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  <div class="section" id="profile-api">
<span id="profile"></span><h1>Profile API<a class="headerlink" href="#profile-api" title="Permalink to this headline"></a></h1>
<p>The <a class="reference internal" href="implementation.html#profile-implementation"><span class="std std-ref">Profile object</span></a> is used for the search of the gene with Hmmer. A <em>“Profile”</em> must match a HMM protein profile file, which name is based on the profile name. For instance, the <em>gspG</em> gene has the corresponding “gspG.hmm” profile file provided at a dedicated location.</p>
<div class="section" id="profilefactory-api-reference">
<h2>ProfileFactory API reference<a class="headerlink" href="#profilefactory-api-reference" title="Permalink to this headline"></a></h2>
<blockquote>
<div><span class="target" id="module-macsypy.gene"></span><dl class="class">
<dt id="macsypy.gene.ProfileFactory">
<em class="property">class </em><code class="descclassname">macsypy.gene.</code><code class="descname">ProfileFactory</code><a class="reference internal" href="_modules/macsypy/gene.html#ProfileFactory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.ProfileFactory" title="Permalink to this definition"></a></dt>
<dd><p>Build and store all Profile objects. Profiles must not be instanciated directly.
The profile_factory must be used. The profile_factory ensures there is only one instance
of profile for a given name.
To get a profile, use the method get_profile. If the profile is already cached, this instance is returned.
Otherwise a new profile is built, stored in the profile_factory and then returned.</p>
<dl class="attribute">
<dt id="macsypy.gene.ProfileFactory.__weakref__">
<code class="descname">__weakref__</code><a class="headerlink" href="#macsypy.gene.ProfileFactory.__weakref__" title="Permalink to this definition"></a></dt>
<dd><p>list of weak references to the object (if defined)</p>
</dd></dl>

<dl class="method">
<dt id="macsypy.gene.ProfileFactory.get_profile">
<code class="descname">get_profile</code><span class="sig-paren">(</span><em>gene</em>, <em>cfg</em>, <em>profiles_registry</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#ProfileFactory.get_profile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.ProfileFactory.get_profile" title="Permalink to this definition"></a></dt>
<dd><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 simple">
<li><strong>gene</strong> (<a class="reference internal" href="gene.html#macsypy.gene.Gene" title="macsypy.gene.Gene"><code class="xref py py-class docutils literal"><span class="pre">macsypy.gene.Gene</span></code></a> or <a class="reference internal" href="gene.html#macsypy.gene.Homolog" title="macsypy.gene.Homolog"><code class="xref py py-class docutils literal"><span class="pre">macsypy.gene.Homolog</span></code></a> or <a class="reference internal" href="gene.html#macsypy.gene.Analog" title="macsypy.gene.Analog"><code class="xref py py-class docutils literal"><span class="pre">macsypy.gene.Analog</span></code></a> object) – the gene associated to this profile</li>
<li><strong>profiles_registry</strong> (<em>the registry of profiles</em>) – the registry where are stored the path of the profiles</li>
<li><strong>profiles_registry</strong><code class="xref py py-class docutils literal"><span class="pre">macsypy.registries.ProfilesRegistry</span></code> instance.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">the profile corresponding to the name.
If the profile already exists, return it. Otherwise build it, store it and return it.</p>
</td>
</tr>
<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="#macsypy.gene.Profile" title="macsypy.gene.Profile"><code class="xref py py-class docutils literal"><span class="pre">macsypy.gene.Profile</span></code></a> object</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

</div></blockquote>
</div>
<div class="section" id="module-macsypy.gene">
<span id="profile-api-reference"></span><h2>Profile API reference<a class="headerlink" href="#module-macsypy.gene" title="Permalink to this headline"></a></h2>
<dl class="class">
<dt id="macsypy.gene.Profile">
<em class="property">class </em><code class="descclassname">macsypy.gene.</code><code class="descname">Profile</code><span class="sig-paren">(</span><em>gene</em>, <em>cfg</em>, <em>path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile" title="Permalink to this definition"></a></dt>
<dd><p>Handle a HMM protein profile</p>
<dl class="method">
<dt id="macsypy.gene.Profile.__init__">
<code class="descname">__init__</code><span class="sig-paren">(</span><em>gene</em>, <em>cfg</em>, <em>path</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile.__init__" title="Permalink to this definition"></a></dt>
<dd><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>gene</strong> – the gene corresponding to this profile</li>
<li><strong>cfg</strong> (<code class="xref py py-class docutils literal"><span class="pre">macsypy.config.Config</span></code> object) – the configuration</li>
<li><strong>path</strong> (<em>string</em>) – the path to the hmm profile.</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="macsypy.gene.Profile.__len__">
<code class="descname">__len__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile.__len__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile.__len__" title="Permalink to this definition"></a></dt>
<dd><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">Returns:</th><td class="field-body">the length of the HMM protein profile</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">int</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="macsypy.gene.Profile.__str__">
<code class="descname">__str__</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile.__str__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile.__str__" title="Permalink to this definition"></a></dt>
<dd><p>Print the name of the corresponding gene and the path to the HMM profile.</p>
</dd></dl>

<dl class="attribute">
<dt id="macsypy.gene.Profile.__weakref__">
<code class="descname">__weakref__</code><a class="headerlink" href="#macsypy.gene.Profile.__weakref__" title="Permalink to this definition"></a></dt>
<dd><p>list of weak references to the object (if defined)</p>
</dd></dl>

<dl class="method">
<dt id="macsypy.gene.Profile._len">
<code class="descname">_len</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile._len"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile._len" title="Permalink to this definition"></a></dt>
<dd><p>Parse the HMM profile file to get and store the length.
This private method is called at the Profile init.</p>
</dd></dl>

<dl class="method">
<dt id="macsypy.gene.Profile.execute">
<code class="descname">execute</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/macsypy/gene.html#Profile.execute"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#macsypy.gene.Profile.execute" title="Permalink to this definition"></a></dt>
<dd><p>Launch the Hmmer search (hmmsearch executable) with this profile</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">Returns:</th><td class="field-body">an object storing information on th results of the HMM search (HMMReport)</td>
</tr>
<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="HMMReport.html#macsypy.report.HMMReport" title="macsypy.report.HMMReport"><code class="xref py py-class docutils literal"><span class="pre">macsypy.report.HMMReport</span></code></a> object</td>
</tr>
</tbody>
</table>
</dd></dl>

</dd></dl>

</div>
</div>


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  <h3><a href="index.html">Table Of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">Profile API</a><ul>
<li><a class="reference internal" href="#profilefactory-api-reference">ProfileFactory API reference</a></li>
<li><a class="reference internal" href="#module-macsypy.gene">Profile API reference</a></li>
</ul>
</li>
</ul>

  <h4>Previous topic</h4>
  <p class="topless"><a href="gene.html"
                        title="previous chapter">Gene API</a></p>
  <h4>Next topic</h4>
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                        title="next chapter">HMMReport API</a></p>
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