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<title>Bio.Motif.Parsers.MEME.MEMEMotif</title>
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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Motif-module.html">Package Motif</a> ::
<a href="Bio.Motif.Parsers-module.html">Package Parsers</a> ::
<a href="Bio.Motif.Parsers.MEME-module.html">Module MEME</a> ::
Class MEMEMotif
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class MEMEMotif</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Motif.Parsers.MEME-pysrc.html#MEMEMotif">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Motif._Motif.Motif-class.html">_Motif.Motif</a> --+
|
<strong class="uidshort">MEMEMotif</strong>
</pre>
<hr />
<p>A subclass of Motif used in parsing MEME (and MAST) output.</p>
<p>This sublcass defines functions and data specific to MEME motifs. This
includes the evalue for a motif and the PSSM of the motif.</p>
<p>Methods: add_instance_from_values (name = 'default', pvalue = 1,
sequence = 'ATA', start = 0, strand = +): create a new instance of the
motif with the specified values. add_to_pssm (position): add a new
position to the pssm. The position should be a list of nucleotide/amino
acid frequencies add_to_logodds (position): add a new position to the log
odds matrix. The position should be a tuple of log odds values for the
nucleotide/amino acid at that position. compare_motifs (other_motif):
returns the maximum correlation between this motif and other_motif</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Motif.Parsers.MEME.MEMEMotif-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
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<span class="codelink"><a href="Bio.Motif.Parsers.MEME-pysrc.html#MEMEMotif.__init__">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.Motif.Parsers.MEME-pysrc.html#MEMEMotif._numoccurrences">source code</a></span>
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<span class="summary-type"> </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.Motif.Parsers.MEME-pysrc.html#MEMEMotif.get_instance_by_name">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="add_instance_from_values"></a><span class="summary-sig-name">add_instance_from_values</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">default</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">pvalue</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">sequence</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">ATA</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">strand</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">+</code><code class="variable-quote">'</code></span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif.Parsers.MEME-pysrc.html#MEMEMotif.add_instance_from_values">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_evalue"></a><span class="summary-sig-name">_evalue</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">evalue</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif.Parsers.MEME-pysrc.html#MEMEMotif._evalue">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Motif._Motif.Motif-class.html">_Motif.Motif</a></code></b>:
<code><a href="Bio.Motif._Motif.Motif-class.html#__getitem__">__getitem__</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#__len__">__len__</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#__str__">__str__</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#add_instance">add_instance</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#anticonsensus">anticonsensus</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#consensus">consensus</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_dpq">dist_dpq</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_dpq_at">dist_dpq_at</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_pearson">dist_pearson</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_pearson_at">dist_pearson_at</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_product">dist_product</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#dist_product_at">dist_product_at</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#exp_score">exp_score</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#format">format</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#ic">ic</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#log_odds">log_odds</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#make_counts_from_instances">make_counts_from_instances</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#make_instances_from_counts">make_instances_from_counts</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#max_score">max_score</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#min_score">min_score</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#pwm">pwm</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#reverse_complement">reverse_complement</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#scanPWM">scanPWM</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#score_hit">score_hit</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#search_instances">search_instances</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#search_pwm">search_pwm</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#set_mask">set_mask</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#weblogo">weblogo</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Motif._Motif.Motif-class.html">_Motif.Motif</a></code></b> (private):
<code><a href="Bio.Motif._Motif.Motif-class.html#_check_alphabet" onclick="show_private();">_check_alphabet</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_check_length" onclick="show_private();">_check_length</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_from_horiz_matrix" onclick="show_private();">_from_horiz_matrix</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_pfm" onclick="show_private();">_from_jaspar_pfm</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_sites" onclick="show_private();">_from_jaspar_sites</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_from_vert_matrix" onclick="show_private();">_from_vert_matrix</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_pwm_calculate" onclick="show_private();">_pwm_calculate</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_read" onclick="show_private();">_read</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_to_fasta" onclick="show_private();">_to_fasta</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_to_horizontal_matrix" onclick="show_private();">_to_horizontal_matrix</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_to_jaspar_pfm" onclick="show_private();">_to_jaspar_pfm</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_to_transfac" onclick="show_private();">_to_transfac</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_to_vertical_matrix" onclick="show_private();">_to_vertical_matrix</a></code>,
<code><a href="Bio.Motif._Motif.Motif-class.html#_write" onclick="show_private();">_write</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__subclasshook__</code>
</p>
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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>
<br /><em class="fname">(Constructor)</em>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif.Parsers.MEME-pysrc.html#MEMEMotif.__init__">source code</a></span>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
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