>72</i>         <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l73"
+               class="code sev- "><tt><i>73</i>         <span class="bp">self</span><span class="o">.</span><span class="n">locals_var_dict</span> <span class="o">=</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l74"
+               class="code sev- "><tt><i>74</i> &nbsp;</tt>
+            </div>
+            <div id="l75"
+               class="code sev- "><tt><i>75</i>         <span class="c1"># Input/Output files</span></tt>
+            </div>
+            <div id="l76"
+               class="code sev- "><tt><i>76</i>         <span class="bp">self</span><span class="o">.</span><span class="n">io_dict</span> <span class="o">=</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l77"
+               class="code sev- "><tt><i>77</i>             <span class="s2">&quot;in&quot;</span><span class="p">:</span> <span class="p">{</span></tt>
+            </div>
+            <div id="l78"
+               class="code sev- "><tt><i>78</i>                 <span class="s2">&quot;input_ser_path&quot;</span><span class="p">:</span> <span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l79"
+               class="code sev- "><tt><i>79</i>             <span class="p">},</span></tt>
+            </div>
+            <div id="l80"
+               class="code sev- "><tt><i>80</i>             <span class="s2">&quot;out&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;output_zip_path&quot;</span><span class="p">:</span> <span class="n">output_zip_path</span><span class="p">},</span></tt>
+            </div>
+            <div id="l81"
+               class="code sev- "><tt><i>81</i>         <span class="p">}</span></tt>
+            </div>
+            <div id="l82"
+               class="code sev- "><tt><i>82</i> &nbsp;</tt>
+            </div>
+            <div id="l83"
+               class="code sev- "><tt><i>83</i>         <span class="bp">self</span><span class="o">.</span><span class="n">properties</span> <span class="o">=</span> <span class="n">properties</span></tt>
+            </div>
+            <div id="l84"
+               class="code sev- "><tt><i>84</i>         <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;sequence&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l85"
+               class="code sev- "><tt><i>85</i>         <span class="bp">self</span><span class="o">.</span><span class="n">bins</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;bins&quot;</span><span class="p">,</span> <span class="s2">&quot;auto&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l86"
+               class="code sev- "><tt><i>86</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stride</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;stride&quot;</span><span class="p">,</span> <span class="mi">10</span><span class="p">)</span></tt>
+            </div>
+            <div id="l87"
+               class="code sev- "><tt><i>87</i>         <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l88"
+               class="code sev- "><tt><i>88</i>             <span class="nb">int</span><span class="p">(</span><span class="n">elem</span><span class="p">)</span> <span class="k">for</span> <span class="n">elem</span> <span class="ow">in</span> <span class="n">_from_string_to_list</span><span class="p">(</span><span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;seqpos&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">))</span></tt>
+            </div>
+            <div id="l89"
+               class="code sev- "><tt><i>89</i>         <span class="p">]</span></tt>
+            </div>
+            <div id="l90"
+               class="code sev- "><tt><i>90</i>         <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">properties</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;helpar_name&quot;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span></tt>
+            </div>
+            <div id="l91"
+               class="code sev- "><tt><i>91</i> &nbsp;</tt>
+            </div>
+            <div id="l92"
+               class="code sev- "><tt><i>92</i>         <span class="c1"># get helical parameter from filename if not specified</span></tt>
+            </div>
+            <div id="l93"
+               class="code sev- "><tt><i>93</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l94"
+               class="code sev- "><tt><i>94</i>             <span class="k">for</span> <span class="n">hp</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l95"
+               class="code sev- "><tt><i>95</i>                 <span class="k">if</span> <span class="n">hp</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">Path</span><span class="p">(</span><span class="n">input_ser_path</span><span class="p">)</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span></tt>
+            </div>
+            <div id="l96"
+               class="code sev- "><tt><i>96</i>                     <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="o">=</span> <span class="n">hp</span></tt>
+            </div>
+            <div id="l97"
+               class="code sev- "><tt><i>97</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span></tt>
+            </div>
+            <div id="l98"
+               class="code sev- "><tt><i>98</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l99"
+               class="code sev- "><tt><i>99</i>                     <span class="s2">&quot;Helical parameter name can&#39;t be inferred from file, &quot;</span></tt>
+            </div>
+            <div id="l100"
+               class="code sev- "><tt><i>100</i>                     <span class="s2">&quot;so it must be specified!&quot;</span></tt>
+            </div>
+            <div id="l101"
+               class="code sev- "><tt><i>101</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l102"
+               class="code sev- "><tt><i>102</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l103"
+               class="code sev- "><tt><i>103</i>             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="p">:</span></tt>
+            </div>
+            <div id="l104"
+               class="code sev- "><tt><i>104</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l105"
+               class="code sev- "><tt><i>105</i>                     <span class="s2">&quot;Helical parameter name is invalid! &quot;</span></tt>
+            </div>
+            <div id="l106"
+               class="code sev- "><tt><i>106</i>                     <span class="sa">f</span><span class="s2">&quot;Options: </span><span class="si">{</span><span class="n">constants</span><span class="o">.</span><span class="n">helical_parameters</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l107"
+               class="code sev- "><tt><i>107</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l108"
+               class="code sev- "><tt><i>108</i> &nbsp;</tt>
+            </div>
+            <div id="l109"
+               class="code sev- "><tt><i>109</i>         <span class="c1"># get base length from helical parameter name</span></tt>
+            </div>
+            <div id="l110"
+               class="code sev- "><tt><i>110</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_singlebases</span><span class="p">:</span></tt>
+            </div>
+            <div id="l111"
+               class="code sev- "><tt><i>111</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l112"
+               class="code sev- "><tt><i>112</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l113"
+               class="code sev- "><tt><i>113</i>             <span class="bp">self</span><span class="o">.</span><span class="n">baselen</span> <span class="o">=</span> <span class="mi">1</span></tt>
+            </div>
+            <div id="l114"
+               class="code sev- "><tt><i>114</i>         <span class="c1"># get unit from helical parameter name</span></tt>
+            </div>
+            <div id="l115"
+               class="code sev- "><tt><i>115</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_angular</span><span class="p">:</span></tt>
+            </div>
+            <div id="l116"
+               class="code sev- "><tt><i>116</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Degrees&quot;</span></tt>
+            </div>
+            <div id="l117"
+               class="code sev- "><tt><i>117</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l118"
+               class="code sev- "><tt><i>118</i>             <span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span> <span class="o">=</span> <span class="s2">&quot;Angstroms&quot;</span></tt>
+            </div>
+            <div id="l119"
+               class="code sev- "><tt><i>119</i> &nbsp;</tt>
+            </div>
+            <div id="l120"
+               class="code sev- "><tt><i>120</i>         <span class="c1"># Check the properties</span></tt>
+            </div>
+            <div id="l121"
+               class="code sev- "><tt><i>121</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_properties</span><span class="p">(</span><span class="n">properties</span><span class="p">)</span></tt>
+            </div>
+            <div id="l122"
+               class="code sev- "><tt><i>122</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">()</span></tt>
+            </div>
+            <div id="l123"
+               class="code sev- "><tt><i>123</i> &nbsp;</tt>
+            </div>
+            <div id="l124"
+               class="code sev- "><tt><i>124</i>     <span class="nd">@launchlogger</span></tt>
+            </div>
+            <div id="l125"
+               class="code sev- "><tt><i>125</i>     <span class="k">def</span> <span class="nf">launch</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l126"
+               class="code sev- "><tt><i>126</i> <span class="w">        </span><span class="sd">&quot;&quot;&quot;Execute the :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries&gt;` object.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l127"
+               class="code sev- "><tt><i>127</i> &nbsp;</tt>
+            </div>
+            <div id="l128"
+               class="code sev- "><tt><i>128</i>         <span class="c1"># Setup Biobb</span></tt>
+            </div>
+            <div id="l129"
+               class="code sev- "><tt><i>129</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">check_restart</span><span class="p">():</span></tt>
+            </div>
+            <div id="l130"
+               class="code sev- "><tt><i>130</i>             <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l131"
+               class="code sev- "><tt><i>131</i>         <span class="bp">self</span><span class="o">.</span><span class="n">stage_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l132"
+               class="code sev- "><tt><i>132</i> &nbsp;</tt>
+            </div>
+            <div id="l133"
+               class="code sev- "><tt><i>133</i>         <span class="c1"># check sequence</span></tt>
+            </div>
+            <div id="l134"
+               class="code sev- "><tt><i>134</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">2</span><span class="p">:</span></tt>
+            </div>
+            <div id="l135"
+               class="code sev- "><tt><i>135</i>             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;sequence is null or too short!&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l136"
+               class="code sev- "><tt><i>136</i> &nbsp;</tt>
+            </div>
+            <div id="l137"
+               class="code sev- "><tt><i>137</i>         <span class="c1"># calculate cols with 0 index</span></tt>
+            </div>
+            <div id="l138"
+               class="code sev- "><tt><i>138</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">:</span></tt>
+            </div>
+            <div id="l139"
+               class="code sev- "><tt><i>139</i>             <span class="n">cols</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">]</span></tt>
+            </div>
+            <div id="l140"
+               class="code sev- "><tt><i>140</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l141"
+               class="code sev- "><tt><i>141</i>             <span class="n">cols</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)))</span></tt>
+            </div>
+            <div id="l142"
+               class="code sev- "><tt><i>142</i> &nbsp;</tt>
+            </div>
+            <div id="l143"
+               class="code sev- "><tt><i>143</i>         <span class="c1"># sort cols in ascending order</span></tt>
+            </div>
+            <div id="l144"
+               class="code sev- "><tt><i>144</i>         <span class="n">cols</span><span class="o">.</span><span class="n">sort</span><span class="p">()</span></tt>
+            </div>
+            <div id="l145"
+               class="code sev- "><tt><i>145</i> &nbsp;</tt>
+            </div>
+            <div id="l146"
+               class="code sev- "><tt><i>146</i>         <span class="c1"># check seqpos for base pairs</span></tt>
+            </div>
+            <div id="l147"
+               class="code sev- "><tt><i>147</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l148"
+               class="code sev- "><tt><i>148</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">2</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">):</span></tt>
+            </div>
+            <div id="l149"
+               class="code sev- "><tt><i>149</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l150"
