From 1f8fe8560d2f8c5e0c89d4ef6cb79a9dd745c3f7 Mon Sep 17 00:00:00 2001
From: PauAndrio <andriopau@gmail.com>
Date: Fri, 15 Nov 2024 13:25:56 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
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             <a class="nav" href="z_97f47455ed834d2d_test_correlation_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_100f5897bddc1993_test_averages_py.html b/coverage/z_100f5897bddc1993_test_averages_py.html
index 2ab43437..3039122c 100644
--- a/coverage/z_100f5897bddc1993_test_averages_py.html
+++ b/coverage/z_100f5897bddc1993_test_averages_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -114,7 +114,7 @@ <h2>
             <a class="nav" href="z_100f5897bddc1993_test_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_bimodality_py.html b/coverage/z_100f5897bddc1993_test_bimodality_py.html
index ec10c7ca..687c42af 100644
--- a/coverage/z_100f5897bddc1993_test_bimodality_py.html
+++ b/coverage/z_100f5897bddc1993_test_bimodality_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -110,7 +110,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_timeseries_py.html b/coverage/z_100f5897bddc1993_test_timeseries_py.html
index 5fa3d63d..f01efdca 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_100f5897bddc1993_test_timeseries_unzip_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -112,7 +112,7 @@ <h2>
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             &nbsp; &nbsp; &nbsp;
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+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
index f6c0bcac..3e7a4a5e 100644
--- a/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
+++ b/coverage/z_100f5897bddc1993_test_timeseries_unzip_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_cda7f8e8576a7189_test_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -115,7 +115,7 @@ <h2>
             <a class="nav" href="z_cda7f8e8576a7189_test_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_159731231e5c9c9d___init___py.html b/coverage/z_159731231e5c9c9d___init___py.html
index 9e60ef69..9821bb00 100644
--- a/coverage/z_159731231e5c9c9d___init___py.html
+++ b/coverage/z_159731231e5c9c9d___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_159731231e5c9c9d_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -94,7 +94,7 @@ <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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_159731231e5c9c9d_bipopulations_py.html b/coverage/z_159731231e5c9c9d_bipopulations_py.html
index 53fd3039..ae8e1a47 100644
--- a/coverage/z_159731231e5c9c9d_bipopulations_py.html
+++ b/coverage/z_159731231e5c9c9d_bipopulations_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_159731231e5c9c9d_canonicalag_py.html b/coverage/z_159731231e5c9c9d_canonicalag_py.html
index 85eb8ae9..922bcfe4 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;
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-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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             <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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_159731231e5c9c9d_puckering_py.html b/coverage/z_159731231e5c9c9d_puckering_py.html
index 220d5105..6c569956 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91___init___py.html b/coverage/z_3afbcd666ed82c91___init___py.html
index 34a9facb..6c2fd8eb 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 13:20 +0000
+            created at 2024-11-15 13:25 +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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_averages_py.html b/coverage/z_3afbcd666ed82c91_dna_averages_py.html
index cac12a39..15cdb22c 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html b/coverage/z_3afbcd666ed82c91_dna_bimodality_py.html
index bea4c104..4b4c76c5 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html b/coverage/z_3afbcd666ed82c91_dna_timeseries_py.html
index ded489b8..58a5c334 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +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 296d3e57..ba1f60a7 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc___init___py.html b/coverage/z_64e03be4370b7ecc___init___py.html
index 8aae06d3..b781a9dd 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 13:20 +0000
+            created at 2024-11-15 13:25 +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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrabpcorr_py.html
index f2c106b5..408db656 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html b/coverage/z_64e03be4370b7ecc_intrahpcorr_py.html
index 30e9a0ed..5a553941 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html b/coverage/z_64e03be4370b7ecc_intraseqcorr_py.html
index 4c98f970..901a7a7e 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4___init___py.html b/coverage/z_74fa14c6d0e940a4___init___py.html
index 0f6e9aba..aa88a797 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 13:20 +0000
+            created at 2024-11-15 13:25 +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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canal_py.html
index e800bd41..eac5204d 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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html b/coverage/z_74fa14c6d0e940a4_biobb_canion_py.html
index 5ed362a9..0d45b9d1 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html b/coverage/z_74fa14c6d0e940a4_biobb_curves_py.html
index bfd06648..bc41c460 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html b/coverage/z_74fa14c6d0e940a4_canal_unzip_py.html
index 36b9d376..54a7a296 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_76997f7c8cf1ed45___init___py.html b/coverage/z_76997f7c8cf1ed45___init___py.html
index 2a85506a..c34ba320 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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -108,7 +108,7 @@ <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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html b/coverage/z_8030ef0ea5bfd6aa_test_canal_py.html
index 586999f3..f321a9e8 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 13:20 +0000
+            created at 2024-11-15 13:25 +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 13:20 +0000
+            created at 2024-11-15 13:25 +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 d6732436..aa326ffc 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;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <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;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +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 edc8d0a8..f77588a6 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 13:20 +0000
+            created at 2024-11-15 13:25 +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_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html b/coverage/z_8030ef0ea5bfd6aa_test_curves_py.html
index b83c519d..6beb4ee9 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 13:20 +0000
+            created at 2024-11-15 13:25 +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_100f5897bddc1993_test_averages_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_833b0317e3c43dca___init___py.html b/coverage/z_833b0317e3c43dca___init___py.html
index 855413cd..fb210dfe 100644
--- a/coverage/z_833b0317e3c43dca___init___py.html
+++ b/coverage/z_833b0317e3c43dca___init___py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_common_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 13:20 +0000
+            created at 2024-11-15 13:25 +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_833b0317e3c43dca_common_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_833b0317e3c43dca_common_py.html b/coverage/z_833b0317e3c43dca_common_py.html
index 475a3997..41bb4a71 100644
--- a/coverage/z_833b0317e3c43dca_common_py.html
+++ b/coverage/z_833b0317e3c43dca_common_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_constants_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -119,7 +119,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_constants_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
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-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_833b0317e3c43dca_constants_py.html b/coverage/z_833b0317e3c43dca_constants_py.html
index f26e1d62..c389c898 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;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -162,7 +162,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_loader_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_833b0317e3c43dca_loader_py.html b/coverage/z_833b0317e3c43dca_loader_py.html
index ac9e736a..975b8e68 100644
--- a/coverage/z_833b0317e3c43dca_loader_py.html
+++ b/coverage/z_833b0317e3c43dca_loader_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="z_833b0317e3c43dca_transform_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -133,7 +133,7 @@ <h2>
