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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.MEME-module.html">Package MEME</a> ::
<a href="Bio.MEME.Motif-module.html">Module Motif</a> ::
Class Motif
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Motif</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif">source code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.MEME.Motif.MEMEMotif-class.html">MEMEMotif</a></li> </ul>
</dd></dl>
<hr />
<p>A generic motif class.</p>
<p>A Motif has information about the alphabet used in the motif, the
length of the motif, the motif name, the number of occurrences, and the
individual instances of the motif. Each of the instances is an object of
the Instance class.</p>
<p>Methods: add_instance(instance): adds a new instance of the motif.
get_instance_by_name(name): returns an instance with the specified
name.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="add_instance"></a><span class="summary-sig-name">add_instance</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">instance</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif.add_instance">source code</a></span>
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<td><span class="summary-sig"><a name="get_instance_by_name"></a><span class="summary-sig-name">get_instance_by_name</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif.get_instance_by_name">source code</a></span>
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<td><span class="summary-sig"><a name="_alphabet"></a><span class="summary-sig-name">_alphabet</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alphabet</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif._alphabet">source code</a></span>
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<td><span class="summary-sig"><a name="_length"></a><span class="summary-sig-name">_length</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">length</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif._length">source code</a></span>
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<td><span class="summary-sig"><a name="_name"></a><span class="summary-sig-name">_name</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif._name">source code</a></span>
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<td><span class="summary-sig"><a name="_consensus"></a><span class="summary-sig-name">_consensus</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">consensus</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif._consensus">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_numoccurrences"></a><span class="summary-sig-name">_numoccurrences</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">number</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif._numoccurrences">source code</a></span>
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<td><span class="summary-sig"><a name="make_pssm"></a><span class="summary-sig-name">make_pssm</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif.make_pssm">source code</a></span>
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<td><span class="summary-sig"><a name="make_consensus"></a><span class="summary-sig-name">make_consensus</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">minimum_frequency</span>=<span class="summary-sig-default">0.6</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MEME.Motif-pysrc.html#Motif.make_consensus">source code</a></span>
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