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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignAce-module.html">Package AlignAce</a> ::
<a href="Bio.AlignAce.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.AlignAce.Motif-pysrc.html#Motif">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Motif</strong>
</pre>
<hr />
<p>A class representing sequence motifs.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="_check_length"></a><span class="summary-sig-name">_check_length</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">len</span>)</span></td>
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<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif._check_length">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_check_alphabet"></a><span class="summary-sig-name">_check_alphabet</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alphabet</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif._check_alphabet">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"></a><span class="summary-sig-name">add_instance</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">instance</span>)</span><br />
adds new instance to the motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.add_instance">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#set_mask" class="summary-sig-name">set_mask</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">mask</span>)</span><br />
sets the mask for the motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.set_mask">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="pwm"></a><span class="summary-sig-name">pwm</span>(<span class="summary-sig-arg">self</span>)</span><br />
returns the PWM computed for the set of instances</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.pwm">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="search_instances"></a><span class="summary-sig-name">search_instances</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence</span>)</span><br />
a generator function, returning found positions of instances of the
motif in a given sequence</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.search_instances">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="score_hit"></a><span class="summary-sig-name">score_hit</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence</span>,
<span class="summary-sig-arg">position</span>,
<span class="summary-sig-arg">normalized</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">masked</span>=<span class="summary-sig-default">0</span>)</span><br />
give the pwm score for a given position</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.score_hit">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="search_pwm"></a><span class="summary-sig-name">search_pwm</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence</span>,
<span class="summary-sig-arg">threshold</span>=<span class="summary-sig-default">0.0</span>,
<span class="summary-sig-arg">normalized</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">masked</span>=<span class="summary-sig-default">1</span>)</span><br />
a generator function, returning found hits in a given sequence with
the pwm score higher than the threshold</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.search_pwm">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#sim" class="summary-sig-name">sim</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>,
<span class="summary-sig-arg">masked</span>=<span class="summary-sig-default">0</span>)</span><br />
return the similarity score for the given motif against self.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.sim">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#read" class="summary-sig-name">read</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>)</span><br />
reads the motif from the stream</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.read">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
string representation of motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.__str__">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="write"></a><span class="summary-sig-name">write</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>)</span><br />
writes the motif to the stream</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.write">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="to_fasta"></a><span class="summary-sig-name">to_fasta</span>(<span class="summary-sig-arg">self</span>)</span><br />
FASTA representation of motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.to_fasta">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.AlignAce.Motif.Motif-class.html#weblogo" class="summary-sig-name">weblogo</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">fname</span>,
<span class="summary-sig-arg">format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">PNG</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**kwds</span>)</span><br />
uses the Berkeley weblogo service to download and save a weblogo of
itself</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.weblogo">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>
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<!-- ==================== PROPERTIES ==================== -->
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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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>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.__init__">source code</a></span>
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<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
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<a name="set_mask"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">set_mask</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">mask</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.set_mask">source code</a></span>
</td>
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<p>sets the mask for the motif</p>
<p>The mask should be a string containing asterisks in the position of
significant columns and spaces in other columns</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="sim"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">sim</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">motif</span>,
<span class="sig-arg">masked</span>=<span class="sig-default">0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.sim">source code</a></span>
</td>
</tr></table>
<p>return the similarity score for the given motif against self.</p>
<p>We use the Pearson's correlation of the respective probabilities. If
the motifs have different length or mask raise the ValueError.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="read"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">read</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">stream</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.read">source code</a></span>
</td>
</tr></table>
<p>reads the motif from the stream</p>
<p>the self.alphabet variable must be set before</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__str__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.__str__">source code</a></span>
</td>
</tr></table>
<p>string representation of motif</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
<a name="weblogo"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">weblogo</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">fname</span>,
<span class="sig-arg">format</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">PNG</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**kwds</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.AlignAce.Motif-pysrc.html#Motif.weblogo">source code</a></span>
</td>
</tr></table>
<p>uses the Berkeley weblogo service to download and save a weblogo of
itself</p>
<p>requires an internet connection. The parameters from **kwds are passed
directly to the weblogo server.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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