Add the +listpos command to docs and rebuild

docs/_sources/cli.rst.txt

@@ -96,6 +96,21 @@ Extra Utilities
     For every extra utility (that is not part of the main workflow), the name
     begins with ``+``.
 
+.. _cli_listpos:
+
+.. click:: seismicrna.lists.listpos:cli
+    :prog: seismic +listpos
+
+.. _cli_addclust:
+
+.. click:: seismicrna.cluster.addclust:cli
+    :prog: seismic +addclust
+
+.. _cli_delclust:
+
+.. click:: seismicrna.cluster.delclust:cli
+    :prog: seismic +delclust
+
 .. _cli_cleanfa:
 
 .. click:: seismicrna.cleanfa:cli

docs/_sources/howto/adjclust.rst.txt

@@ -2,7 +2,7 @@
 Add/Delete Orders to/from an Already-Clustered Dataset
 --------------------------------------------------------------------------------
 
-Background about adjusting the order  clusters
+Background about adding/deleting orders of clusters
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 You can use ``+addclust`` and ``+delclust`` to adjust the maximum number of

docs/_sources/howto/cleanfa.rst.txt

@@ -19,7 +19,6 @@ nucleotides and ``N``, such as the `IUPAC extended nucleotide codes`_.
 For details on the valid FASTA format for SEISMIC-RNA and the rationale
 behind it, see :doc:`../../formats/data/fasta`.
 
-
 Algorithm for cleaning FASTA files
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -38,7 +37,6 @@ The FASTA file cleaner of SEISMIC-RNA follows the following procedure:
   `IUPAC extended nucleotide codes`_ are replaced with ``N``.
   If any illegal characters remain after that, then an error is raised.
 
-
 How to clean FASTA files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -64,7 +62,6 @@ To force overwriting, use the option ``--force``::
 
     seismic +cleanfa --force refs.fa
 
-
 Troubleshooting cleaning FASTA files
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

docs/_sources/howto/index.rst.txt

@@ -7,6 +7,7 @@ How To
 
     run/index
     graph/index
+    lists
     adjclust
     cleanfa
     inputs

docs/_sources/howto/lists.rst.txt

@@ -0,0 +1,39 @@
+
+List Positions Matching Criteria
+--------------------------------------------------------------------------------
+
+Background about lists
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can use ``+listpos`` to list positions meeting specific criteria in tables.
+
+Purpose of listing positions
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+After you run ``seismic table``, you may want to find the positions that meet
+certain criteria, such as the mutation rate being less/greater than a threshold.
+
+How to list positions from a table
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. _listpos:
+
+Command line for listing positions
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+Suppose you have already run ``seismic table``::
+
+    seismic table out/sample/*/ref/sect
+
+You can list the positions meeting certain criteria with ::
+
+    seismic +listpos out/sample/table/ref/sect
+
+This command will output one list file for each table file, with the same path
+except ``table/`` is replaced by ``list/``.
+
+You can filter the positions using options such as ``--max-fmut-pos 0.01``,
+which will output all positions with a mutation rate of 0.01 or less.
+Using ``--complement`` lists the complement of the positions; for example,
+``--complement --max-fmut-pos 0.01`` would output all positions with a mutation
+rate greater than 0.01.