             <a class="nav" href="z_833b0317e3c43dca_transform_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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_833b0317e3c43dca_transform_py.html b/coverage/z_833b0317e3c43dca_transform_py.html
index 19a5d978..d4581339 100644
--- a/coverage/z_833b0317e3c43dca_transform_py.html
+++ b/coverage/z_833b0317e3c43dca_transform_py.html
@@ -65,7 +65,7 @@ <h2>
             <a id="nextFileLink" class="nav" href="index.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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,7 +102,7 @@ <h2>
             <a class="nav" href="index.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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_8a2a7f872cf1434f___init___py.html b/coverage/z_8a2a7f872cf1434f___init___py.html
index a5481c72..0cfa31e4 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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
         <aside class="hidden">
             <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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interbpcorr_py.html
index 23ab2f55..67ce986d 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html b/coverage/z_8a2a7f872cf1434f_interhpcorr_py.html
index 8699808f..89c64bdf 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html b/coverage/z_8a2a7f872cf1434f_interseqcorr_py.html
index 442413b1..7d1a8b26 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_957b841f7413f0a1___init___py.html b/coverage/z_957b841f7413f0a1___init___py.html
index 24c53054..39df838c 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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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         <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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
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diff --git a/coverage/z_97f47455ed834d2d_test_correlation_py.html b/coverage/z_97f47455ed834d2d_test_correlation_py.html
index 0c0d6129..4c78e634 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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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         <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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_9de9475b0a6fab52___init___py.html b/coverage/z_9de9475b0a6fab52___init___py.html
index bc7afe4a..555d7788 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 13:20 +0000
+            created at 2024-11-15 13:25 +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;
             <a class="nav" href="https://coverage.readthedocs.io/en/7.6.5">coverage.py v7.6.5</a>,
-            created at 2024-11-15 13:20 +0000
+            created at 2024-11-15 13:25 +0000
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diff --git a/coverage/z_9de9475b0a6fab52_average_stiffness_py.html b/coverage/z_9de9475b0a6fab52_average_stiffness_py.html
index 0df101b0..86720b3b 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html b/coverage/z_9de9475b0a6fab52_basepair_stiffness_py.html
index 36a44bba..ccd7db04 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 13:20 +0000
+            created at 2024-11-15 13:25 +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="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="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="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="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="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="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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_cda7f8e8576a7189_test_stiffness_py.html b/coverage/z_cda7f8e8576a7189_test_stiffness_py.html
index 7c818380..e54f2219 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 13:20 +0000
+            created at 2024-11-15 13:25 +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 13:20 +0000
+            created at 2024-11-15 13:25 +0000
         </p>
     </div>
 </footer>
diff --git a/flake8/biobb_dna.dna.dna_averages.report.html b/flake8/biobb_dna.dna.dna_averages.report.html
deleted file mode 100644
index 49419b66..00000000
--- a/flake8/biobb_dna.dna.dna_averages.report.html
+++ /dev/null
@@ -1,83 +0,0 @@
-<!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
deleted file mode 100644
index db5d0a64..00000000
--- a/flake8/biobb_dna.dna.dna_averages.source.html
+++ /dev/null
@@ -1,890 +0,0 @@
-<!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
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deleted file mode 100644
index 9c998414..00000000
--- a/flake8/biobb_dna.dna.dna_timeseries.report.html
+++ /dev/null
@@ -1,73 +0,0 @@
-<!DOCTYPE html>
-<html>
-   <head>
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-               href="biobb_dna.dna.dna_timeseries.source.html">
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-            </a></p>
-         <h1>
-            <a href="index.html">
-               <img src="back.svg" alt="&#x2B05;">
-               biobb_dna/dna/dna_timeseries.py
-            </a>
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-
-         <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>
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diff --git a/flake8/biobb_dna.dna.dna_timeseries.source.html b/flake8/biobb_dna.dna.dna_timeseries.source.html
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@@ -1,1037 +0,0 @@
-<!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>
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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;500 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 13:19:59,217 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.canonicalag Version: 5.0.1\n2024-11-15 13:19:59,217 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1 directory successfully created\n2024-11-15 13:19:59,218 [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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\n2024-11-15 13:19:59,219 [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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\n2024-11-15 13:19:59,220 [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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\n2024-11-15 13:19:59,220 [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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\n2024-11-15 13:19:59,630 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_77/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_77/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1 directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\nINFO     /tmp/biobb/unitests_77/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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\nINFO     /tmp/biobb/unitests_77/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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\nINFO     /tmp/biobb/unitests_77/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_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1\nINFO     /tmp/biobb/unitests_77/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/canonicalag/sandbox_f6235f3a-5900-4fbc-beeb-62c84689bac1&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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;679 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;679 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 13:19:59,721 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.1\n2024-11-15 13:19:59,721 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb directory successfully created\n2024-11-15 13:19:59,722 [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_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb\n2024-11-15 13:19:59,723 [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_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb\n2024-11-15 13:20:00,310 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb&amp;#x27;]\n2024-11-15 13:20:00,310 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_77/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb\nINFO     /tmp/biobb/unitests_77/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_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb\nINFO     /tmp/biobb/unitests_77/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/puckering/sandbox_5c8f7791-f7ca-4f09-b2e6-6376d3b26ddb&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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;402 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;402 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 13:20:00,405 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\n2024-11-15 13:20:00,405 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3 directory successfully created\n2024-11-15 13:20:00,406 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,406 