Add listpos to docs and rebuild

rouskinlab · Feb 25, 2024 · 3ca37cd · 3ca37cd
1 parent 82c3c04
commit 3ca37cd
Show file tree

Hide file tree

Showing 119 changed files with 1,133 additions and 209 deletions.
diff --git a/docs/.doctrees/api/seismicrna.core.doctree b/docs/.doctrees/api/seismicrna.core.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.seq.doctree b/docs/.doctrees/api/seismicrna.core.seq.doctree
diff --git a/docs/.doctrees/api/seismicrna.core.seq.tests.doctree b/docs/.doctrees/api/seismicrna.core.seq.tests.doctree
diff --git a/docs/.doctrees/api/seismicrna.doctree b/docs/.doctrees/api/seismicrna.doctree
diff --git a/docs/.doctrees/api/seismicrna.lists.doctree b/docs/.doctrees/api/seismicrna.lists.doctree
diff --git a/docs/.doctrees/api/seismicrna.mask.doctree b/docs/.doctrees/api/seismicrna.mask.doctree
diff --git a/docs/.doctrees/api/seismicrna.table.doctree b/docs/.doctrees/api/seismicrna.table.doctree
diff --git a/docs/.doctrees/api/seismicrna.wf.doctree b/docs/.doctrees/api/seismicrna.wf.doctree
diff --git a/docs/.doctrees/cli.doctree b/docs/.doctrees/cli.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/formats/index.doctree b/docs/.doctrees/formats/index.doctree
diff --git a/docs/.doctrees/formats/list/index.doctree b/docs/.doctrees/formats/list/index.doctree
diff --git a/docs/.doctrees/formats/list/listpos.doctree b/docs/.doctrees/formats/list/listpos.doctree
diff --git a/docs/.doctrees/formats/meta/index.doctree b/docs/.doctrees/formats/meta/index.doctree
diff --git a/docs/.doctrees/formats/meta/joined.doctree b/docs/.doctrees/formats/meta/joined.doctree
diff --git a/docs/.doctrees/formats/meta/refs.doctree b/docs/.doctrees/formats/meta/refs.doctree
diff --git a/docs/.doctrees/formats/meta/samples.doctree b/docs/.doctrees/formats/meta/samples.doctree
diff --git a/docs/.doctrees/formats/meta/sections.doctree b/docs/.doctrees/formats/meta/sections.doctree
diff --git a/docs/.doctrees/howto/run/mask.doctree b/docs/.doctrees/howto/run/mask.doctree
diff --git a/docs/_sources/api/seismicrna.lists.rst.txt b/docs/_sources/api/seismicrna.lists.rst.txt
@@ -0,0 +1,22 @@
+seismicrna.lists package
+========================
+
+.. automodule:: seismicrna.lists
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+
+.. automodule:: seismicrna.lists.listpos
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+.. automodule:: seismicrna.lists.lists
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/_sources/api/seismicrna.rst.txt b/docs/_sources/api/seismicrna.rst.txt
@@ -21,6 +21,7 @@ Subpackages
    seismicrna.fold
    seismicrna.graph
    seismicrna.join
+   seismicrna.lists
    seismicrna.mask
    seismicrna.pool
    seismicrna.relate

diff --git a/docs/_sources/formats/index.rst.txt b/docs/_sources/formats/index.rst.txt
@@ -6,6 +6,7 @@ File Formats
 .. toctree::
     :maxdepth: 2
 
-    report/index
     data/index
+    list/index
     meta/index
+    report/index
diff --git a/docs/_sources/formats/list/index.rst.txt b/docs/_sources/formats/list/index.rst.txt
@@ -0,0 +1,16 @@
+
+List Formats
+================================================================================
+
+Using list files, one can list positions and reads that meet certain criteria,
+as well as provide them to other commands.
+All list files are in comma-separated values (CSV) format, which is advantageous
+because it is both human-readable and widely supported by software including
+Microsoft Excel and Python.
+An example in CSV format is given for each type of list file.
+
+
+.. toctree::
+    :maxdepth: 2
+
+    listpos
diff --git a/docs/_sources/formats/list/listpos.rst.txt b/docs/_sources/formats/list/listpos.rst.txt
@@ -0,0 +1,58 @@
+
+List of Positions
+--------------------------------------------------------------------------------
+
+List of Positions: Fields
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+========= ==== ========================================================= ========
+Name      Type Description                                               Required
+========= ==== ========================================================= ========
+Reference str  Name of the reference sequence                            yes
+Position  int  Position in the reference sequence                        yes
+...       n/a  Additional field (ignored)                                no
+========= ==== ========================================================= ========
+
+List of Positions file: Uses
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+List of Positions as input file
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+- The ``mask`` command accepts a List of Positions file via ``--exclude-file``.
+
+List of Positions as output file
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+- The ``+listpos`` command outputs a List of Positions file for each table file.
+
+Example List of Positions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+List of Positions as a pretty table
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+========= ========
+Reference Position
+========= ========
+refA            11
+refA            16
+refA            20
+refB            11
+refB            46
+refB            83
+========= ========
+
+List of Positions as plain text
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+::
+
+    Reference,Position
+    refA,11
+    refA,16
+    refA,20
+    refB,11
+    refB,46
+    refB,83
+
+This text can be copied into a new CSV file.
diff --git a/docs/_sources/formats/meta/index.rst.txt b/docs/_sources/formats/meta/index.rst.txt
@@ -1,12 +1,12 @@
 
 Metadata Formats
-========================================================================
+================================================================================
 
 Using metadata files, information can be given about samples, reference
 sequences, and sections.
-All metadata files must be in comma-separated values (CSV) format, which
-is advantageous because it is both human-readable and widely supported
-by software including Microsoft Excel and Python.
+All metadata files are in comma-separated values (CSV) format, which is
+advantageous because it is both human-readable and widely supported by software
+including Microsoft Excel and Python.
 An example in CSV format is given for each type of metadata file.
 