docs/cli.html

@@ -76,6 +76,9 @@
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#extra-utilities">Extra Utilities</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#seismic-listpos">seismic +listpos</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#seismic-addclust">seismic +addclust</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#seismic-delclust">seismic +delclust</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#seismic-cleanfa">seismic +cleanfa</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#seismic-renumct">seismic +renumct</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#seismic-test">seismic +test</a></li>
@@ -2504,6 +2507,129 @@ <h2>Extra Utilities<a class="headerlink" href="#extra-utilities" title="Permalin
 <p>For every extra utility (that is not part of the main workflow), the name
 begins with <code class="docutils literal notranslate"><span class="pre">+</span></code>.</p>
 </div>
+<section id="seismic-listpos">
+<span id="cli-listpos"></span><h3>seismic +listpos<a class="headerlink" href="#seismic-listpos" title="Permalink to this headline"></a></h3>
+<p>Add more clusters to a dataset that was already clustered.</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>seismic<span class="w"> </span>+listpos<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUT_PATH<span class="o">]</span>...
+</pre></div>
+</div>
+<p class="rubric">Options</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-max-fmut-pos">
+<span class="sig-name descname"><span class="pre">--max-fmut-pos</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_fmut_pos&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-listpos-max-fmut-pos" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum mutation fraction at a position to use it</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-complement">
+<span id="cmdoption-seismic-listpos-no-complement"></span><span class="sig-name descname"><span class="pre">--complement</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--no-complement</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-listpos-complement" title="Permalink to this definition"></a></dt>
+<dd><p>List the complement</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-force">
+<span id="cmdoption-seismic-listpos-no-force"></span><span class="sig-name descname"><span class="pre">--force</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--no-force</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-listpos-force" title="Permalink to this definition"></a></dt>
+<dd><p>Force all tasks to run, even those whose output files already exist</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-max-procs">
+<span class="sig-name descname"><span class="pre">--max-procs</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_procs&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-listpos-max-procs" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum number of simultaneous processes</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-parallel">
+<span id="cmdoption-seismic-listpos-serial"></span><span class="sig-name descname"><span class="pre">--parallel</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--serial</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-listpos-parallel" title="Permalink to this definition"></a></dt>
+<dd><p>Run tasks in parallel</p>
+</dd></dl>
+
+<p class="rubric">Arguments</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-listpos-arg-INPUT_PATH">
+<span id="cmdoption-seismic-listpos-arg-input-path"></span><span class="sig-name descname"><span class="pre">INPUT_PATH</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-listpos-arg-INPUT_PATH" title="Permalink to this definition"></a></dt>
+<dd><p>Optional argument(s)</p>
+</dd></dl>
+
+</section>
+<section id="seismic-addclust">
+<span id="cli-addclust"></span><h3>seismic +addclust<a class="headerlink" href="#seismic-addclust" title="Permalink to this headline"></a></h3>
+<p>Add more clusters to a dataset that was already clustered.</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>seismic<span class="w"> </span>+addclust<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUT_PATH<span class="o">]</span>...
+</pre></div>
+</div>
+<p class="rubric">Options</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-addclust-k">
+<span id="cmdoption-seismic-addclust-max-clusters"></span><span class="sig-name descname"><span class="pre">-k</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--max-clusters</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_clusters&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-addclust-k" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum number of clusters to attempt (0 to disable)</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-addclust-brotli-level">
+<span class="sig-name descname"><span class="pre">--brotli-level</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;brotli_level&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-addclust-brotli-level" title="Permalink to this definition"></a></dt>
+<dd><p>Compression level for brotli (0 - 11)</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-addclust-max-procs">
+<span class="sig-name descname"><span class="pre">--max-procs</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_procs&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-addclust-max-procs" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum number of simultaneous processes</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-addclust-parallel">
+<span id="cmdoption-seismic-addclust-serial"></span><span class="sig-name descname"><span class="pre">--parallel</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--serial</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-addclust-parallel" title="Permalink to this definition"></a></dt>
+<dd><p>Run tasks in parallel</p>
+</dd></dl>
+
+<p class="rubric">Arguments</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-addclust-arg-INPUT_PATH">
+<span id="cmdoption-seismic-addclust-arg-input-path"></span><span class="sig-name descname"><span class="pre">INPUT_PATH</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-addclust-arg-INPUT_PATH" title="Permalink to this definition"></a></dt>
+<dd><p>Optional argument(s)</p>
+</dd></dl>
+
+</section>
+<section id="seismic-delclust">
+<span id="cli-delclust"></span><h3>seismic +delclust<a class="headerlink" href="#seismic-delclust" title="Permalink to this headline"></a></h3>
+<p>Delete clusters from a dataset that was already clustered.</p>
+<div class="highlight-shell notranslate"><div class="highlight"><pre><span></span>seismic<span class="w"> </span>+delclust<span class="w"> </span><span class="o">[</span>OPTIONS<span class="o">]</span><span class="w"> </span><span class="o">[</span>INPUT_PATH<span class="o">]</span>...
+</pre></div>
+</div>
+<p class="rubric">Options</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-delclust-k">
+<span id="cmdoption-seismic-delclust-max-clusters"></span><span class="sig-name descname"><span class="pre">-k</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--max-clusters</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_clusters&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-delclust-k" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum number of clusters to attempt (0 to disable)</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-delclust-brotli-level">
+<span class="sig-name descname"><span class="pre">--brotli-level</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;brotli_level&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-delclust-brotli-level" title="Permalink to this definition"></a></dt>
+<dd><p>Compression level for brotli (0 - 11)</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-delclust-max-procs">
+<span class="sig-name descname"><span class="pre">--max-procs</span></span><span class="sig-prename descclassname"> <span class="pre">&lt;max_procs&gt;</span></span><a class="headerlink" href="#cmdoption-seismic-delclust-max-procs" title="Permalink to this definition"></a></dt>
+<dd><p>Maximum number of simultaneous processes</p>
+</dd></dl>
+
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-delclust-parallel">
+<span id="cmdoption-seismic-delclust-serial"></span><span class="sig-name descname"><span class="pre">--parallel</span></span><span class="sig-prename descclassname"></span><span class="sig-prename descclassname"><span class="pre">,</span> </span><span class="sig-name descname"><span class="pre">--serial</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-delclust-parallel" title="Permalink to this definition"></a></dt>
+<dd><p>Run tasks in parallel</p>
+</dd></dl>
+
+<p class="rubric">Arguments</p>
+<dl class="std option">
+<dt class="sig sig-object std" id="cmdoption-seismic-delclust-arg-INPUT_PATH">
+<span id="cmdoption-seismic-delclust-arg-input-path"></span><span class="sig-name descname"><span class="pre">INPUT_PATH</span></span><span class="sig-prename descclassname"></span><a class="headerlink" href="#cmdoption-seismic-delclust-arg-INPUT_PATH" title="Permalink to this definition"></a></dt>
+<dd><p>Optional argument(s)</p>
+</dd></dl>
+
+</section>
 <section id="seismic-cleanfa">
 <span id="cli-cleanfa"></span><h3>seismic +cleanfa<a class="headerlink" href="#seismic-cleanfa" title="Permalink to this headline"></a></h3>
 <p>Clean the names and sequences in FASTA files.</p>