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,406 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,407 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,407 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,407 [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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\n2024-11-15 13:20:00,719 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3&amp;#x27;]\n2024-11-15 13:20:00,720 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_77/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3 directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/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_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3\nINFO     /tmp/biobb/unitests_77/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/interhpcorr/sandbox_8511ad65-6166-400f-b41c-03c952a5e1c3&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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;395 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;395 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 13:20:00,806 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\n2024-11-15 13:20:00,806 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff directory successfully created\n2024-11-15 13:20:00,807 [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_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff\n2024-11-15 13:20:01,111 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff&amp;#x27;]\n2024-11-15 13:20:01,111 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_77/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff\nINFO     /tmp/biobb/unitests_77/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/interseqcorr/sandbox_42f1d051-5404-4749-9cbc-d04b168e5eff&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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;949 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;949 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 13:20:01,209 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\n2024-11-15 13:20:01,210 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263 directory successfully created\n2024-11-15 13:20:01,211 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:01,211 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:01,212 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:01,213 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:01,214 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:01,214 [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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\n2024-11-15 13:20:02,057 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263&amp;#x27;]\n2024-11-15 13:20:02,058 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_77/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263 directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/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_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263\nINFO     /tmp/biobb/unitests_77/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/interbpcorr/sandbox_2408b9c5-6a69-435f-b95d-4e9d4cf13263&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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 13:20:02,154 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\n2024-11-15 13:20:02,154 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117 directory successfully created\n2024-11-15 13:20:02,154 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,155 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,155 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,155 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,156 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,156 [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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\n2024-11-15 13:20:02,368 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117&amp;#x27;]\n2024-11-15 13:20:02,368 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_77/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117 directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/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_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117\nINFO     /tmp/biobb/unitests_77/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/intrahpcorr/sandbox_98a2c710-6aa0-49d3-8a79-fef4e5247117&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_77\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;391 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;391 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 13:20:02,454 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\n2024-11-15 13:20:02,455 [MainThread  ] [INFO ]  /tmp/biobb/unitests_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694 directory successfully created\n2024-11-15 13:20:02,455 [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_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694\n2024-11-15 13:20:02,759 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694&amp;#x27;]\n2024-11-15 13:20:02,759 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_77/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_77/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_77/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_77/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_77/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694 directory successfully created\nINFO     /tmp/biobb/unitests_77/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_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694\nINFO     /tmp/biobb/unitests_77/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_77/intraseqcorr/sandbox_40e4deea-8c42-4f9d-a5e6-e1314b48b694&amp;#x27;]\nINFO     /tmp/biobb/unitests_77/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;954 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;954 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 13:20:02,845 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\n2024-11-15 13:20:02,845 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19 directory successfully created\n2024-11-15 13:20:02,846 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:02,847 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:02,847 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:02,848 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:02,849 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:02,849 [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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\n2024-11-15 13:20:03,706 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19&amp;#x27;]\n2024-11-15 13:20:03,706 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_78/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_78/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_78/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/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_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19\nINFO     /tmp/biobb/unitests_78/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/intrabpcorr/sandbox_a98b32c6-b374-4e9b-bbf0-17cc360f3f19&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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 13:20:03,799 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\n2024-11-15 13:20:03,800 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953 directory successfully created\n2024-11-15 13:20:03,811 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953\n2024-11-15 13:20:03,812 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:20:03,812 [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 13:20:10,968 [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 13:20:10,968 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:20:11,119 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953&amp;#x27;]\n2024-11-15 13:20:11,120 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_78/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953\nINFO     /tmp/biobb/unitests_78/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_78/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_78/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_78/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_78/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_canal/sandbox_8e51bc99-8ffb-4155-9011-c8b9c838c953&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;91 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;91 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 13:20:11,174 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\n2024-11-15 13:20:11,174 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457 directory successfully created\n2024-11-15 13:20:11,204 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457\n2024-11-15 13:20:11,211 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457/canal_unzip_output.ser.