 

diff --git a/docs/_sources/formats/meta/joined.rst.txt b/docs/_sources/formats/meta/joined.rst.txt
@@ -40,12 +40,6 @@ joined cluster in the joined clusters metadata file.
     of ways to join those sections is *k*\ :sup:`n`.
 
 
-Commands that use metadata for sections
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- ``seismic wf``
-- ``seismic join``
-
 Fields of metadata for joined clusters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/_sources/formats/meta/refs.rst.txt b/docs/_sources/formats/meta/refs.rst.txt
@@ -7,15 +7,10 @@ About metadata for references
 
 Purpose of metadata for references
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
 Define metadata about reference sequences, such as the coordinates at
 which barcodes are located.
 
-Commands that use metadata for references
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- ``seismic export``
-
-
 Fields of metadata for references
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -33,7 +28,6 @@ Notes about metadata for references
 - Additional fields with arbitrary names can be given.
   Their data types will be inferred as strings, integers, or floats.
 
-
 Example metadata for references
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/_sources/formats/meta/samples.rst.txt b/docs/_sources/formats/meta/samples.rst.txt
@@ -12,11 +12,6 @@ Define metadata about samples, such as the cell line or buffer in which
 the RNA was probed, the type and concentration of the chemical probe,
 and the temperature during chemical probing.
 
-Commands that use metadata for samples
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- ``seismic export``
-
 
 Fields of metadata for samples
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/_sources/formats/meta/sections.rst.txt b/docs/_sources/formats/meta/sections.rst.txt
@@ -14,13 +14,6 @@ and traceable to define the sections in a file than on the command line,
 using the option ``--sections-file`` (``-s``).
 The sections file additionally permits giving each section a name.
 
-Commands that use metadata for sections
-""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-- ``seismic wf``
-- ``seismic mask``
-- ``seismic fold``
-
 
 Fields of metadata for sections
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/docs/_sources/howto/run/mask.rst.txt b/docs/_sources/howto/run/mask.rst.txt
@@ -101,10 +101,8 @@ Exclude arbitary positions
 You can also exclude any arbitary positions from any reference sequence.
 A common reason to exclude a position is if the base is modified endogenously
 in a way that causes mutations during reverse transcription.
-To exclude an arbitrary position, use ``--exclude-pos`` followed by the name of
-the reference and the position to exclude.
-For example, ``--exclude-pos lititz 48`` would exclude positions 48 from the
-reference "lititz".
+To exclude an arbitrary position, use ``--exclude-file`` followed by a file of
+all positions to exclude, in :doc:`../../formats/list/listpos` format.
 
 Mask setting: Filter reads
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

diff --git a/docs/api/seismicrna.align.html b/docs/api/seismicrna.align.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.align.tests.html b/docs/api/seismicrna.align.tests.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.cleanfa.html b/docs/api/seismicrna.cleanfa.html
@@ -65,6 +65,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.cluster.html b/docs/api/seismicrna.cluster.html
@@ -65,6 +65,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.core.arg.html b/docs/api/seismicrna.core.arg.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.core.batch.html b/docs/api/seismicrna.core.batch.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.core.extern.html b/docs/api/seismicrna.core.extern.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>

diff --git a/docs/api/seismicrna.core.html b/docs/api/seismicrna.core.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>
@@ -2104,12 +2105,12 @@ <h3>Purpose<a class="headerlink" href="#purpose" title="Permalink to this headli
 <span class="target" id="module-seismicrna.core.version"></span><p>Version information for SEISMIC-RNA</p>
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.format_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">13</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">format_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">major</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">minor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">14</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">patch</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.format_version" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">
 <dt class="sig sig-object py" id="seismicrna.core.version.parse_version">
-<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.13.1'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Permalink to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">seismicrna.core.version.</span></span><span class="sig-name descname"><span class="pre">parse_version</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">version</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'0.14.0'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#seismicrna.core.version.parse_version" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <span class="target" id="module-seismicrna.core.write"></span><dl class="py function">

diff --git a/docs/api/seismicrna.core.io.html b/docs/api/seismicrna.core.io.html
@@ -66,6 +66,7 @@
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.fold.html">seismicrna.fold package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.graph.html">seismicrna.graph package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.join.html">seismicrna.join package</a></li>
+<li class="toctree-l3"><a class="reference internal" href="seismicrna.lists.html">seismicrna.lists package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.mask.html">seismicrna.mask package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.pool.html">seismicrna.pool package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="seismicrna.relate.html">seismicrna.relate package</a></li>