+               class="code sev- "><tt><i>150</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="w"> </span><span class="o">-</span><span class="w"> </span><span class="mi">1</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l151"
+               class="code sev- "><tt><i>151</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l152"
+               class="code sev- "><tt><i>152</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l153"
+               class="code sev- "><tt><i>153</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l154"
+               class="code sev- "><tt><i>154</i>         <span class="c1"># check seqpos for non base pairs</span></tt>
+            </div>
+            <div id="l155"
+               class="code sev- "><tt><i>155</i>         <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span> <span class="ow">and</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l156"
+               class="code sev- "><tt><i>156</i>             <span class="k">if</span> <span class="p">(</span><span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&gt;</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">0</span><span class="p">):</span></tt>
+            </div>
+            <div id="l157"
+               class="code sev- "><tt><i>157</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span></tt>
+            </div>
+            <div id="l158"
+               class="code sev- "><tt><i>158</i>                     <span class="sa">f</span><span class="s2">&quot;seqpos values must be between 1 and </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l159"
+               class="code sev- "><tt><i>159</i>                 <span class="p">)</span></tt>
+            </div>
+            <div id="l160"
+               class="code sev- "><tt><i>160</i>             <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span><span class="nb">isinstance</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">seqpos</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">):</span></tt>
+            </div>
+            <div id="l161"
+               class="code sev- "><tt><i>161</i>                 <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;seqpos must be a list of at least two integers&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l162"
+               class="code sev- "><tt><i>162</i> &nbsp;</tt>
+            </div>
+            <div id="l163"
+               class="code sev- "><tt><i>163</i>         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span> <span class="ow">in</span> <span class="n">constants</span><span class="o">.</span><span class="n">hp_basepairs</span><span class="p">:</span></tt>
+            </div>
+            <div id="l164"
+               class="code sev- "><tt><i>164</i>             <span class="c1"># remove first and last base pairs from cols if they match 0 and len(sequence)</span></tt>
+            </div>
+            <div id="l165"
+               class="code sev- "><tt><i>165</i>             <span class="k">if</span> <span class="nb">min</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span></tt>
+            </div>
+            <div id="l166"
+               class="code sev- "><tt><i>166</i>                 <span class="n">cols</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span></tt>
+            </div>
+            <div id="l167"
+               class="code sev- "><tt><i>167</i>             <span class="k">if</span> <span class="nb">max</span><span class="p">(</span><span class="n">cols</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">:</span></tt>
+            </div>
+            <div id="l168"
+               class="code sev- "><tt><i>168</i>                 <span class="n">cols</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span></tt>
+            </div>
+            <div id="l169"
+               class="code sev- "><tt><i>169</i> &nbsp;</tt>
+            </div>
+            <div id="l170"
+               class="code sev- "><tt><i>170</i>             <span class="c1"># discard first and last base(pairs) from sequence</span></tt>
+            </div>
+            <div id="l171"
+               class="code sev- "><tt><i>171</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span><span class="p">[</span><span class="mi">1</span><span class="p">:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span></tt>
+            </div>
+            <div id="l172"
+               class="code sev- "><tt><i>172</i>             <span class="c1"># create indices list</span></tt>
+            </div>
+            <div id="l173"
+               class="code sev- "><tt><i>173</i>             <span class="n">indices</span> <span class="o">=</span> <span class="n">cols</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l174"
+               class="code sev- "><tt><i>174</i>             <span class="c1"># create subunits list from cols</span></tt>
+            </div>
+            <div id="l175"
+               class="code sev- "><tt><i>175</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="o">-</span><span class="mi">1</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span></tt>
+            </div>
+            <div id="l176"
+               class="code sev- "><tt><i>176</i>             <span class="c1"># clean subunits (leave only basepairs)</span></tt>
+            </div>
+            <div id="l177"
+               class="code sev- "><tt><i>177</i>             <span class="n">pattern</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">compile</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\d+_[A-Za-z]</span><span class="si">{2}</span><span class="s2">&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l178"
+               class="code sev- "><tt><i>178</i>             <span class="c1"># get removed items</span></tt>
+            </div>
+            <div id="l179"
+               class="code sev- "><tt><i>179</i>             <span class="n">removed_items</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">subunits</span> <span class="k">if</span> <span class="ow">not</span> <span class="n">pattern</span><span class="o">.</span><span class="n">fullmatch</span><span class="p">(</span><span class="n">s</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l180"
+               class="code sev- "><tt><i>180</i>             <span class="c1"># get indices of removed items (in integer format and starting from 0)</span></tt>
+            </div>
+            <div id="l181"
+               class="code sev- "><tt><i>181</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="p">[</span></tt>
+            </div>
+            <div id="l182"
+               class="code sev- "><tt><i>182</i>                 <span class="nb">int</span><span class="p">(</span><span class="n">match</span><span class="o">.</span><span class="n">group</span><span class="p">())</span></tt>
+            </div>
+            <div id="l183"
+               class="code sev- "><tt><i>183</i>                 <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">removed_items</span></tt>
+            </div>
+            <div id="l184"
+               class="code sev- "><tt><i>184</i>                 <span class="k">if</span> <span class="p">(</span><span class="n">match</span> <span class="o">:=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">&quot;\d+&quot;</span><span class="p">,</span> <span class="n">item</span><span class="p">))</span></tt>
+            </div>
+            <div id="l185"
+               class="code sev- "><tt><i>185</i>             <span class="p">]</span></tt>
+            </div>
+            <div id="l186"
+               class="code sev- "><tt><i>186</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">removed_numbers</span><span class="p">))</span></tt>
+            </div>
+            <div id="l187"
+               class="code sev- "><tt><i>187</i>             <span class="n">removed_numbers</span> <span class="o">=</span> <span class="p">[</span><span class="nb">int</span><span class="p">(</span><span class="n">i</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">removed_numbers</span><span class="p">]</span></tt>
+            </div>
+            <div id="l188"
+               class="code sev- "><tt><i>188</i>             <span class="c1"># remove non basepairs from subunits and indices</span></tt>
+            </div>
+            <div id="l189"
+               class="code sev- "><tt><i>189</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">subunits</span> <span class="k">if</span> <span class="n">pattern</span><span class="o">.</span><span class="n">fullmatch</span><span class="p">(</span><span class="n">s</span><span class="p">)]</span></tt>
+            </div>
+            <div id="l190"
+               class="code sev- "><tt><i>190</i>             <span class="n">indices</span> <span class="o">=</span> <span class="p">[</span><span class="n">i</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">indices</span> <span class="k">if</span> <span class="n">i</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">removed_numbers</span><span class="p">]</span></tt>
+            </div>
+            <div id="l191"
+               class="code sev- "><tt><i>191</i>         <span class="k">else</span><span class="p">:</span></tt>
+            </div>
+            <div id="l192"
+               class="code sev- "><tt><i>192</i>             <span class="n">sequence</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">sequence</span></tt>
+            </div>
+            <div id="l193"
+               class="code sev- "><tt><i>193</i>             <span class="c1"># create indices list</span></tt>
+            </div>
+            <div id="l194"
+               class="code sev- "><tt><i>194</i>             <span class="n">indices</span> <span class="o">=</span> <span class="n">cols</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span></tt>
+            </div>
+            <div id="l195"
+               class="code sev- "><tt><i>195</i>             <span class="c1"># trick for getting the index column from the .ser file</span></tt>
+            </div>
+            <div id="l196"
+               class="code sev- "><tt><i>196</i>             <span class="n">indices</span><span class="o">.</span><span class="n">insert</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span></tt>
+            </div>
+            <div id="l197"
+               class="code sev- "><tt><i>197</i>             <span class="c1"># create subunits list from cols</span></tt>
+            </div>
+            <div id="l198"
+               class="code sev- "><tt><i>198</i>             <span class="n">subunits</span> <span class="o">=</span> <span class="p">[</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">sequence</span><span class="p">[</span><span class="n">i</span><span class="p">:</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="o">+</span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="p">]</span><span class="si">}</span><span class="s2">&quot;</span> <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="n">cols</span><span class="p">]</span></tt>
+            </div>
+            <div id="l199"
+               class="code sev- "><tt><i>199</i> &nbsp;</tt>
+            </div>
+            <div id="l200"
+               class="code sev- "><tt><i>200</i>         <span class="c1"># read input .ser file</span></tt>
+            </div>
+            <div id="l201"
+               class="code sev- "><tt><i>201</i>         <span class="n">ser_data</span> <span class="o">=</span> <span class="n">read_series</span><span class="p">(</span></tt>
+            </div>
+            <div id="l202"
+               class="code sev- "><tt><i>202</i>             <span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">][</span><span class="s2">&quot;input_ser_path&quot;</span><span class="p">],</span> <span class="n">usecols</span><span class="o">=</span><span class="n">indices</span></tt>
+            </div>
+            <div id="l203"
+               class="code sev- "><tt><i>203</i>         <span class="p">)</span></tt>
+            </div>
+            <div id="l204"
+               class="code sev- "><tt><i>204</i> &nbsp;</tt>
+            </div>
+            <div id="l205"
+               class="code sev- "><tt><i>205</i>         <span class="c1"># get columns for selected bases</span></tt>
+            </div>
+            <div id="l206"
+               class="code sev- "><tt><i>206</i>         <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">subunits</span></tt>
+            </div>
+            <div id="l207"
+               class="code sev- "><tt><i>207</i> &nbsp;</tt>
+            </div>
+            <div id="l208"
+               class="code sev- "><tt><i>208</i>         <span class="c1"># write output files for all selected bases (one per column)</span></tt>
+            </div>
+            <div id="l209"
+               class="code sev- "><tt><i>209</i>         <span class="n">zf</span> <span class="o">=</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="p">[</span><span class="s2">&quot;out&quot;</span><span class="p">][</span><span class="s2">&quot;output_zip_path&quot;</span><span class="p">]),</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l210"
+               class="code sev- "><tt><i>210</i>         <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">ser_data</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span></tt>
+            </div>
+            <div id="l211"
+               class="code sev- "><tt><i>211</i>             <span class="c1"># unstack columns to prevent errors from repeated base pairs</span></tt>
+            </div>
+            <div id="l212"