\n2024-11-15 13:20:11,216 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457&amp;#x27;]\n2024-11-15 13:20:11,217 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_78/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_78/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_78/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_78/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457\nINFO     /tmp/biobb/unitests_78/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_78/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/canal_unzip/sandbox_053daddd-7ff7-4887-bd41-665bded7a457&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;387 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;387 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 13:20:11,266 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\n2024-11-15 13:20:11,266 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607 directory successfully created\n2024-11-15 13:20:11,553 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\n2024-11-15 13:20:11,553 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\n2024-11-15 13:20:11,553 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\n2024-11-15 13:20:11,554 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:20:11,554 [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 13:20:11,558 [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 13:20:11,559 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:20:11,605 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607&amp;#x27;]\n2024-11-15 13:20:11,605 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_78/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\nINFO     /tmp/biobb/unitests_78/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_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\nINFO     /tmp/biobb/unitests_78/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_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607\nINFO     /tmp/biobb/unitests_78/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_78/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_78/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_78/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_78/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_canion/sandbox_c953e6e7-b31f-4d8e-87ce-4f70ede9e607&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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 13:20:11,661 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\n2024-11-15 13:20:11,661 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472 directory successfully created\n2024-11-15 13:20:11,732 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472\n2024-11-15 13:20:11,732 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472\n2024-11-15 13:20:11,735 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-15 13:20:11,735 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:20:11,735 [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 13:20:18,244 [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 13:20:18,244 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:20:18,292 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472&amp;#x27;]\n2024-11-15 13:20:18,292 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_78/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_78/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_78/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_78/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: 19963d81-77f4-4efa-8dee-ad1bb8a8e8e9/curves_output.cdi\n        File_B: 87072841-2c9e-4b17-a948-9546265ee704/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_78/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472\nINFO     /tmp/biobb/unitests_78/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_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472\nINFO     /tmp/biobb/unitests_78/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_78/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_78/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_78/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_78/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_78/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/biobb_curves/sandbox_6c91ccd7-a77a-48de-aa55-66e4aeeb4472&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;250 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;250 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 13:20:18,401 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.1\n2024-11-15 13:20:18,401 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af directory successfully created\n2024-11-15 13:20:18,402 [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_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af\n2024-11-15 13:20:18,566 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af&amp;#x27;]\n2024-11-15 13:20:18,567 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_78/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_78/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_78/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af\nINFO     /tmp/biobb/unitests_78/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_averages/sandbox_47ebb001-78f2-466c-b865-cc4d8b6329af&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;543 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;543 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 13:20:18,655 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\n2024-11-15 13:20:18,656 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74 directory successfully created\n2024-11-15 13:20:18,656 [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_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74\n2024-11-15 13:20:19,146 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74&amp;#x27;]\n2024-11-15 13:20:19,147 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_78/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_78/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74\nINFO     /tmp/biobb/unitests_78/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_bimodality/sandbox_6f292403-25f9-42ea-92df-667985ad5a74&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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 13:20:19,196 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\n2024-11-15 13:20:19,196 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac directory successfully created\n2024-11-15 13:20:19,197 [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_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac\n2024-11-15 13:20:24,171 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac&amp;#x27;]\n2024-11-15 13:20:24,172 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_78/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac\nINFO     /tmp/biobb/unitests_78/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_timeseries/sandbox_d39ac29e-2d8e-4d89-8a1c-1b1d149191ac&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;85 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;85 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 13:20:24,223 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\n2024-11-15 13:20:24,223 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306 directory successfully created\n2024-11-15 13:20:24,224 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306\n2024-11-15 13:20:24,225 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306/dna_timeseries_unzip.csv.\n2024-11-15 13:20:24,225 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306/dna_timeseries_unzip.jpg.