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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._Motif-module.html" onclick="show_private();">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.Motif._Motif-pysrc.html#Motif">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Motif</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.Motif.Parsers.MEME.MEMEMotif-class.html">Parsers.MEME.MEMEMotif</a></li> </ul>
</dd></dl>
<hr />
<p>A class representing sequence motifs.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#__getitem__" class="summary-sig-name">__getitem__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">index</span>)</span><br />
Returns the probability distribution over symbols at a given
position, padding with background.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__getitem__">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.Motif._Motif.Motif-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">IUPACUnambiguousDNA()</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__init__">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#__len__" class="summary-sig-name">__len__</a>(<span class="summary-sig-arg">self</span>)</span><br />
return the length of a motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__len__">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.Motif._Motif.Motif-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">masked</span>=<span class="summary-sig-default">False</span>)</span><br />
string representation of a motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__str__">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="_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.Motif._Motif-pysrc.html#Motif._check_alphabet">source code</a></span>
</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="_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>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._check_length">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_from_horiz_matrix"></a><span class="summary-sig-name">_from_horiz_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">letters</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">make_instances</span>=<span class="summary-sig-default">False</span>)</span><br />
reads a horizontal count matrix from stream and fill in the counts.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._from_horiz_matrix">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_pfm" class="summary-sig-name" onclick="show_private();">_from_jaspar_pfm</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">make_instances</span>=<span class="summary-sig-default">False</span>)</span><br />
reads the motif from Jaspar .pfm file</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._from_jaspar_pfm">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>
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<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_sites" class="summary-sig-name" onclick="show_private();">_from_jaspar_sites</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>)</span><br />
reads the motif from Jaspar .sites file</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._from_jaspar_sites">source code</a></span>
</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="_from_vert_matrix"></a><span class="summary-sig-name">_from_vert_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>,
<span class="summary-sig-arg">letters</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">make_instances</span>=<span class="summary-sig-default">False</span>)</span><br />
reads a vertical count matrix from stream and fill in the counts.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._from_vert_matrix">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_pwm_calculate"></a><span class="summary-sig-name">_pwm_calculate</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sequence</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._pwm_calculate">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#_read" class="summary-sig-name" onclick="show_private();">_read</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">stream</span>)</span><br />
Reads the motif from the stream (in AlignAce format).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._read">source code</a></span>
</td>
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</td>
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<tr class="private">
<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.Motif._Motif-pysrc.html#Motif._to_fasta">source code</a></span>
</td>
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</td>
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<tr class="private">
<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_horizontal_matrix"></a><span class="summary-sig-name">_to_horizontal_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">letters</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">normalized</span>=<span class="summary-sig-default">True</span>)</span><br />
Return string representation of the motif as a matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._to_horizontal_matrix">source code</a></span>
</td>
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</td>
</tr>
<tr class="private">
<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="_to_jaspar_pfm"></a><span class="summary-sig-name">_to_jaspar_pfm</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the pfm representation of the motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._to_jaspar_pfm">source code</a></span>
</td>
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</td>
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<tr class="private">
<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_transfac"></a><span class="summary-sig-name">_to_transfac</span>(<span class="summary-sig-arg">self</span>)</span><br />
Write the representation of a motif in TRANSFAC format</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._to_transfac">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="_to_vertical_matrix"></a><span class="summary-sig-name">_to_vertical_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">letters</span>=<span class="summary-sig-default">None</span>)</span><br />
Return string representation of the motif as a matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._to_vertical_matrix">source code</a></span>
</td>
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</td>
</tr>
<tr class="private">
<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="_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.Motif._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="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.Motif._Motif-pysrc.html#Motif.add_instance">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="anticonsensus"></a><span class="summary-sig-name">anticonsensus</span>(<span class="summary-sig-arg">self</span>)</span><br />
returns the least probable pattern to be generated from this motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.anticonsensus">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="consensus"></a><span class="summary-sig-name">consensus</span>(<span class="summary-sig-arg">self</span>)</span><br />
Returns the consensus sequence of a motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.consensus">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 href="Bio.Motif._Motif.Motif-class.html#dist_dpq" class="summary-sig-name">dist_dpq</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