+               class="code sev- "><tt><i>212</i>             <span class="n">column_data</span> <span class="o">=</span> <span class="n">ser_data</span><span class="p">[[</span><span class="n">col</span><span class="p">]]</span><span class="o">.</span><span class="n">unstack</span><span class="p">()</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l213"
+               class="code sev- "><tt><i>213</i>             <span class="n">column_data</span><span class="o">.</span><span class="n">name</span> <span class="o">=</span> <span class="n">col</span></tt>
+            </div>
+            <div id="l214"
+               class="code sev- "><tt><i>214</i>             <span class="n">fu</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Computing base number </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">...&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l215"
+               class="code sev- "><tt><i>215</i> &nbsp;</tt>
+            </div>
+            <div id="l216"
+               class="code sev- "><tt><i>216</i>             <span class="c1"># column series</span></tt>
+            </div>
+            <div id="l217"
+               class="code sev- "><tt><i>217</i>             <span class="n">series_colfn</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;series_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l218"
+               class="code sev- "><tt><i>218</i>             <span class="n">column_data</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span></tt>
+            </div>
+            <div id="l219"
+               class="code sev- "><tt><i>219</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span></tt>
+            </div>
+            <div id="l220"
+               class="code sev- "><tt><i>220</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l221"
+               class="code sev- "><tt><i>221</i>             <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l222"
+               class="code sev- "><tt><i>222</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l223"
+               class="code sev- "><tt><i>223</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l224"
+               class="code sev- "><tt><i>224</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l225"
+               class="code sev- "><tt><i>225</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l226"
+               class="code sev- "><tt><i>226</i> &nbsp;</tt>
+            </div>
+            <div id="l227"
+               class="code sev- "><tt><i>227</i>             <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l228"
+               class="code sev- "><tt><i>228</i>             <span class="n">reduced_data</span> <span class="o">=</span> <span class="n">column_data</span><span class="o">.</span><span class="n">iloc</span><span class="p">[::</span> <span class="bp">self</span><span class="o">.</span><span class="n">stride</span><span class="p">]</span></tt>
+            </div>
+            <div id="l229"
+               class="code sev- "><tt><i>229</i>             <span class="n">axs</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">reduced_data</span><span class="o">.</span><span class="n">index</span><span class="p">,</span> <span class="n">reduced_data</span><span class="o">.</span><span class="n">to_numpy</span><span class="p">())</span></tt>
+            </div>
+            <div id="l230"
+               class="code sev- "><tt><i>230</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;Time (Snapshots)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l231"
+               class="code sev- "><tt><i>231</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l232"
+               class="code sev- "><tt><i>232</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_title</span><span class="p">(</span></tt>
+            </div>
+            <div id="l233"
+               class="code sev- "><tt><i>233</i>                 <span class="sa">f</span><span class="s2">&quot;Helical Parameter vs Time: </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> &quot;</span></tt>
+            </div>
+            <div id="l234"
+               class="code sev- "><tt><i>234</i>                 <span class="s2">&quot;(base pair &quot;</span></tt>
+            </div>
+            <div id="l235"
+               class="code sev-2  le">
+               <ul class="violations">
+               
+                  <li>
+                     <span class="count sev-2">
+                        E225
+                     </span>
+                     Missing whitespace around operator</li>
+               
+               </ul><tt><i>235</i>                 <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="s1">&#39;step&#39;</span><span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="bp">self</span><span class="o">.</span><span class="n">baselen</span><span class="o">==</span><span class="mi">1</span><span class="w"> </span><span class="k">else</span><span class="w"> </span><span class="s1">&#39;&#39;</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">)&quot;</span></tt>
+            </div>
+            <div id="l236"
+               class="code sev- "><tt><i>236</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l237"
+               class="code sev- "><tt><i>237</i>             <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span></tt>
+            </div>
+            <div id="l238"
+               class="code sev- "><tt><i>238</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l239"
+               class="code sev- "><tt><i>239</i>                 <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l240"
+               class="code sev- "><tt><i>240</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l241"
+               class="code sev- "><tt><i>241</i>             <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l242"
+               class="code sev- "><tt><i>242</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l243"
+               class="code sev- "><tt><i>243</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l244"
+               class="code sev- "><tt><i>244</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">series_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l245"
+               class="code sev- "><tt><i>245</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l246"
+               class="code sev- "><tt><i>246</i>             <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l247"
+               class="code sev- "><tt><i>247</i> &nbsp;</tt>
+            </div>
+            <div id="l248"
+               class="code sev- "><tt><i>248</i>             <span class="c1"># columns histogram</span></tt>
+            </div>
+            <div id="l249"
+               class="code sev- "><tt><i>249</i>             <span class="n">hist_colfn</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;hist_</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">col</span><span class="si">}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l250"
+               class="code sev- "><tt><i>250</i>             <span class="n">fig</span><span class="p">,</span> <span class="n">axs</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">dpi</span><span class="o">=</span><span class="mi">300</span><span class="p">,</span> <span class="n">tight_layout</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></tt>
+            </div>
+            <div id="l251"
+               class="code sev- "><tt><i>251</i>             <span class="n">ybins</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">axs</span><span class="o">.</span><span class="n">hist</span><span class="p">(</span><span class="n">column_data</span><span class="p">,</span> <span class="n">bins</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">bins</span><span class="p">)</span></tt>
+            </div>
+            <div id="l252"
+               class="code sev- "><tt><i>252</i>             <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="p">:</span> <span class="n">x</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="s2">&quot;density&quot;</span><span class="p">:</span> <span class="n">ybins</span><span class="p">})</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span></tt>
+            </div>
+            <div id="l253"
+               class="code sev- "><tt><i>253</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l254"
+               class="code sev- "><tt><i>254</i>                 <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span></tt>
+            </div>
+            <div id="l255"
+               class="code sev- "><tt><i>255</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l256"
+               class="code sev- "><tt><i>256</i>             <span class="c1"># save table</span></tt>
+            </div>
+            <div id="l257"
+               class="code sev- "><tt><i>257</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l258"
+               class="code sev- "><tt><i>258</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l259"
+               class="code sev- "><tt><i>259</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.csv&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l260"
+               class="code sev- "><tt><i>260</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l261"
+               class="code sev- "><tt><i>261</i> &nbsp;</tt>
+            </div>
+            <div id="l262"
+               class="code sev- "><tt><i>262</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;Density&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l263"
+               class="code sev- "><tt><i>263</i>             <span class="n">axs</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">helpar_name</span><span class="o">.</span><span class="n">capitalize</span><span class="p">()</span><span class="si">}</span><span class="s2"> (</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">hp_unit</span><span class="si">}</span><span class="s2">)&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l264"
+               class="code sev- "><tt><i>264</i>             <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span></tt>
+            </div>
+            <div id="l265"
+               class="code sev- "><tt><i>265</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l266"
+               class="code sev- "><tt><i>266</i>                 <span class="nb">format</span><span class="o">=</span><span class="s2">&quot;jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l267"
+               class="code sev- "><tt><i>267</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l268"
+               class="code sev- "><tt><i>268</i>             <span class="c1"># save plot</span></tt>
+            </div>
+            <div id="l269"
+               class="code sev- "><tt><i>269</i>             <span class="n">zf</span><span class="o">.</span><span class="n">write</span><span class="p">(</span></tt>
+            </div>
+            <div id="l270"
+               class="code sev- "><tt><i>270</i>                 <span class="n">Path</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">))</span> <span class="o">/</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l271"
+               class="code sev- "><tt><i>271</i>                 <span class="n">arcname</span><span class="o">=</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">hist_colfn</span><span class="si">}</span><span class="s2">.jpg&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l272"
+               class="code sev- "><tt><i>272</i>             <span class="p">)</span></tt>
+            </div>
+            <div id="l273"
+               class="code sev- "><tt><i>273</i>             <span class="n">plt</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l274"
+               class="code sev- "><tt><i>274</i>         <span class="n">zf</span><span class="o">.</span><span class="n">close</span><span class="p">()</span></tt>
+            </div>
+            <div id="l275"
+               class="code sev- "><tt><i>275</i> &nbsp;</tt>
+            </div>
+            <div id="l276"
+               class="code sev- "><tt><i>276</i>         <span class="c1"># Copy files to host</span></tt>
+            </div>
+            <div id="l277"
+               class="code sev- "><tt><i>277</i>         <span class="bp">self</span><span class="o">.</span><span class="n">copy_to_host</span><span class="p">()</span></tt>
+            </div>
+            <div id="l278"
+               class="code sev- "><tt><i>278</i> &nbsp;</tt>
+            </div>
+            <div id="l279"
+               class="code sev- "><tt><i>279</i>         <span class="c1"># Remove temporary file(s)</span></tt>
+            </div>
+            <div id="l280"
+               class="code sev- "><tt><i>280</i>         <span class="bp">self</span><span class="o">.</span><span class="n">tmp_files</span><span class="o">.</span><span class="n">extend</span><span class="p">([</span><span class="bp">self</span><span class="o">.</span><span class="n">stage_io_dict</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;unique_dir&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">)])</span></tt>
+            </div>
+            <div id="l281"
+               class="code sev- "><tt><i>281</i>         <span class="bp">self</span><span class="o">.</span><span class="n">remove_tmp_files</span><span class="p">()</span></tt>
+            </div>
+            <div id="l282"
+               class="code sev- "><tt><i>282</i> &nbsp;</tt>
+            </div>
+            <div id="l283"
+               class="code sev- "><tt><i>283</i>         <span class="bp">self</span><span class="o">.</span><span class="n">check_arguments</span><span class="p">(</span><span class="n">output_files_created</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">raise_exception</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span></tt>