\n2024-11-15 13:20:24,226 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306&amp;#x27;]\n2024-11-15 13:20:24,226 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_78/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_78/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_78/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_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306\nINFO     /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/dna_timeseries_unzip/sandbox_520b5062-c5be-4393-8881-fc9912b22306&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;259 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;259 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 13:20:24,307 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\n2024-11-15 13:20:24,308 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3 directory successfully created\n2024-11-15 13:20:24,308 [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_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3\n2024-11-15 13:20:24,484 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3&amp;#x27;]\n2024-11-15 13:20:24,484 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_78/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_78/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_78/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3\nINFO     /tmp/biobb/unitests_78/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/average_stiffness/sandbox_03d4a70b-f797-4ee0-8aa4-4b8646d4e1c3&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;271 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;271 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 13:20:24,567 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\n2024-11-15 13:20:24,567 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0 directory successfully created\n2024-11-15 13:20:24,568 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,568 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,568 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,569 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,569 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,569 [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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\n2024-11-15 13:20:24,758 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_78/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_78/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_78/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/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_78/basepair_stiffness/sandbox_11011352-e2f0-495b-b748-63bf2f3582f0\nINFO     /tmp/biobb/unitests_78/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_78\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;3.9.20&#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;515 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;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 13:25:20,104 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.bipopulations Version: 5.0.1\n2024-11-15 13:25:20,105 [MainThread  ] [INFO ]  /tmp/biobb/unitests_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853 directory successfully created\n2024-11-15 13:25:20,106 [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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\n2024-11-15 13:25:20,106 [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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\n2024-11-15 13:25:20,107 [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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\n2024-11-15 13:25:20,108 [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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\n2024-11-15 13:25:20,516 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853&amp;#x27;]\n2024-11-15 13:25:20,516 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_78/bipopulations/bipop.csv\nChecking if empty file: /tmp/biobb/unitests_78/bipopulations/bipop.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_78/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_78/bipopulations/bipopulations_log.out:file_utils.py:409 Module: biobb_dna.backbone.bipopulations Version: 5.0.1\nINFO     /tmp/biobb/unitests_78/bipopulations/bipopulations_log.out:file_utils.py:82 /tmp/biobb/unitests_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853 directory successfully created\nINFO     /tmp/biobb/unitests_78/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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\nINFO     /tmp/biobb/unitests_78/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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\nINFO     /tmp/biobb/unitests_78/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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\nINFO     /tmp/biobb/unitests_78/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_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853\nINFO     /tmp/biobb/unitests_78/bipopulations/bipopulations_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_78/bipopulations/sandbox_db08b0c5-bcb1-40d7-9b9b-dc3583770853&amp;#x27;]\nINFO     /tmp/biobb/unitests_78/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;463 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;463 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 13:25:20,639 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.canonicalag Version: 5.0.1\n2024-11-15 13:25:20,640 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900 directory successfully created\n2024-11-15 13:25:20,641 [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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\n2024-11-15 13:25:20,641 [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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\n2024-11-15 13:25:20,642 [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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\n2024-11-15 13:25:20,643 [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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\n2024-11-15 13:25:21,013 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_79/canonicalag/canonag.csv\nChecking if empty file: /tmp/biobb/unitests_79/canonicalag/canonag.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/canonicalag/canonicalag_log.out:file_utils.py:409 Module: biobb_dna.backbone.canonicalag Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/canonicalag/canonicalag_log.out:file_utils.py:82 /tmp/biobb/unitests_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\nINFO     /tmp/biobb/unitests_79/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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\nINFO     /tmp/biobb/unitests_79/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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\nINFO     /tmp/biobb/unitests_79/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_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900\nINFO     /tmp/biobb/unitests_79/canonicalag/canonicalag_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/canonicalag/sandbox_b557b128-22b4-4609-aa34-55c607854900&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;555 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;555 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 13:25:21,105 [MainThread  ] [INFO ]  Module: biobb_dna.backbone.puckering Version: 5.0.1\n2024-11-15 13:25:21,105 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303 directory successfully created\n2024-11-15 13:25:21,106 [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_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303\n2024-11-15 13:25:21,107 [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_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303\n2024-11-15 13:25:21,574 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303&amp;#x27;]\n2024-11-15 13:25:21,575 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/puckering/puckering.csv\nChecking if empty file: /tmp/biobb/unitests_79/puckering/puckering.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/puckering/puckering_log.out:file_utils.py:409 Module: biobb_dna.backbone.puckering Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/puckering/puckering_log.out:file_utils.py:82 /tmp/biobb/unitests_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303\nINFO     /tmp/biobb/unitests_79/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_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303\nINFO     /tmp/biobb/unitests_79/puckering/puckering_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/puckering/sandbox_883c4de7-1dcd-439b-b54c-11330cfb1303&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/puckering/puckering_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;342 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;342 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 13:25:21,664 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\n2024-11-15 13:25:21,664 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03 directory successfully created\n2024-11-15 13:25:21,664 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,665 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,665 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,665 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,665 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,666 [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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\n2024-11-15 13:25:21,922 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03&amp;#x27;]\n2024-11-15 13:25:21,922 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/interhpcorr/inter_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_79/interhpcorr/inter_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/interhpcorr/log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interhpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/interhpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/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_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03\nINFO     /tmp/biobb/unitests_79/interhpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/interhpcorr/sandbox_9bcb1d5b-8b9b-41ec-9c9f-7c507a5bac03&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/interhpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;351 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;351 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 13:25:22,005 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\n2024-11-15 13:25:22,006 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11 directory successfully created\n2024-11-15 13:25:22,006 [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_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11\n2024-11-15 13:25:22,275 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11&amp;#x27;]\n2024-11-15 13:25:22,275 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/interseqcorr/inter_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_79/interseqcorr/inter_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/interseqcorr/interseqcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/interseqcorr/interseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11\nINFO     /tmp/biobb/unitests_79/interseqcorr/interseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/interseqcorr/sandbox_ed245b89-7dbf-4a86-9ed6-16a038fcac11&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/interseqcorr/interseqcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;870 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;870 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 13:25:22,359 [MainThread  ] [INFO ]  Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\n2024-11-15 13:25:22,359 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2 directory successfully created\n2024-11-15 13:25:22,360 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:22,361 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:22,361 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:22,362 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:22,363 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:22,363 [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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\n2024-11-15 13:25:23,139 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2&amp;#x27;]\n2024-11-15 13:25:23,140 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/interbpcorr/inter_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_79/interbpcorr/inter_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/interbpcorr/interbpcorr_log.out:file_utils.py:409 Module: biobb_dna.interbp_correlations.interbpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/interbpcorr/interbpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/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_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2\nINFO     /tmp/biobb/unitests_79/interbpcorr/interbpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/interbpcorr/sandbox_2f9655e2-f85b-4954-ba67-aca24df8c9e2&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/interbpcorr/interbpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;278 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;278 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 13:25:23,229 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\n2024-11-15 13:25:23,230 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6 directory successfully created\n2024-11-15 13:25:23,230 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,230 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,231 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,231 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,231 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,231 [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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\n2024-11-15 13:25:23,426 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6&amp;#x27;]\n2024-11-15 13:25:23,427 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/intrahpcorr/intra_hpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_79/intrahpcorr/intra_hpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/intrahpcorr/log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrahpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/intrahpcorr/log.out:file_utils.py:82 /tmp/biobb/unitests_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/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_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6\nINFO     /tmp/biobb/unitests_79/intrahpcorr/log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/intrahpcorr/sandbox_b59ac164-07ff-4dc9-b5b6-d1e31902b3a6&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/intrahpcorr/log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_79\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;582 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;582 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 13:25:23,509 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\n2024-11-15 13:25:23,509 [MainThread  ] [INFO ]  /tmp/biobb/unitests_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94 directory successfully created\n2024-11-15 13:25:23,510 [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_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94\n2024-11-15 13:25:24,001 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94&amp;#x27;]\n2024-11-15 13:25:24,001 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_79/intraseqcorr/intra_seqcorr.csv\nChecking if empty file: /tmp/biobb/unitests_79/intraseqcorr/intra_seqcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_79/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_79/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intraseqcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_79/intraseqcorr/intraseqcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94 directory successfully created\nINFO     /tmp/biobb/unitests_79/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_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94\nINFO     /tmp/biobb/unitests_79/intraseqcorr/intraseqcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_79/intraseqcorr/sandbox_a7a4cae7-a0e5-4240-a7d6-3395d0739b94&amp;#x27;]\nINFO     /tmp/biobb/unitests_79/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;848 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;848 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 13:25:24,093 [MainThread  ] [INFO ]  Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\n2024-11-15 13:25:24,093 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd directory successfully created\n2024-11-15 13:25:24,094 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,095 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,095 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,096 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,097 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,098 [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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\n2024-11-15 13:25:24,851 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd&amp;#x27;]\n2024-11-15 13:25:24,851 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/intrabpcorr/intra_bpcorr.csv\nChecking if empty file: /tmp/biobb/unitests_80/intrabpcorr/intra_bpcorr.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_80/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_80/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Module: biobb_dna.intrabp_correlations.intrabpcorr Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/intrabpcorr/intrabpcorr_log.out:file_utils.py:82 /tmp/biobb/unitests_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/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_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd\nINFO     /tmp/biobb/unitests_80/intrabpcorr/intrabpcorr_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/intrabpcorr/sandbox_07e05360-7ffc-4c55-b8f8-07edcc6e89dd&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/intrabpcorr/intrabpcorr_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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 13:25:24,942 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\n2024-11-15 13:25:24,942 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2 directory successfully created\n2024-11-15 13:25:24,953 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/curves_output.cda to /tmp/biobb/unitests_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2\n2024-11-15 13:25:24,953 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:25:24,953 [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 13:25:32,105 [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 13:25:32,105 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:25:32,262 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2&amp;#x27;]\n2024-11-15 13:25:32,262 