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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.Pattern-module.html">Module Pattern</a> ::
Class PatternRepository
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class PatternRepository</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository">source code</a></span></p>
<p>This holds a list of specific patterns found in sequences.</p>
<p>This is designed to be a general holder for a set of patterns and
should be subclassed for specific implementations (ie. holding Motifs or
Signatures.</p>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pattern_info</span>)</span><br />
Initialize a repository with patterns,</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="get_all"></a><span class="summary-sig-name">get_all</span>(<span class="summary-sig-arg">self</span>)</span><br />
Retrieve all of the patterns in the repository.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_all">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#get_random" class="summary-sig-name">get_random</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">num_patterns</span>)</span><br />
Retrieve the specified number of patterns randomly.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_random">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#get_top_percentage" class="summary-sig-name">get_top_percentage</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">percent</span>)</span><br />
Return a percentage of the patterns.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_top_percentage">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#get_top" class="summary-sig-name">get_top</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">num_patterns</span>)</span><br />
Return the specified number of most frequently occurring patterns</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_top">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#get_differing" class="summary-sig-name">get_differing</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">top_num</span>,
<span class="summary-sig-arg">bottom_num</span>)</span><br />
Retrieve patterns that are at the extreme ranges.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_differing">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#remove_polyA" class="summary-sig-name">remove_polyA</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">at_percentage</span>=<span class="summary-sig-default">0.9</span>)</span><br />
Remove patterns which are likely due to polyA tails from the lists.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.remove_polyA">source code</a></span>
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<td><span class="summary-sig"><a name="count"></a><span class="summary-sig-name">count</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pattern</span>)</span><br />
Return the number of times the specified pattern is found.</td>
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<span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.count">source code</a></span>
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<a name="__init__"></a>
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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">pattern_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 a repository with patterns,</p>
<p>Arguments:</p>
<p>o pattern_info - A representation of all of the patterns found in a
*Finder search. This should be a dictionary, where the keys are patterns,
and the values are the number of times a pattern is found.</p>
<p>The patterns are represented interally as a list of two tuples, where
the first element is the number of times a pattern occurs, and the second
is the pattern itself. This makes it easy to sort the list and return the
top N patterns.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_random</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">num_patterns</span>)</span>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_random">source code</a></span>
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<p>Retrieve the specified number of patterns randomly.</p>
<p>Randomly selects patterns from the list and returns them.</p>
<p>Arguments:</p>
<p>o num_patterns - The total number of patterns to return.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_top_percentage</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">percent</span>)</span>
</h3>
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><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_top_percentage">source code</a></span>
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<p>Return a percentage of the patterns.</p>
<p>This returns the top 'percent' percentage of the patterns in the
repository.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_top</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">num_patterns</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_top">source code</a></span>
</td>
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<p>Return the specified number of most frequently occurring patterns</p>
<p>Arguments:</p>
<p>o num_patterns - The number of patterns to return.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_differing</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">top_num</span>,
<span class="sig-arg">bottom_num</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.get_differing">source code</a></span>
</td>
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<p>Retrieve patterns that are at the extreme ranges.</p>
<p>This returns both patterns at the top of the list (ie. the same as
returned by get_top) and at the bottom of the list. This is especially
useful for patterns that are the differences between two sets of
patterns.</p>
<p>Arguments:</p>
<p>o top_num - The number of patterns to take from the top of the
list.</p>
<p>o bottom_num - The number of patterns to take from the bottom of the
list.</p>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">remove_polyA</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">at_percentage</span>=<span class="sig-default">0.9</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.NeuralNetwork.Gene.Pattern-pysrc.html#PatternRepository.remove_polyA">source code</a></span>
</td>
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<p>Remove patterns which are likely due to polyA tails from the
lists.</p>
<p>This is just a helper function to remove pattenrs which are likely
just due to polyA tails, and thus are not really great motifs. This will
also get rid of stuff like ATATAT, which might be a useful motif, so use
at your own discretion.</p>
<p>XXX Could we write a more general function, based on info content or
something like that?</p>
<p>Arguments:</p>
<p>o at_percentage - The percentage of A and T residues in a pattern that
qualifies it for being removed.</p>
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