+            </div>
+            <div id="l284"
+               class="code sev- "><tt><i>284</i> &nbsp;</tt>
+            </div>
+            <div id="l285"
+               class="code sev- "><tt><i>285</i>         <span class="k">return</span> <span class="mi">0</span></tt>
+            </div>
+            <div id="l286"
+               class="code sev- "><tt><i>286</i> &nbsp;</tt>
+            </div>
+            <div id="l287"
+               class="code sev- "><tt><i>287</i> &nbsp;</tt>
+            </div>
+            <div id="l288"
+               class="code sev- "><tt><i>288</i> <span class="k">def</span> <span class="nf">dna_timeseries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l289"
+               class="code sev- "><tt><i>289</i>     <span class="n">input_ser_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l290"
+               class="code sev- "><tt><i>290</i>     <span class="n">output_zip_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span></tt>
+            </div>
+            <div id="l291"
+               class="code sev- "><tt><i>291</i>     <span class="n">properties</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">dict</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span></tt>
+            </div>
+            <div id="l292"
+               class="code sev- "><tt><i>292</i>     <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l293"
+               class="code sev- "><tt><i>293</i> <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">int</span><span class="p">:</span></tt>
+            </div>
+            <div id="l294"
+               class="code sev- "><tt><i>294</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Create :class:`HelParTimeSeries &lt;dna.dna_timeseries.HelParTimeSeries&gt;` class and</span></tt>
+            </div>
+            <div id="l295"
+               class="code sev- "><tt><i>295</i> <span class="sd">    execute the :meth:`launch() &lt;dna.dna_timeseries.HelParTimeSeries.launch&gt;` method.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l296"
+               class="code sev- "><tt><i>296</i> &nbsp;</tt>
+            </div>
+            <div id="l297"
+               class="code sev- "><tt><i>297</i>     <span class="k">return</span> <span class="n">HelParTimeSeries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l298"
+               class="code sev- "><tt><i>298</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l299"
+               class="code sev- "><tt><i>299</i>         <span class="n">output_zip_path</span><span class="o">=</span><span class="n">output_zip_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l300"
+               class="code sev- "><tt><i>300</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l301"
+               class="code sev- "><tt><i>301</i>         <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span></tt>
+            </div>
+            <div id="l302"
+               class="code sev- "><tt><i>302</i>     <span class="p">)</span><span class="o">.</span><span class="n">launch</span><span class="p">()</span></tt>
+            </div>
+            <div id="l303"
+               class="code sev- "><tt><i>303</i> &nbsp;</tt>
+            </div>
+            <div id="l304"
+               class="code sev- "><tt><i>304</i> &nbsp;</tt>
+            </div>
+            <div id="l305"
+               class="code sev- "><tt><i>305</i> <span class="k">def</span> <span class="nf">main</span><span class="p">():</span></tt>
+            </div>
+            <div id="l306"
+               class="code sev- "><tt><i>306</i> <span class="w">    </span><span class="sd">&quot;&quot;&quot;Command line execution of this building block. Please check the command line documentation.&quot;&quot;&quot;</span></tt>
+            </div>
+            <div id="l307"
+               class="code sev- "><tt><i>307</i>     <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span></tt>
+            </div>
+            <div id="l308"
+               class="code sev- "><tt><i>308</i>         <span class="n">description</span><span class="o">=</span><span class="s2">&quot;Created time series and histogram plots for each base pair from a helical parameter series file.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l309"
+               class="code sev- "><tt><i>309</i>         <span class="n">formatter_class</span><span class="o">=</span><span class="k">lambda</span> <span class="n">prog</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">RawTextHelpFormatter</span><span class="p">(</span><span class="n">prog</span><span class="p">,</span> <span class="n">width</span><span class="o">=</span><span class="mi">99999</span><span class="p">),</span></tt>
+            </div>
+            <div id="l310"
+               class="code sev- "><tt><i>310</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l311"
+               class="code sev- "><tt><i>311</i>     <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">&quot;--config&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Configuration file&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l312"
+               class="code sev- "><tt><i>312</i> &nbsp;</tt>
+            </div>
+            <div id="l313"
+               class="code sev- "><tt><i>313</i>     <span class="n">required_args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument_group</span><span class="p">(</span><span class="s2">&quot;required arguments&quot;</span><span class="p">)</span></tt>
+            </div>
+            <div id="l314"
+               class="code sev- "><tt><i>314</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l315"
+               class="code sev- "><tt><i>315</i>         <span class="s2">&quot;--input_ser_path&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l316"
+               class="code sev- "><tt><i>316</i>         <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span></tt>
+            </div>
+            <div id="l317"
+               class="code sev- "><tt><i>317</i>         <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Helical parameter input ser file path. Accepted formats: ser.&quot;</span><span class="p">,</span></tt>
+            </div>
+            <div id="l318"
+               class="code sev- "><tt><i>318</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l319"
+               class="code sev- "><tt><i>319</i>     <span class="n">required_args</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span></tt>
+            </div>
+            <div id="l320"
+               class="code sev- "><tt><i>320</i>         <span class="s2">&quot;--output_zip_path&quot;</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">&quot;Path to output directory.&quot;</span></tt>
+            </div>
+            <div id="l321"
+               class="code sev- "><tt><i>321</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l322"
+               class="code sev- "><tt><i>322</i> &nbsp;</tt>
+            </div>
+            <div id="l323"
+               class="code sev- "><tt><i>323</i>     <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></tt>
+            </div>
+            <div id="l324"
+               class="code sev- "><tt><i>324</i>     <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">config</span> <span class="ow">or</span> <span class="s2">&quot;</span><span class="si">{}</span><span class="s2">&quot;</span></tt>
+            </div>
+            <div id="l325"
+               class="code sev- "><tt><i>325</i>     <span class="n">properties</span> <span class="o">=</span> <span class="n">settings</span><span class="o">.</span><span class="n">ConfReader</span><span class="p">(</span><span class="n">config</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">config</span><span class="p">)</span><span class="o">.</span><span class="n">get_prop_dic</span><span class="p">()</span></tt>
+            </div>
+            <div id="l326"
+               class="code sev- "><tt><i>326</i> &nbsp;</tt>
+            </div>
+            <div id="l327"
+               class="code sev- "><tt><i>327</i>     <span class="n">dna_timeseries</span><span class="p">(</span></tt>
+            </div>
+            <div id="l328"
+               class="code sev- "><tt><i>328</i>         <span class="n">input_ser_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">input_ser_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l329"
+               class="code sev- "><tt><i>329</i>         <span class="n">output_zip_path</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">output_zip_path</span><span class="p">,</span></tt>
+            </div>
+            <div id="l330"
+               class="code sev- "><tt><i>330</i>         <span class="n">properties</span><span class="o">=</span><span class="n">properties</span><span class="p">,</span></tt>
+            </div>
+            <div id="l331"
+               class="code sev- "><tt><i>331</i>     <span class="p">)</span></tt>
+            </div>
+            <div id="l332"
+               class="code sev- "><tt><i>332</i> &nbsp;</tt>
+            </div>
+            <div id="l333"
+               class="code sev- "><tt><i>333</i> &nbsp;</tt>
+            </div>
+            <div id="l334"
+               class="code sev- "><tt><i>334</i> <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span></tt>
+            </div>
+            <div id="l335"
+               class="code sev- "><tt><i>335</i>     <span class="n">main</span><span class="p">()</span></tt>
+            </div>
+            
+         </div>
+      </div>
+   </body>
+</html>
\ No newline at end of file
diff --git a/flake8/flake8badge.svg b/flake8/flake8badge.svg
index 55710d42..1b70a3be 100644
--- a/flake8/flake8badge.svg
+++ b/flake8/flake8badge.svg
@@ -1 +1 @@
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\ No newline at end of file
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" width="128" height="20" role="img" aria-label="Flake8: 0 C, 8 W, 0 I"><title>Flake8: 0 C, 8 W, 0 I</title><linearGradient id="s" x2="0" y2="100%"><stop offset="0" stop-color="#bbb" stop-opacity=".1"/><stop offset="1" stop-opacity=".1"/></linearGradient><clipPath id="r"><rect width="128" height="20" rx="3" fill="#fff"/></clipPath><g clip-path="url(#r)"><rect width="47" height="20" fill="#555"/><rect x="47" width="81" height="20" fill="#fe7d37"/><rect width="128" height="20" fill="url(#s)"/></g><g fill="#fff" text-anchor="middle" font-family="Verdana,Geneva,DejaVu Sans,sans-serif" text-rendering="geometricPrecision" font-size="110"><text aria-hidden="true" x="245" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="370">Flake8</text><text x="245" y="140" transform="scale(.1)" fill="#fff" textLength="370">Flake8</text><text aria-hidden="true" x="865" y="150" fill="#010101" fill-opacity=".3" transform="scale(.1)" textLength="710">0 C, 8 W, 0 I</text><text x="865" y="140" transform="scale(.1)" fill="#fff" textLength="710">0 C, 8 W, 0 I</text></g></svg>
\ No newline at end of file
diff --git a/flake8/flake8stats.txt b/flake8/flake8stats.txt
index 883e4fd8..099cfd6b 100644
--- a/flake8/flake8stats.txt
+++ b/flake8/flake8stats.txt
@@ -1 +1,2 @@
+4     E225 missing whitespace around operator
 4     W503 line break before binary operator
diff --git a/flake8/index.html b/flake8/index.html
index 48dc5971..7b8c1b61 100644
--- a/flake8/index.html
+++ b/flake8/index.html
@@ -9,11 +9,20 @@
       <div id="masthead" class="sev-2"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-11-15 12:09
+         <p id="versions">Generated on 2024-11-15 12:14
             with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
          </p>
          <ul id="index">
          
+         <li>
+            <a href="biobb_dna.dna.dna_averages.report.html">
+               <span class="count sev-2">
+                  3
+               </span>
+               biobb_dna/dna/dna_averages.py
+            </a>
+         </li>
+         
          <li>
             <a href="biobb_dna.interbp_correlations.interbpcorr.report.html">
                <span class="count sev-2">
@@ -32,6 +41,15 @@ <h1>flake8 violations</h1>
             </a>
          </li>
          
+         <li>
+            <a href="biobb_dna.dna.dna_timeseries.report.html">
+               <span class="count sev-2">
+                  1
+               </span>
+               biobb_dna/dna/dna_timeseries.py
+            </a>
+         </li>
+         
          </ul>
       </div>
    </body>
diff --git a/junit/junit.xml b/junit/junit.xml