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/biobb_canal/canal_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_80/biobb_canal/biobb_canal_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canal Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/biobb_canal/biobb_canal_log.out:file_utils.py:82 /tmp/biobb/unitests_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2 directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2\nINFO     /tmp/biobb/unitests_80/biobb_canal/biobb_canal_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_80/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_80/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_80/biobb_canal/biobb_canal_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_80/biobb_canal/biobb_canal_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_canal/sandbox_48a75843-6b29-4f27-af10-d1d5fcd0c7c2&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/biobb_canal/biobb_canal_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;95 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;95 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 13:25:32,320 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\n2024-11-15 13:25:32,321 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa directory successfully created\n2024-11-15 13:25:32,355 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/canal_output.zip to /tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa\n2024-11-15 13:25:32,359 [MainThread  ] [INFO ]  canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa/canal_unzip_output.ser.\n2024-11-15 13:25:32,364 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa&amp;#x27;]\n2024-11-15 13:25:32,365 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/canal_unzip/canal_unzip_output.ser\nChecking if empty file: /tmp/biobb/unitests_80/canal_unzip/canal_unzip_output.txt\nComparing: \n        File_A: /tmp/biobb/unitests_80/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_80/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_80/canal_unzip/canal_unzip_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.canal_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/canal_unzip/canal_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa\nINFO     /tmp/biobb/unitests_80/canal_unzip/canal_unzip_log.out:file_utils.py:409 canal_output_alphaC.his exists, copying into /tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa/canal_unzip_output.ser.\nINFO     /tmp/biobb/unitests_80/canal_unzip/canal_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/canal_unzip/sandbox_6e74ab92-a189-4792-8848-85ac330d01aa&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/canal_unzip/canal_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;438 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;438 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 13:25:32,417 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\n2024-11-15 13:25:32,418 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0 directory successfully created\n2024-11-15 13:25:32,745 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_K.cdi to /tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\n2024-11-15 13:25:32,745 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA.afr to /tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\n2024-11-15 13:25:32,746 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/THGA_avg.pdb to /tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\n2024-11-15 13:25:32,746 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:25:32,746 [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 13:25:32,759 [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 13:25:32,760 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:25:32,804 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0&amp;#x27;]\n2024-11-15 13:25:32,804 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/biobb_canion/canion_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_80/biobb_canion/biobb_canion_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_canion Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/biobb_canion/biobb_canion_log.out:file_utils.py:82 /tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0 directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\nINFO     /tmp/biobb/unitests_80/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_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\nINFO     /tmp/biobb/unitests_80/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_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0\nINFO     /tmp/biobb/unitests_80/biobb_canion/biobb_canion_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_80/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_80/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_80/biobb_canion/biobb_canion_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_80/biobb_canion/biobb_canion_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_canion/sandbox_65092e30-f120-45ed-a567-84ce3dff95a0&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/biobb_canion/biobb_canion_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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 13:25:32,857 [MainThread  ] [INFO ]  Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\n2024-11-15 13:25:32,857 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d directory successfully created\n2024-11-15 13:25:32,930 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.trj to /tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d\n2024-11-15 13:25:32,931 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/curvesplus/structure.stripped.top to /tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d\n2024-11-15 13:25:32,932 [MainThread  ] [INFO ]  Appending provided topology to command\n2024-11-15 13:25:32,932 [MainThread  ] [INFO ]  Creating command line with instructions and required arguments\n2024-11-15 13:25:32,933 [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 13:25:39,612 [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 13:25:39,613 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-15 13:25:39,654 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d&amp;#x27;]\n2024-11-15 13:25:39,655 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/biobb_curves/curves_output.cda\nChecking if empty file: /tmp/biobb/unitests_80/biobb_curves/curves_output.lis\nChecking if empty file: /tmp/biobb/unitests_80/biobb_curves/curves_output.zip\nComparing ignoring lines containing this words: [2]\n     FILE_A: /tmp/biobb/unitests_80/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_80/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: 2b5004e0-6ae6-4155-be0c-c0df8ee1d317/curves_output.cdi\n        File_B: 32518fb1-6f7a-42ed-b6bc-1070b98e1f1d/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_80/biobb_curves/biobb_curves_log.out:file_utils.py:409 Module: biobb_dna.curvesplus.biobb_curves Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/biobb_curves/biobb_curves_log.out:file_utils.py:82 /tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d\nINFO     /tmp/biobb/unitests_80/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_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d\nINFO     /tmp/biobb/unitests_80/biobb_curves/biobb_curves_log.out:file_utils.py:409 Appending provided topology to command\nINFO     /tmp/biobb/unitests_80/biobb_curves/biobb_curves_log.out:file_utils.py:409 Creating command line with instructions and required arguments\nINFO     /tmp/biobb/unitests_80/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_80/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_80/biobb_curves/biobb_curves_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_80/biobb_curves/biobb_curves_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/biobb_curves/sandbox_d0ae37de-755f-46f1-8ac1-47733eda3e0d&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/biobb_curves/biobb_curves_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;336 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;336 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 13:25:39,763 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_averages Version: 5.0.1\n2024-11-15 13:25:39,763 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9 directory successfully created\n2024-11-15 13:25:39,764 [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_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9\n2024-11-15 13:25:40,014 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9&amp;#x27;]\n2024-11-15 13:25:40,014 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/dna_averages/avg_out.csv\nChecking if empty file: /tmp/biobb/unitests_80/dna_averages/avg_out.