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<span class="target" id="module-GAllele"></span><div class="section" id="gallele-the-genome-alleles-module">
<h1><a class="reference internal" href="#module-GAllele" title="GAllele"><code class="xref py py-mod docutils literal"><span class="pre">GAllele</span></code></a> – the genome alleles module<a class="headerlink" href="#gallele-the-genome-alleles-module" title="Permalink to this headline">¶</a></h1>
<p>In this module, there are the <a class="reference internal" href="#GAllele.GAlleles" title="GAllele.GAlleles"><code class="xref py py-class docutils literal"><span class="pre">GAllele.GAlleles</span></code></a> class (which is the
class that holds the allele types) and all the
allele types to use with the supported chromosomes.</p>
<dl class="class">
<dt id="GAllele.GAlleleList">
<em class="property">class </em><code class="descclassname">GAllele.</code><code class="descname">GAlleleList</code><span class="sig-paren">(</span><em>options=None</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleList" title="Permalink to this definition">¶</a></dt>
<dd><p>GAlleleList Class - The list allele type</p>
<dl class="docutils">
<dt>Example:</dt>
<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">alleles</span> <span class="o">=</span> <span class="n">GAlleles</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">choices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">4</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">lst</span> <span class="o">=</span> <span class="n">GAlleleList</span><span class="p">(</span><span class="n">choices</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">alleles</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">lst</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">alleles</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getRandomAllele</span><span class="p">()</span> <span class="ow">in</span> <span class="n">lst</span>
<span class="go">True</span>
</pre></div>
</div>
</dd>
</dl>
<dl class="method">
<dt id="GAllele.GAlleleList.add">
<code class="descname">add</code><span class="sig-paren">(</span><em>option</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleList.add" title="Permalink to this definition">¶</a></dt>
<dd><p>Appends one option to the options list</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>option</strong> – option to be added in the list</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleList.clear">
<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleList.clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes all the allele options from the list</p>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleList.getRandomAllele">
<code class="descname">getRandomAllele</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleList.getRandomAllele" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns one random choice from the options list</p>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleList.remove">
<code class="descname">remove</code><span class="sig-paren">(</span><em>option</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleList.remove" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes the option from list</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>option</strong> – remove the option from the list</td>
</tr>
</tbody>
</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="GAllele.GAlleleRange">
<em class="property">class </em><code class="descclassname">GAllele.</code><code class="descname">GAlleleRange</code><span class="sig-paren">(</span><em>begin=0</em>, <em>end=100</em>, <em>real=False</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange" title="Permalink to this definition">¶</a></dt>
<dd><p>GAlleleRange Class - The range allele type</p>
<dl class="docutils">
<dt>Example:</dt>
<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">ranges</span> <span class="o">=</span> <span class="n">GAlleleRange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">100</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">ranges</span><span class="o">.</span><span class="n">getRandomAllele</span><span class="p">()</span> <span class="o">>=</span> <span class="mi">0</span> <span class="ow">and</span> <span class="n">ranges</span><span class="o">.</span><span class="n">getRandomAllele</span><span class="p">()</span> <span class="o"><=</span> <span class="mi">100</span>
<span class="go">True</span>
</pre></div>
</div>
</dd>
</dl>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>begin</strong> – the begin of the range</li>
<li><strong>end</strong> – the end of the range</li>
<li><strong>real</strong> – if True, the range will be of real values</li>
</ul>
</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="GAllele.GAlleleRange.add">
<code class="descname">add</code><span class="sig-paren">(</span><em>begin</em>, <em>end</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.add" title="Permalink to this definition">¶</a></dt>
<dd><p>Add a new range</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>begin</strong> – the begin of range</li>
<li><strong>end</strong> – the end of the range</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.clear">
<code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.clear" title="Permalink to this definition">¶</a></dt>
<dd><p>Removes all ranges</p>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.getMaximum">
<code class="descname">getMaximum</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.getMaximum" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the maximum of all the ranges</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">the maximum value</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.getMinimum">
<code class="descname">getMinimum</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.getMinimum" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the minimum of all the ranges</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">the minimum value</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.getRandomAllele">
<code class="descname">getRandomAllele</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.getRandomAllele" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns one random choice between the range</p>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.getReal">
<code class="descname">getReal</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.getReal" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns True if the range is real or False if it is integer</p>
</dd></dl>
<dl class="method">
<dt id="GAllele.GAlleleRange.setReal">
<code class="descname">setReal</code><span class="sig-paren">(</span><em>flag=True</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleleRange.setReal" title="Permalink to this definition">¶</a></dt>
<dd><p>Sets True if the range is real or False if is integer</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>flag</strong> – True or False</td>
</tr>
</tbody>
</table>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="GAllele.GAlleles">
<em class="property">class </em><code class="descclassname">GAllele.</code><code class="descname">GAlleles</code><span class="sig-paren">(</span><em>allele_list=None</em>, <em>homogeneous=False</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleles" title="Permalink to this definition">¶</a></dt>
<dd><p>GAlleles Class - The set of alleles</p>
<dl class="docutils">
<dt>Example:</dt>
<dd><div class="first last highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">alleles</span> <span class="o">=</span> <span class="n">GAlleles</span><span class="p">()</span>
<span class="gp">>>> </span><span class="n">choices</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">4</span><span class="p">]</span>
<span class="gp">>>> </span><span class="n">lst</span> <span class="o">=</span> <span class="n">GAlleleList</span><span class="p">(</span><span class="n">choices</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">alleles</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">lst</span><span class="p">)</span>
<span class="gp">>>> </span><span class="n">alleles</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">getRandomAllele</span><span class="p">()</span> <span class="ow">in</span> <span class="n">lst</span>
<span class="go">True</span>
</pre></div>
</div>
</dd>
</dl>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>allele_list</strong> – the list of alleles</li>
<li><strong>homogeneous</strong> – if is True, all the alleles will be use only the first added</li>
</ul>
</td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="GAllele.GAlleles.add">
<code class="descname">add</code><span class="sig-paren">(</span><em>allele</em><span class="sig-paren">)</span><a class="headerlink" href="#GAllele.GAlleles.add" title="Permalink to this definition">¶</a></dt>
<dd><p>Appends one allele to the alleles list</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>allele</strong> – allele to be added</td>
</tr>
</tbody>
</table>
</dd></dl>
</dd></dl>
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