index 73066c51..00c3b583 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="19" time="27.055" timestamp="2024-11-15T12:09:46.517059+00:00" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.515" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.461" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.568" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.289" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.369" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.881" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.365" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.441" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="0.884" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="7.305" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.081" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.363" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.790" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.229" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.419" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="4.461" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.081" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.299" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.258" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="19" time="30.340" timestamp="2024-11-15T12:15:12.917879+00:00" hostname="biobb-runners"><testcase classname="biobb_dna.test.unitests.test_backbone.test_bipopulations.TestBIPopulations" name="test_bipopulations" time="0.579" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_canonical_alpha_gamma.TestCanonicalAlphaGamma" name="test_canonicalag" time="0.497" /><testcase classname="biobb_dna.test.unitests.test_backbone.test_puckering.TestPuckering" name="test_puckering" time="0.706" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterHelparCorrelation" name="test_helparcorrelation" time="0.298" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterSequenceCorrelation" name="test_sequencecorrelation" time="0.388" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestInterBasepairCorrelation" name="test_basepaircorrelation" time="0.968" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraHelparCorrelation" name="test_helparcorrelation" time="0.297" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraSequenceCorrelation" name="test_sequencecorrelation" time="0.574" /><testcase classname="biobb_dna.test.unitests.test_correlation.test_correlation.TestIntraBasepairCorrelation" name="test_basepaircorrelation" time="0.963" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal.TestCanal" name="test_canal" time="7.358" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canal_unzip.TestCanalUnzip" name="test_canal_unzip" time="0.094" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_canion.TestCanal" name="test_canion" time="0.382" /><testcase classname="biobb_dna.test.unitests.test_curvesplus.test_curves.TestCurves" name="test_curves" time="6.815" /><testcase classname="biobb_dna.test.unitests.test_dna.test_averages.TestAverages" name="test_helparaverages" time="0.247" /><testcase classname="biobb_dna.test.unitests.test_dna.test_bimodality.TestBimodality" name="test_helparbimodality" time="0.605" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries.TestTimeSeries" name="test_helpartimeseries" time="5.200" /><testcase classname="biobb_dna.test.unitests.test_dna.test_timeseries_unzip.TestCanalUnzip" name="test_dna_timeseries_unzip" time="0.082" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestAvgStiffness" name="test_averagestiffness" time="0.266" /><testcase classname="biobb_dna.test.unitests.test_stiffness.test_stiffness.TestBasePairStiffness" name="test_basepairstiffness" time="0.282" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 64d6898d..1f9c4e7b 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 15-Nov-2024 at 12:10:13 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 15-Nov-2024 at 12:15:43 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">19 tests took 00:00:25.</p>
+        <p class="run-count">19 tests took 00:00:27.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
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class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;515 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nseqpos::::::::\n[]\n2024-11-15 12:09:48,281 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.0\n2024-11-15 12:09:48,281 [MainThread  ] [INFO ]  /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee directory successfully created\n2024-11-15 12:09:48,282 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\n2024-11-15 12:09:48,283 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\n2024-11-15 12:09:48,284 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\n2024-11-15 12:09:48,284 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\n2024-11-15 12:09:48,703 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee&amp;#x27;]\n2024-11-15 12:09:48,704 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_62/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_62/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_62/bipopulations/bipop.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/bipop_ref.jpg\n     IMAGE_A HASH: ff8981818181c9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8981818180c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.0\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee directory successfully created\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_62/bipopulations/sandbox_23401fe8-831d-48e8-8988-15af33cb86ee&amp;#x27;]\nINFO     /tmp/biobb/unitests_62/bipopulations/bipopulations_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;461 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td 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/home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\n2024-11-15 12:09:48,808 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\n2024-11-15 12:09:48,809 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\n2024-11-15 12:09:49,187 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_63/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_63/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/canonicalag/canonag.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef directory successfully created\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef\nINFO     /tmp/biobb/unitests_63/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/canonicalag/sandbox_8e02d745-a473-4f04-aeb5-cd4718791bef&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;568 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;568 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:49,268 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.0\n2024-11-15 12:09:49,268 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d directory successfully created\n2024-11-15 12:09:49,269 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d\n2024-11-15 12:09:49,270 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d\n2024-11-15 12:09:49,754 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d&amp;#x27;]\n2024-11-15 12:09:49,755 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_63/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/puckering/puckering.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d directory successfully created\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/puckering/sandbox_429edcea-9431-41c6-954d-1e127d605a4d&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;289 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;289 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:49,843 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\n2024-11-15 12:09:49,843 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f directory successfully created\n2024-11-15 12:09:49,843 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:49,844 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:49,844 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:49,844 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:49,844 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:49,845 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\n2024-11-15 12:09:50,044 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f&amp;#x27;]\n2024-11-15 12:09:50,046 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_63/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f directory successfully created\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/interhpcorr/sandbox_31ea5af7-46d6-460b-bae1-e25c7ad2d79f&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;369 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;369 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:50,131 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\n2024-11-15 12:09:50,131 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4 directory successfully created\n2024-11-15 12:09:50,132 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4\n2024-11-15 12:09:50,416 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4&amp;#x27;]\n2024-11-15 12:09:50,417 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_63/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4 directory successfully created\nINFO     /tmp/biobb/unitests_63/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4\nINFO     /tmp/biobb/unitests_63/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/interseqcorr/sandbox_a01ac475-c807-4af7-8a28-1878e51b83d4&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;881 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;881 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:50,504 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\n2024-11-15 12:09:50,505 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5 directory successfully created\n2024-11-15 12:09:50,505 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:50,506 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:50,507 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:50,508 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:50,509 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:50,509 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\n2024-11-15 12:09:51,293 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5&amp;#x27;]\n2024-11-15 12:09:51,294 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_63/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5 directory successfully created\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/interbpcorr/sandbox_afaa6b39-aa78-4caf-b2d0-00293f7510b5&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;365 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;365 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:51,385 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\n2024-11-15 12:09:51,385 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9 directory successfully created\n2024-11-15 12:09:51,386 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,386 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,386 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,387 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,387 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,387 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\n2024-11-15 12:09:51,669 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9&amp;#x27;]\n2024-11-15 12:09:51,670 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_63/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9 directory successfully created\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/intrahpcorr/sandbox_e52f317e-68e6-48f4-b255-3968e8e347f9&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_63\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;441 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;441 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:51,751 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\n2024-11-15 12:09:51,751 [MainThread  ] [INFO ]  /tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2 directory successfully created\n2024-11-15 12:09:51,752 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2\n2024-11-15 12:09:52,106 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2&amp;#x27;]\n2024-11-15 12:09:52,107 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_63/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_63/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_63/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_63/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_63/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2 directory successfully created\nINFO     /tmp/biobb/unitests_63/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2\nINFO     /tmp/biobb/unitests_63/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_63/intraseqcorr/sandbox_b8860531-83ee-48a0-ba40-f8085969f4a2&amp;#x27;]\nINFO     /tmp/biobb/unitests_63/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;884 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;884 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:52,197 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\n2024-11-15 12:09:52,197 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167 directory successfully created\n2024-11-15 12:09:52,198 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,199 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,199 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,200 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,201 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,202 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\n2024-11-15 12:09:52,990 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167&amp;#x27;]\n2024-11-15 12:09:52,991 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_64/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167 directory successfully created\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/intrabpcorr/sandbox_bcbc46b5-74f3-4883-ab46-4b71c8883167&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:09:53,078 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\n2024-11-15 12:09:53,078 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7 directory successfully created\n2024-11-15 12:09:53,090 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7\n2024-11-15 12:09:53,090 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:09:53,090 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-11-15 12:10:00,189 [MainThread  ] [INFO ]  Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\n2024-11-15 12:10:00,190 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:10:00,336 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7&amp;#x27;]\n2024-11-15 12:10:00,336 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7 directory successfully created\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_canal/sandbox_b23e4727-aef8-4b36-9487-8f2c719e82e7&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;81 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;81 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:00,386 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\n2024-11-15 12:10:00,386 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76 directory successfully created\n2024-11-15 12:10:00,416 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76\n2024-11-15 12:10:00,418 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76/canal_unzip_output.ser.