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Finished first major doc update

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<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
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<link rel="search" title="Search" href="search.html" />
<link rel="next" title="License" href="license.html" />
<link rel="prev" title="Input files" href="input_files.html" />
<script src="_static/js/modernizr.min.js"></script>
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<div class="wy-grid-for-nav">
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<p>FASTA headers are generated with the following pattern:</p>
<p><code class="docutils literal notranslate"><span class="pre">&gt;&lt;ID&gt;_&lt;G1&gt;:&lt;G1_C&gt;_&lt;G2&gt;:&lt;G2_C&gt;_p:&lt;P&gt;_mindepth:&lt;D&gt;</span></code></p>
<ul class="simple">
<li>&lt;ID&gt;: marker ID in the markers depth table</li>
<li>&lt;G1&gt;: name of the first compared group</li>
<li>&lt;G1_C&gt;: number of individuals from the first compared group in which the marker is present</li>
<li>&lt;G2&gt;: name of the second compared group</li>
<li>&lt;G2_C&gt;: number of individuals from the second compared group in which the marker is present</li>
<li>&lt;P&gt;: p-value of association with group</li>
<li>&lt;D&gt;: minimum depth to consider a marker present in an individual</li>
<li><p>&lt;ID&gt;: marker ID in the markers depth table</p></li>
<li><p>&lt;G1&gt;: name of the first compared group</p></li>
<li><p>&lt;G1_C&gt;: number of individuals from the first compared group in which the marker is present</p></li>
<li><p>&lt;G2&gt;: name of the second compared group</p></li>
<li><p>&lt;G2_C&gt;: number of individuals from the second compared group in which the marker is present</p></li>
<li><p>&lt;P&gt;: p-value of association with group</p></li>
<li><p>&lt;D&gt;: minimum depth to consider a marker present in an individual</p></li>
</ul>
<p>Example:</p>
<p><code class="docutils literal notranslate"><span class="pre">&gt;4495827_F:0_M:21_p:1.14577e-07_mindepth:10</span></code></p>
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docs/html/search.html
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<script type="text/javascript" src="_static/js/modernizr.min.js"></script>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
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<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">RADSex usage</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#process">process</a></li>
<li class="toctree-l2"><a class="reference internal" href="#distrib">distrib</a></li>
<li class="toctree-l2"><a class="reference internal" href="#subset">subset</a></li>
<li class="toctree-l2"><a class="reference internal" href="#signif">signif</a></li>
<li class="toctree-l2"><a class="reference internal" href="#map">map</a></li>
<li class="toctree-l2"><a class="reference internal" href="#subset">subset</a></li>
<li class="toctree-l2"><a class="reference internal" href="#freq">freq</a></li>
<li class="toctree-l2"><a class="reference internal" href="#depth">depth</a></li>
</ul>
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<div class="section" id="radsex-usage">
<span id="full-usage"></span><h1>RADSex usage<a class="headerlink" href="#radsex-usage" title="Permalink to this headline"></a></h1>
<p>The RADSex software presents the general command-line interface:</p>
<p>The RADSex software implements the general command-line interface:</p>
<p><code class="docutils literal notranslate"><span class="pre">radsex</span> <span class="pre">&lt;command&gt;</span> <span class="pre">[options]</span></code></p>
<p><strong>Available commands</strong></p>
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<tr class="row-odd"><th class="head">Command</th>
<th class="head">Description</th>
<thead>
<tr class="row-odd"><th class="head"><p>Command</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>depth</td>
<td>Compute marker depth statistics for each individual</td>
<tbody>
<tr class="row-even"><td><p>depth</p></td>
<td><p>Compute marker depth statistics for each individual</p></td>
</tr>
<tr class="row-odd"><td>distrib</td>
<td>Compute the distribution of markers between compared groups</td>
<tr class="row-odd"><td><p>distrib</p></td>
<td><p>Compute the distribution of markers between compared groups</p></td>
</tr>
<tr class="row-even"><td>freq</td>
<td>Compute the distribution of markers in all individuals</td>
<tr class="row-even"><td><p>freq</p></td>
<td><p>Compute the distribution of markers in all individuals</p></td>
</tr>
<tr class="row-odd"><td>map</td>
<td>Align markers to a genome and compute metrics for each aligned marker</td>
<tr class="row-odd"><td><p>map</p></td>
<td><p>Align markers to a genome and compute metrics for each aligned marker</p></td>
</tr>
<tr class="row-even"><td>process</td>
<td>Compute a table of marker depths from a set of demultiplexed reads files</td>
<tr class="row-even"><td><p>process</p></td>
<td><p>Compute a table of marker depths from a set of demultiplexed reads files</p></td>
</tr>
<tr class="row-odd"><td>signif</td>
<td>Extract markers significantly associated with phenotypic group from a marker depths table</td>
<tr class="row-odd"><td><p>signif</p></td>
<td><p>Extract markers significantly associated with phenotypic group from a marker depths table</p></td>
</tr>
<tr class="row-even"><td>subset</td>
<td>Extract a subset of markers from a marker depths table</td>
<tr class="row-even"><td><p>subset</p></td>
<td><p>Extract a subset of markers from a marker depths table</p></td>
</tr>
</tbody>
</table>
<hr class="docutils" />
<div class="section" id="process">
<span id="process-usage"></span><h2>process<a class="headerlink" href="#process" title="Permalink to this headline"></a></h2>
<p>Generate a table containing the depth of each marker in each individual from the dataset.</p>
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</pre></div>
</div>
<p><strong>Options</strong></p>
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<tr class="row-odd"><th class="head">Option</th>
<th class="head">Description</th>
<thead>
<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
</thead>
