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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 Schema
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Schema</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema">source code</a></span></p>
<p>Deal with motifs that have ambiguity characters in it.</p>
<p>This motif class allows specific ambiguity characters and tries to
speed up finding motifs using regular expressions.</p>
<p>This is likely to be a replacement for the Schema representation,
since it allows multiple ambiguity characters to be used.</p>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ambiguity_info</span>)</span><br />
Initialize with ambiguity information.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html#encode_motif" class="summary-sig-name">encode_motif</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>)</span><br />
Encode the passed motif as a regular expression pattern object.</td>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html#find_ambiguous" class="summary-sig-name">find_ambiguous</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>)</span><br />
Return the location of ambiguous items in the motif.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema.find_ambiguous">source code</a></span>
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<td><span class="summary-sig"><a name="num_ambiguous"></a><span class="summary-sig-name">num_ambiguous</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>)</span><br />
Return the number of ambiguous letters in a given motif.</td>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Schema.Schema-class.html#find_matches" class="summary-sig-name">find_matches</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>,
<span class="summary-sig-arg">query</span>)</span><br />
Return all non-overlapping motif matches in the query string.</td>
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<td><span class="summary-sig"><a name="num_matches"></a><span class="summary-sig-name">num_matches</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>,
<span class="summary-sig-arg">query</span>)</span><br />
Find the number of non-overlapping times motif occurs in query.</td>
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<td><span class="summary-sig"><a name="all_unambiguous"></a><span class="summary-sig-name">all_unambiguous</span>(<span class="summary-sig-arg">self</span>)</span><br />
Return a listing of all unambiguous letters allowed in motifs.</td>
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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">ambiguity_info</span>)</span>
<br /><em class="fname">(Constructor)</em>
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</td><td align="right" valign="top"
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<p>Initialize with ambiguity information.</p>
<p>Arguments:</p>
<p>o ambiguity_info - A dictionary which maps letters in the motifs to
the ambiguous characters which they might represent. For example, {'R' :
'AG'} specifies that Rs in the motif can match a A or a G. All letters in
the motif must be represented in the ambiguity_info dictionary.</p>
<dl class="fields">
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<a name="encode_motif"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">encode_motif</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">motif</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema.encode_motif">source code</a></span>
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<p>Encode the passed motif as a regular expression pattern object.</p>
<p>Arguments:</p>
<p>o motif - The motif we want to encode. This should be a string.</p>
<p>Returns: A compiled regular expression pattern object that can be used
for searching strings.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">find_ambiguous</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">motif</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema.find_ambiguous">source code</a></span>
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<p>Return the location of ambiguous items in the motif.</p>
<p>This just checks through the motif and compares each letter against
the ambiguity information. If a letter stands for multiple items, it is
ambiguous.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">find_matches</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">motif</span>,
<span class="sig-arg">query</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Schema-pysrc.html#Schema.find_matches">source code</a></span>
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<p>Return all non-overlapping motif matches in the query string.</p>
<p>This utilizes the regular expression findall function, and will return
a list of all non-overlapping occurances in query that match the
ambiguous motif.</p>
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</dl>
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