\n2024-11-15 12:10:00,423 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76&amp;#x27;]\n2024-11-15 12:10:00,424 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_64/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_64/canal_unzip/canal_unzip_output.ser\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_64/canal_unzip/canal_unzip_output.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76 directory successfully created\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/canal_unzip/sandbox_e8f3c4dd-2b92-41be-9f93-9fbd654d3a76&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;363 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;363 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:00,467 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\n2024-11-15 12:10:00,467 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5 directory successfully created\n2024-11-15 12:10:00,740 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\n2024-11-15 12:10:00,740 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\n2024-11-15 12:10:00,741 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\n2024-11-15 12:10:00,741 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:10:00,741 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2024-11-15 12:10:00,745 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2024-11-15 12:10:00,745 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:10:00,787 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5&amp;#x27;]\n2024-11-15 12:10:00,788 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5 directory successfully created\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_canion/sandbox_6fcd669e-d337-42af-b829-94fa47a87ff5&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:00,832 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\n2024-11-15 12:10:00,833 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917 directory successfully created\n2024-11-15 12:10:00,895 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917\n2024-11-15 12:10:00,895 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917\n2024-11-15 12:10:00,897 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-15 12:10:00,897 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:10:00,897 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2024-11-15 12:10:07,488 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2024-11-15 12:10:07,489 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:10:07,527 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917&amp;#x27;]\n2024-11-15 12:10:07,528 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_64/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_64/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_64/biobb_curves/curves_output.lis\n     FILE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.lis\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_64/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: 25264895-b1b6-4fcd-a83f-4705a04fa040/curves_output.cdi\n        File_B: 1337f017-86b2-4538-92ae-72e52e2af666/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917 directory successfully created\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/biobb_curves/sandbox_6ab143ce-9d67-4c4d-aef2-0fc3b4725917&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;229 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;229 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:07,623 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.0\n2024-11-15 12:10:07,623 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc directory successfully created\n2024-11-15 12:10:07,623 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc\n2024-11-15 12:10:07,777 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc&amp;#x27;]\n2024-11-15 12:10:07,777 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_64/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/dna_averages/avg_out.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc directory successfully created\nINFO     /tmp/biobb/unitests_64/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc\nINFO     /tmp/biobb/unitests_64/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_averages/sandbox_a4a03540-3bbb-4d31-8b3f-accd96d7e6fc&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;419 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;419 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:07,854 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\n2024-11-15 12:10:07,854 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428 directory successfully created\n2024-11-15 12:10:07,854 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428\n2024-11-15 12:10:08,230 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428&amp;#x27;]\n2024-11-15 12:10:08,230 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_64/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428 directory successfully created\nINFO     /tmp/biobb/unitests_64/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428\nINFO     /tmp/biobb/unitests_64/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_bimodality/sandbox_2c9e3950-911b-48a2-9360-e02445dc0428&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:04&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:04&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:08,275 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\n2024-11-15 12:10:08,276 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438 directory successfully created\n2024-11-15 12:10:08,276 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438\n2024-11-15 12:10:12,693 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438&amp;#x27;]\n2024-11-15 12:10:12,693 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438 directory successfully created\nINFO     /tmp/biobb/unitests_64/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438\nINFO     /tmp/biobb/unitests_64/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_timeseries/sandbox_250b097c-8466-4708-a0ae-3079961a6438&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;81 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;81 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:12,739 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\n2024-11-15 12:10:12,739 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3 directory successfully created\n2024-11-15 12:10:12,740 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3\n2024-11-15 12:10:12,740 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3/dna_timeseries_unzip.csv.\n2024-11-15 12:10:12,741 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3/dna_timeseries_unzip.jpg.\n2024-11-15 12:10:12,742 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3&amp;#x27;]\n2024-11-15 12:10:12,742 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3 directory successfully created\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/dna_timeseries_unzip/sandbox_94ce9273-77c9-4e96-b304-3d32fb3733b3&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;299 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;299 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:12,878 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\n2024-11-15 12:10:12,879 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b directory successfully created\n2024-11-15 12:10:12,879 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b\n2024-11-15 12:10:13,044 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b&amp;#x27;]\n2024-11-15 12:10:13,044 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_64/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b directory successfully created\nINFO     /tmp/biobb/unitests_64/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b\nINFO     /tmp/biobb/unitests_64/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/average_stiffness/sandbox_f05fb8d9-c3dd-4501-bce3-17a945f1f24b&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;258 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;258 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:10:13,119 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\n2024-11-15 12:10:13,120 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52 directory successfully created\n2024-11-15 12:10:13,120 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\n2024-11-15 12:10:13,120 [MainThread  ] [INFO ]  Copy: 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/home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\n2024-11-15 12:10:13,300 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_64/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52 directory successfully created\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_64/basepair_stiffness/sandbox_166aa4f6-e1ee-4a11-ba0f-83ada72eab52\nINFO     /tmp/biobb/unitests_64/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_64\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.12.7&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&#34;, &#34;duration&#34;: &#34;579 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_bipopulations.py::TestBIPopulations::test_bipopulations&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;579 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\nseqpos::::::::\n[]\n2024-11-15 12:15:16,448 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.0\n2024-11-15 12:15:16,449 [MainThread  ] [INFO ]  /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84 directory successfully created\n2024-11-15 12:15:16,450 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\n2024-11-15 12:15:16,450 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\n2024-11-15 12:15:16,451 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\n2024-11-15 12:15:16,452 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\n2024-11-15 12:15:16,909 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84&amp;#x27;]\n2024-11-15 12:15:16,910 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_64/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_64/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_64/bipopulations/bipop.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/bipop_ref.jpg\n     IMAGE_A HASH: ff8981818181c9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8981818180c9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 1 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.0\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84 directory successfully created\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilC.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_epsilW.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaC.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_zetaW.ser to /tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_64/bipopulations/sandbox_e1fa0524-37f5-474d-ae1b-cd1be2d92e84&amp;#x27;]\nINFO     /tmp/biobb/unitests_64/bipopulations/bipopulations_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&#34;, &#34;duration&#34;: &#34;497 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_canonical_alpha_gamma.py::TestCanonicalAlphaGamma::test_canonicalag&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;497 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:17,032 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.canonicalag Version: 5.0.0\n2024-11-15 12:15:17,032 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff directory successfully created\n2024-11-15 12:15:17,033 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\n2024-11-15 12:15:17,034 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\n2024-11-15 12:15:17,034 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\n2024-11-15 12:15:17,035 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\n2024-11-15 12:15:17,442 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_65/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_65/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/canonicalag/canonag.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/canonag_ref.jpg\n     IMAGE_A HASH: ff8081818180f9ff SIZE: 64 bits\n     IMAGE_B HASH: ff8081818180f9ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff directory successfully created\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaC.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_alphaW.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaC.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_gammaW.ser to /tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff\nINFO     /tmp/biobb/unitests_65/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/canonicalag/sandbox_ff977333-a377-49fd-b34c-231170fd5cff&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&#34;, &#34;duration&#34;: &#34;706 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_backbone/test_puckering.py::TestPuckering::test_puckering&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;706 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:17,534 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.0\n2024-11-15 12:15:17,535 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad directory successfully created\n2024-11-15 12:15:17,536 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad\n2024-11-15 12:15:17,537 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad\n2024-11-15 12:15:18,150 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad&amp;#x27;]\n2024-11-15 12:15:18,150 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_65/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/puckering/puckering.