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_80/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_80/dna_averages/dna_averages_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_averages Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/dna_averages/dna_averages_log.out:file_utils.py:82 /tmp/biobb/unitests_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9 directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9\nINFO     /tmp/biobb/unitests_80/dna_averages/dna_averages_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_averages/sandbox_03fdde4b-9f9d-41d2-bc07-d3983fc3aec9&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/dna_averages/dna_averages_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;521 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;521 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 13:25:40,099 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\n2024-11-15 13:25:40,099 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b directory successfully created\n2024-11-15 13:25:40,100 [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_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b\n2024-11-15 13:25:40,571 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b&amp;#x27;]\n2024-11-15 13:25:40,572 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/dna_bimodality/bimod_out.csv\nChecking if empty file: /tmp/biobb/unitests_80/dna_bimodality/bimod_out.jpg\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_80/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_bimodality Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/dna_bimodality/dna_bimodality_log.out:file_utils.py:82 /tmp/biobb/unitests_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b\nINFO     /tmp/biobb/unitests_80/dna_bimodality/dna_bimodality_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_bimodality/sandbox_f30e37f3-3aee-4f24-9965-eedfcbaa868b&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/dna_bimodality/dna_bimodality_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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 13:25:40,622 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\n2024-11-15 13:25:40,623 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5 directory successfully created\n2024-11-15 13:25:40,623 [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_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5\n2024-11-15 13:25:44,884 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5&amp;#x27;]\n2024-11-15 13:25:44,884 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/dna_timeseries/timeseries_output.zip\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_80/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/dna_timeseries/dna_timeseries_log.out:file_utils.py:82 /tmp/biobb/unitests_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5 directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5\nINFO     /tmp/biobb/unitests_80/dna_timeseries/dna_timeseries_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_timeseries/sandbox_9125f100-d118-44f7-963e-42fe39e1f7f5&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/dna_timeseries/dna_timeseries_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;144 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;144 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 13:25:44,991 [MainThread  ] [INFO ]  Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\n2024-11-15 13:25:44,992 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd directory successfully created\n2024-11-15 13:25:44,993 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_dna/biobb_dna/biobb_dna/test/data/dna/timeseries_output.zip to /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd\n2024-11-15 13:25:44,993 [MainThread  ] [INFO ]  hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd/dna_timeseries_unzip.csv.\n2024-11-15 13:25:44,993 [MainThread  ] [INFO ]  hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd/dna_timeseries_unzip.jpg.\n2024-11-15 13:25:44,995 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd&amp;#x27;]\n2024-11-15 13:25:44,995 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip.csv\nChecking if empty file: /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip.jpg\nChecking if empty file: /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip.txt\nComparing: \n        File_A: /tmp/biobb/unitests_80/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_80/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_80/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_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Module: biobb_dna.dna.dna_timeseries_unzip Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:82 /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd\nINFO     /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.csv exists, copying into /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd/dna_timeseries_unzip.csv.\nINFO     /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 hist_shift_5_AA.jpg exists, copying into /tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd/dna_timeseries_unzip.jpg.\nINFO     /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/dna_timeseries_unzip/sandbox_f8132f21-7d9e-4063-a971-7fcd78b080bd&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/dna_timeseries_unzip/dna_timeseries_unzip_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;254 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;254 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 13:25:45,078 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\n2024-11-15 13:25:45,078 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab directory successfully created\n2024-11-15 13:25:45,079 [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_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab\n2024-11-15 13:25:45,251 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab&amp;#x27;]\n2024-11-15 13:25:45,251 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/average_stiffness/avgstiff.csv\nChecking if empty file: /tmp/biobb/unitests_80/average_stiffness/avgstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_80/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_80/average_stiffness/average_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.average_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/average_stiffness/average_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab\nINFO     /tmp/biobb/unitests_80/average_stiffness/average_stiffness_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_80/average_stiffness/sandbox_95a6f92c-170e-41f9-9520-8f917fbdabab&amp;#x27;]\nINFO     /tmp/biobb/unitests_80/average_stiffness/average_stiffness_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_80\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;267 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;267 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 13:25:45,333 [MainThread  ] [INFO ]  Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\n2024-11-15 13:25:45,334 [MainThread  ] [INFO ]  /tmp/biobb/unitests_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2 directory successfully created\n2024-11-15 13:25:45,334 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,334 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,335 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,335 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,335 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,335 [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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\n2024-11-15 13:25:45,516 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_80/basepair_stiffness/bpstiff.csv\nChecking if empty file: /tmp/biobb/unitests_80/basepair_stiffness/bpstiff.jpg\nComparing images of both files:\n     IMAGE_A: /tmp/biobb/unitests_80/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_80/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:409 Module: biobb_dna.stiffness.basepair_stiffness Version: 5.0.1\nINFO     /tmp/biobb/unitests_80/basepair_stiffness/basepair_stiffness_log.out:file_utils.py:82 /tmp/biobb/unitests_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2 directory successfully created\nINFO     /tmp/biobb/unitests_80/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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\nINFO     /tmp/biobb/unitests_80/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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\nINFO     /tmp/biobb/unitests_80/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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\nINFO     /tmp/biobb/unitests_80/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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\nINFO     /tmp/biobb/unitests_80/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_80/basepair_stiffness/sandbox_203328b6-95c8-4802-9ff9-2ee9c2b456f2\nINFO     /tmp/biobb/unitests_80/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 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