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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.NeuralNetwork-module.html">Package NeuralNetwork</a> ::
<a href="Bio.NeuralNetwork.Gene-module.html">Package Gene</a> ::
<a href="Bio.NeuralNetwork.Gene.Schema-module.html">Module Schema</a> ::
Class SchemaCoder
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SchemaCoder</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">SchemaCoder</strong>
</pre>
<hr />
<p>Convert a sequence into a representation of ambiguous motifs
(schemas).</p>
<p>This takes a sequence, and returns the number of times specified
motifs are found in the sequence. This lets you represent a sequence as
just a count of (possibly ambiguous) motifs.</p>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">schemas</span>,
<span class="summary-sig-arg">ambiguous_converter</span>)</span><br />
Initialize the coder to convert sequences</td>
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<span class="summary-sig-arg">sequence</span>)</span><br />
Represent the given input sequence as a bunch of motif counts.</td>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">schemas</span>,
<span class="sig-arg">ambiguous_converter</span>)</span>
<br /><em class="fname">(Constructor)</em>
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<p>Initialize the coder to convert sequences</p>
<p>Arguments:</p>
<p>o schema - A list of all of the schemas we want to search for in input
sequences.</p>
<p>o ambiguous_converter - An Schema class which can be used to convert
motifs into regular expressions for searching.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">representation</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sequence</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#SchemaCoder.representation">source code</a></span>
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<p>Represent the given input sequence as a bunch of motif counts.</p>
<p>Arguments:</p>
<p>o sequence - A Bio.Seq object we are going to represent as
schemas.</p>
<p>This takes the sequence, searches for the motifs within it, and then
returns counts specifying the relative number of times each motifs was
found. The frequencies are in the order the original motifs were passed
into the initializer.</p>
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