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/backbone/puckering_ref.jpg\n     IMAGE_A HASH: eb8181808081ffff SIZE: 64 bits\n     IMAGE_B HASH: eb8181808081ffff SIZE: 64 bits\n     TOLERANCE: 20%, ABS TOLERANCE: 12.8 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad directory successfully created\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseC.ser to /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/backbone/canal_output_phaseW.ser to /tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/puckering/sandbox_830eeb9f-28b7-4504-a293-4b9294c2bfad&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;298 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;298 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:18,241 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\n2024-11-15 12:15:18,241 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b directory successfully created\n2024-11-15 12:15:18,242 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,242 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,242 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,243 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,243 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,243 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\n2024-11-15 12:15:18,455 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b&amp;#x27;]\n2024-11-15 12:15:18,455 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_65/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/interhpcorr/inter_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_hpcorr_ref.jpg\n     IMAGE_A HASH: ff83868890a1c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83868890a1c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b directory successfully created\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/interhpcorr/sandbox_17fa1e55-402e-49b4-b62f-9a56a82b627b&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;388 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;388 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:18,541 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\n2024-11-15 12:15:18,541 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b directory successfully created\n2024-11-15 12:15:18,542 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b\n2024-11-15 12:15:18,842 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b&amp;#x27;]\n2024-11-15 12:15:18,842 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_65/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/interseqcorr/inter_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_seqcorr_roll.jpg\n     IMAGE_A HASH: ff8080889080c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff8080889080c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b directory successfully created\nINFO     /tmp/biobb/unitests_65/interseqcorr/interseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b\nINFO     /tmp/biobb/unitests_65/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/interseqcorr/sandbox_a1e19e38-18f7-49e5-92cb-3e8b58c9bd3b&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;968 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestInterBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;968 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:18,931 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\n2024-11-15 12:15:18,932 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46 directory successfully created\n2024-11-15 12:15:18,933 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:18,933 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:18,934 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:18,935 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:18,936 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:18,937 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\n2024-11-15 12:15:19,807 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46&amp;#x27;]\n2024-11-15 12:15:19,808 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_65/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/interbpcorr/inter_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/inter_bpcorr_ref.jpg\n     IMAGE_A HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     IMAGE_B HASH: fd6d6dfffd6c0183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46 directory successfully created\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shift.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_slide.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_rise.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_tilt.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_roll.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_twist.ser to /tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/interbpcorr/sandbox_5fef08de-5671-41f4-8b58-d318fbcc4c46&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&#34;, &#34;duration&#34;: &#34;297 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraHelparCorrelation::test_helparcorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;297 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:19,901 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\n2024-11-15 12:15:19,901 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3 directory successfully created\n2024-11-15 12:15:19,901 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\n2024-11-15 12:15:19,902 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\n2024-11-15 12:15:19,902 [MainThread  ] [INFO ]  Copy: 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[&amp;#x27;/tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3&amp;#x27;]\n2024-11-15 12:15:20,114 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_65/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/intrahpcorr/intra_hpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_hpcorr_ref.jpg\n     IMAGE_A HASH: fb81848890a0e0ff SIZE: 64 bits\n     IMAGE_B HASH: fb81848890a0e0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3 directory successfully created\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_shear_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stretch_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_stagger_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_buckle_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_propel_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/series_opening_A.csv to /tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/intrahpcorr/sandbox_5f74cbbf-4888-4ffa-8618-392ddf99a8a3&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_65\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&#34;, &#34;duration&#34;: &#34;574 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraSequenceCorrelation::test_sequencecorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;574 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:20,201 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\n2024-11-15 12:15:20,202 [MainThread  ] [INFO ]  /tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39 directory successfully created\n2024-11-15 12:15:20,203 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39\n2024-11-15 12:15:20,690 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39&amp;#x27;]\n2024-11-15 12:15:20,691 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_65/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_65/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_65/intraseqcorr/intra_seqcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_seqcorr_buckle.jpg\n     IMAGE_A HASH: ff83848890a0c0ff SIZE: 64 bits\n     IMAGE_B HASH: ff83848890a0c0ff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_65/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_65/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39 directory successfully created\nINFO     /tmp/biobb/unitests_65/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39\nINFO     /tmp/biobb/unitests_65/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_65/intraseqcorr/sandbox_c1271e99-af57-4f79-886d-0d2f6cdc3b39&amp;#x27;]\nINFO     /tmp/biobb/unitests_65/intraseqcorr/intraseqcorr_log.out:file_utils.py:409\n\n&#34;}], &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&#34;, &#34;duration&#34;: &#34;963 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_correlation/test_correlation.py::TestIntraBasepairCorrelation::test_basepaircorrelation&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;963 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:20,778 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\n2024-11-15 12:15:20,778 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2 directory successfully created\n2024-11-15 12:15:20,779 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:20,780 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:20,781 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:20,781 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:20,782 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:20,783 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\n2024-11-15 12:15:21,646 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2&amp;#x27;]\n2024-11-15 12:15:21,647 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_66/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_66/intrabpcorr/intra_bpcorr.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/correlation/intra_bpcorr_ref.jpg\n     IMAGE_A HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     IMAGE_B HASH: 01f5f7f7fcf40183 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2 directory successfully created\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_shear.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stretch.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_stagger.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_buckle.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_propel.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/correlation/canal_output_opening.ser to /tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/intrabpcorr/sandbox_092e7e7c-bd50-462c-8ab6-443b028b02a2&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal.py::TestCanal::test_canal&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:21,741 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\n2024-11-15 12:15:21,742 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae directory successfully created\n2024-11-15 12:15:21,753 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae\n2024-11-15 12:15:21,753 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:15:21,754 [MainThread  ] [INFO ]  Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\n2024-11-15 12:15:28,896 [MainThread  ] [INFO ]  Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\n2024-11-15 12:15:28,896 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:15:29,048 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae&amp;#x27;]\n2024-11-15 12:15:29,048 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae directory successfully created\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:63 Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd=0,itdel=1,\n  histo=.t.,\n  series=.t.,\n  corr=.t.,\n&amp;amp;end\ncurves_output.cda CGCGAATTCGCG\n!\n\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:36 Executing: Canal &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canal_output,\n  cormin=0.6,\n  lev1=0,lev2=0,\n  itst=0,itnd...\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_canal/sandbox_bd249bb3-de00-42a6-93d1-64eeae70f3ae&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&#34;, &#34;duration&#34;: &#34;94 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canal_unzip.py::TestCanalUnzip::test_canal_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;94 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:29,103 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\n2024-11-15 12:15:29,103 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f directory successfully created\n2024-11-15 12:15:29,136 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f\n2024-11-15 12:15:29,143 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f/canal_unzip_output.ser.\n2024-11-15 12:15:29,148 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f&amp;#x27;]\n2024-11-15 12:15:29,149 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_66/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_66/canal_unzip/canal_unzip_output.ser\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.ser\n        File_A hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\x84{\\xb8:rpBW\\xb4M\\x86\\xfd8I\\xfe\\xd3i\\x19CV_\\xd7\\x91\\xa5\\xf4\\xf4 \\xa6\\xed\\xc1\\xec&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_66/canal_unzip/canal_unzip_output.