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<tr class="row-even"><td><code class="docutils literal notranslate"><span class="pre">--input-dir,</span> <span class="pre">-i</span></code></td>
<td>Path to a folder containing demultiplexed reads</td>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--input-dir,</span> <span class="pre">-i</span></code></p></td>
<td><p>Path to a folder containing demultiplexed reads</p></td>
</tr>
<tr class="row-odd"><td><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></td>
<td>Path to the generated marker depths table</td>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the generated marker depths table</p></td>
</tr>
<tr class="row-even"><td><code class="docutils literal notranslate"><span class="pre">--threads,</span> <span class="pre">-T</span></code></td>
<td>Number of threads to use (default: 1)</td>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--threads,</span> <span class="pre">-T</span></code></p></td>
<td><p>Number of threads to use (default: 1)</p></td>
</tr>
<tr class="row-odd"><td><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></td>
<td>Minimum depth to consider a marker present in an individual (default: 1)</td>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></p></td>
<td><p>Minimum depth to consider a marker present in an individual (default: 1)</p></td>
</tr>
</tbody>
</table>
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</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Input files are automatically dectected from the input directory based on their extensions. Supported extensions are <strong>.fa</strong>, <strong>.fa.gz</strong>, <strong>.fq</strong>, <strong>.fq.gz</strong>, <strong>.fasta</strong>, <strong>.fasta.gz</strong>, <strong>.fastq</strong>, <strong>.fastq.gz</strong>, <strong>.fna</strong>, and <strong>.fna.gz</strong>. Individual IDs in the output table will be inferred from the input files names after removing the extension. For instance, a file named <strong>individual_1.fastq.gz</strong> will be attributed the ID <strong>individual_1</strong>. Make sure to use the same IDs when creating the population map.</p>
<p class="admonition-title">Note</p>
<p>Input files are automatically dectected from the input directory based on their extensions. Supported extensions are <strong>.fa</strong>, <strong>.fa.gz</strong>, <strong>.fq</strong>, <strong>.fq.gz</strong>, <strong>.fasta</strong>, <strong>.fasta.gz</strong>, <strong>.fastq</strong>, <strong>.fastq.gz</strong>, <strong>.fna</strong>, and <strong>.fna.gz</strong>. Individual IDs in the output table will be inferred from the input files names after removing the extension. For instance, a file named <strong>individual_1.fastq.gz</strong> will be attributed the ID <strong>individual_1</strong>. Make sure to use the same IDs when creating the population map.</p>
</div>
<hr class="docutils" />
</div>
<div class="section" id="distrib">
<span id="distrib-usage"></span><h2>distrib<a class="headerlink" href="#distrib" title="Permalink to this headline"></a></h2>
<p>Generate a table containing the distribution of markers between two groups of individuals defined in a <span class="xref std std-ref">popmap-file</span>.</p>
<p>Generate a table containing the distribution of markers between two groups of individuals defined in a <a class="reference internal" href="input_files.html#population-map"><span class="std std-ref">Population map</span></a>.</p>
<p><strong>Command</strong></p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">radsex</span> <span class="n">distrib</span> <span class="o">--</span><span class="n">markers</span><span class="o">-</span><span class="n">table</span> <span class="n">markers_table_path</span> <span class="o">--</span><span class="n">output</span><span class="o">-</span><span class="n">file</span> <span class="n">output_file_path</span> <span class="o">--</span><span class="n">popmap</span> <span class="n">popmap_path</span> <span class="p">[</span> <span class="o">--</span><span class="nb">min</span><span class="o">-</span><span class="n">depth</span> <span class="n">min_depth</span> <span class="o">--</span><span class="n">groups</span> <span class="n">group1</span><span class="p">,</span><span class="n">group2</span> <span class="o">--</span><span class="n">signif</span><span class="o">-</span><span class="n">threshold</span> <span class="n">signif_threshold</span> <span class="o">--</span><span class="n">disable</span><span class="o">-</span><span class="n">correction</span> <span class="p">]</span>
</pre></div>
</div>
<p><strong>Options</strong></p>
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<th class="head">Description</th>
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<tr class="row-odd"><th class="head"><p>Option</p></th>
<th class="head"><p>Description</p></th>
</tr>
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<tr class="row-even"><td><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></td>
<td>Path to a marker depths table generated by “process”</td>
<tbody>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--markers-table,</span> <span class="pre">-t</span></code></p></td>
<td><p>Path to a marker depths table generated by “process”</p></td>
</tr>
<tr class="row-odd"><td><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></td>
<td>Path to a tabulated file specifying groups for all individuals</td>
<tr class="row-odd"><td><p><code class="docutils literal notranslate"><span class="pre">--popmap,</span> <span class="pre">-p</span></code></p></td>
<td><p>Path to a tabulated file specifying groups for all individuals</p></td>
</tr>
<tr class="row-even"><td><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></td>
<td>Path to the output file (distribution of markers between groups)</td>
<tr class="row-even"><td><p><code class="docutils literal notranslate"><span class="pre">--output-file,</span> <span class="pre">-o</span></code></p></td>
<td><p>Path to the output file (distribution of markers between groups)</p></td>
</tr>
<tr class="row-odd"><td><code class="docutils literal notranslate"><span class="pre">--min-depth,</span> <span class="pre">-d</span></code></td>
<td>Minimum depth to consider a marker present in an individual</td>