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/canal_unzip_output.txt\n        File_A hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n        File_B hash: b&amp;#x27;\\x00&amp;gt;\\x1f\\x86\\x87\\xae]^K\\t\\xa5\\x9a3\\x17\\xf1\\x91P\\x97O\\x04q\\xd6\\xd3d\\n\\xec4j\\x1d\\x1a\\x82\\xa5&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f directory successfully created\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/canal_unzip/sandbox_615c99d4-f31b-4752-8a49-820397d7812f&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&#34;, &#34;duration&#34;: &#34;382 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_canion.py::TestCanal::test_canion&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;382 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:29,198 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\n2024-11-15 12:15:29,198 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d directory successfully created\n2024-11-15 12:15:29,483 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\n2024-11-15 12:15:29,484 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\n2024-11-15 12:15:29,484 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\n2024-11-15 12:15:29,485 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:15:29,485 [MainThread  ] [INFO ]  Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\n2024-11-15 12:15:29,489 [MainThread  ] [INFO ]  Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\n2024-11-15 12:15:29,489 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:15:29,533 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d&amp;#x27;]\n2024-11-15 12:15:29,533 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d directory successfully created\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:63 Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_avg,\n  type=K+,\n  dlow=5.8,\n  dhig=7.2,\n  rlow=0,\n  rhig=18,\n  alow=0,\n  ahig=360,\n  itst=0,\n  itnd=0,\n  itdel=1,\n  rmsf=.f.,\n  circ=.f.,\n&amp;amp;end\n!\n\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:36 Executing: Canion &amp;lt;&amp;lt;! \n&amp;amp;inp\n  lis=canion_output,\n  dat=THGA_K,\n  axfrm=THGA,\n  solute=THGA_...\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_canion/sandbox_934d1ad6-9957-472a-8b46-5c78165fb35d&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&#34;, &#34;duration&#34;: &#34;00:00:07&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_curvesplus/test_curves.py::TestCurves::test_curves&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:07&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:29,583 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\n2024-11-15 12:15:29,583 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f directory successfully created\n2024-11-15 12:15:29,644 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f\n2024-11-15 12:15:29,645 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f\n2024-11-15 12:15:29,647 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-15 12:15:29,648 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 12:15:29,648 [MainThread  ] [INFO ]  Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\n2024-11-15 12:15:36,256 [MainThread  ] [INFO ]  Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\n2024-11-15 12:15:36,256 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 12:15:36,298 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f&amp;#x27;]\n2024-11-15 12:15:36,299 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_66/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_66/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_66/biobb_curves/curves_output.lis\n     FILE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.lis\nThis is a ZIP comparison!\nUnzipping:\nCreating a unique_dir for: /tmp/biobb/unitests_66/biobb_curves/curves_output.zip\nCreating a unique_dir for: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/curvesplus/curves_trj_output.zip\nComparing: \n        File_A: 08e4e7da-d71e-472d-8d3a-a383a70b7cae/curves_output.cdi\n        File_B: d3f3d3ad-f633-4c2e-9a40-c694df233ae9/curves_output.cdi\n        File_A hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n        File_B hash: b&amp;#x27;\\xbf\\x13\\x93\\xa0\\xc8\\xba\\x96\\xaa\\xd5sy\\xda\\x0f\\xe1m|\\xab\\xd4\\x9c z\\x9a\\x9d\\xde\\x07\\x7f\\xe3\\x1c\\x0cf_h&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f directory successfully created\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:63 Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  lis=&amp;#x27;curves_output&amp;#x27;,\n  lib=.curvesplus/standard,\n  ions=.t.,\n  test=.f.,\n  line=.f.,\n  fit=.t.,\n  axfrm=.f.,\n  itst=0,itnd=0,itdel=1,\n&amp;amp;end\n2 1 -1 0 0\n1:12\n24:13\n!\n\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:36 Executing: Cur+ &amp;lt;&amp;lt;! \n&amp;amp;inp\n  file=structure.stripped.trj,\n  ftop=structure.stripped.top,\n  l...\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/biobb_curves/sandbox_c0051fde-4f33-4d1b-948e-d9f09132852f&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&#34;, &#34;duration&#34;: &#34;247 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_averages.py::TestAverages::test_helparaverages&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;247 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:36,403 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.0\n2024-11-15 12:15:36,403 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0 directory successfully created\n2024-11-15 12:15:36,404 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0\n2024-11-15 12:15:36,566 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0&amp;#x27;]\n2024-11-15 12:15:36,566 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_66/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_66/dna_averages/avg_out.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/shift_avg.jpg\n     IMAGE_A HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     IMAGE_B HASH: c07e3e32163f3ee3 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0 directory successfully created\nINFO     /tmp/biobb/unitests_66/dna_averages/dna_averages_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0\nINFO     /tmp/biobb/unitests_66/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_averages/sandbox_7c055a13-3a22-49c6-bad4-9144a930bcb0&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&#34;, &#34;duration&#34;: &#34;605 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_bimodality.py::TestBimodality::test_helparbimodality&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;605 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:36,651 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\n2024-11-15 12:15:36,651 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492 directory successfully created\n2024-11-15 12:15:36,652 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492\n2024-11-15 12:15:37,206 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492&amp;#x27;]\n2024-11-15 12:15:37,207 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_66/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492 directory successfully created\nINFO     /tmp/biobb/unitests_66/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/series_shift_AT.csv to /tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492\nINFO     /tmp/biobb/unitests_66/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_bimodality/sandbox_c81a669d-cc97-4eb4-8552-3d8d1b51f492&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&#34;, &#34;duration&#34;: &#34;00:00:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries.py::TestTimeSeries::test_helpartimeseries&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:37,260 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\n2024-11-15 12:15:37,260 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6 directory successfully created\n2024-11-15 12:15:37,261 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6\n2024-11-15 12:15:42,410 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6&amp;#x27;]\n2024-11-15 12:15:42,410 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6 directory successfully created\nINFO     /tmp/biobb/unitests_66/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/canal_output_shift.ser to /tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6\nINFO     /tmp/biobb/unitests_66/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_timeseries/sandbox_d54bdce6-10b3-44c1-83fc-a98d2a90fba6&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&#34;, &#34;duration&#34;: &#34;82 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_dna/test_timeseries_unzip.py::TestCanalUnzip::test_dna_timeseries_unzip&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;82 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:42,460 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\n2024-11-15 12:15:42,460 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51 directory successfully created\n2024-11-15 12:15:42,461 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51\n2024-11-15 12:15:42,462 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51/dna_timeseries_unzip.csv.\n2024-11-15 12:15:42,462 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51/dna_timeseries_unzip.jpg.\n2024-11-15 12:15:42,463 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51&amp;#x27;]\n2024-11-15 12:15:42,463 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.csv\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.csv\n        File_A hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;2\\xf3\\xc2\\xe4\\x137\\xc2\\xfc\\x98\\xc6A\\xe1\\x14T\\xeb\\xb2k\\xad\\xd5\\xe7y\\tx\\xd5\\xa1R\\xd1\\xd6\\xac\\xd1v\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.txt\n        File_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.txt\n        File_A hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\n        File_B hash: b&amp;#x27;\\xe3\\xbc\\x13{\\xa6\\r\\x807]\\x87\\x14|u\\xc6\\xbe\\x9d\\xca\\x8bl\\x96\\x86Z\\xd7\\x973+@+\\x1a\\xe4[\\x1b&amp;#x27;\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/dna/dna_timeseries_unzip.jpg\n     IMAGE_A HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     IMAGE_B HASH: fff7f7e7e3e3c3f7 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51 directory successfully created\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/dna_timeseries_unzip/sandbox_a51c0319-8610-453a-86eb-0ff85a27bd51&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&#34;, &#34;duration&#34;: &#34;266 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestAvgStiffness::test_averagestiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;266 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:42,545 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\n2024-11-15 12:15:42,545 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9 directory successfully created\n2024-11-15 12:15:42,546 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9\n2024-11-15 12:15:42,730 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9&amp;#x27;]\n2024-11-15 12:15:42,731 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_66/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_66/average_stiffness/avgstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg\n     IMAGE_A HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     IMAGE_B HASH: 017f7f7f1d7f7e80 SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9 directory successfully created\nINFO     /tmp/biobb/unitests_66/average_stiffness/average_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/canal_output_roll.ser to /tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9\nINFO     /tmp/biobb/unitests_66/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_66/average_stiffness/sandbox_a72c5523-2001-45a7-affe-b06a757baae9&amp;#x27;]\nINFO     /tmp/biobb/unitests_66/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}], &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&#34;, &#34;duration&#34;: &#34;282 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_dna/test/unitests/test_stiffness/test_stiffness.py::TestBasePairStiffness::test_basepairstiffness&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;282 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-15 12:15:42,811 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\n2024-11-15 12:15:42,812 [MainThread  ] [INFO ]  /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05 directory successfully created\n2024-11-15 12:15:42,812 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:42,812 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:42,813 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:42,813 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:42,813 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:42,814 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\n2024-11-15 12:15:43,011 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_66/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_66/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_66/basepair_stiffness/bpstiff.jpg\n     IMAGE_B: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/reference/stiffness/stiffbp_ref.jpg\n     IMAGE_A HASH: ff8080909080ffff SIZE: 64 bits\n     IMAGE_B HASH: ff8080909080ffff SIZE: 64 bits\n     TOLERANCE: 1.0%, ABS TOLERANCE: 1 bits, DIFFERENCE: 0 bits\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.0\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05 directory successfully created\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_shift_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_slide_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_rise_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_tilt_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_roll_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/stiffness/series_twist_AA.csv to /tmp/biobb/unitests_66/basepair_stiffness/sandbox_f0ea5b4b-efe8-41f3-a5d2-04748fae9c05\nINFO     /tmp/biobb/unitests_66/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_66\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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