Calculates the DPQ distance measure between motifs.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_dpq">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 href="Bio.Motif._Motif.Motif-class.html#dist_dpq_at" class="summary-sig-name">dist_dpq_at</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>,
<span class="summary-sig-arg">offset</span>)</span><br />
calculates the dist_dpq measure with a given offset.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_dpq_at">source code</a></span>
</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 href="Bio.Motif._Motif.Motif-class.html#dist_pearson" class="summary-sig-name">dist_pearson</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 based on pearson correlation for the
given motif against self.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_pearson">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="dist_pearson_at"></a><span class="summary-sig-name">dist_pearson_at</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">motif</span>,
<span class="summary-sig-arg">offset</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_pearson_at">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<td><span class="summary-sig"><a name="dist_product"></a><span class="summary-sig-name">dist_product</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
A similarity measure taking into account a product probability of
generating overlaping instances of two motifs</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_product">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="dist_product_at"></a><span class="summary-sig-name">dist_product_at</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>,
<span class="summary-sig-arg">offset</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_product_at">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="exp_score"></a><span class="summary-sig-name">exp_score</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">st_dev</span>=<span class="summary-sig-default">False</span>)</span><br />
Computes expected score of motif's instance and its standard
deviation</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.exp_score">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#format" class="summary-sig-name">format</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">format</span>)</span><br />
Returns a string representation of the Motif in a given format</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.format">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="ic"></a><span class="summary-sig-name">ic</span>(<span class="summary-sig-arg">self</span>)</span><br />
Method returning the information content of a motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.ic">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="log_odds"></a><span class="summary-sig-name">log_odds</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">laplace</span>=<span class="summary-sig-default">True</span>)</span><br />
returns the logg odds matrix computed for the set of instances</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.log_odds">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="make_counts_from_instances"></a><span class="summary-sig-name">make_counts_from_instances</span>(<span class="summary-sig-arg">self</span>)</span><br />
Creates the count matrix for a motif with instances.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.make_counts_from_instances">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#make_instances_from_counts" class="summary-sig-name">make_instances_from_counts</a>(<span class="summary-sig-arg">self</span>)</span><br />
Creates "fake" instances for a motif created from a count
matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.make_instances_from_counts">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#max_score" class="summary-sig-name">max_score</a>(<span class="summary-sig-arg">self</span>)</span><br />
Maximal possible score for this motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.max_score">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#min_score" class="summary-sig-name">min_score</a>(<span class="summary-sig-arg">self</span>)</span><br />
Minimal possible score for this motif.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.min_score">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#pwm" class="summary-sig-name">pwm</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">laplace</span>=<span class="summary-sig-default">True</span>)</span><br />
returns the PWM computed for the set of instances</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.pwm">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="reverse_complement"></a><span class="summary-sig-name">reverse_complement</span>(<span class="summary-sig-arg">self</span>)</span><br />
Gives the reverse complement of the motif</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.reverse_complement">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._Motif.Motif-class.html#scanPWM" class="summary-sig-name">scanPWM</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seq</span>)</span><br />
Matrix of log-odds scores for a nucleotide sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.scanPWM">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<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">0</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.Motif._Motif-pysrc.html#Motif.score_hit">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<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.Motif._Motif-pysrc.html#Motif.search_instances">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<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">normalized</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">masked</span>=<span class="summary-sig-default">0</span>,
<span class="summary-sig-arg">threshold</span>=<span class="summary-sig-default">0.0</span>,
<span class="summary-sig-arg">both</span>=<span class="summary-sig-default">True</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.Motif._Motif-pysrc.html#Motif.search_pwm">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._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.Motif._Motif-pysrc.html#Motif.set_mask">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Motif._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.Motif._Motif-pysrc.html#Motif.weblogo">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<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>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__getitem__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__getitem__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">index</span>)</span>
<br /><em class="fname">(Indexing operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__getitem__">source code</a></span>
</td>
</tr></table>
<p>Returns the probability distribution over symbols at a given position,
padding with background.</p>
<p>If the requested index is out of bounds, the returned distribution
comes from background.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">IUPACUnambiguousDNA()</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="__len__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__len__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Length operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__len__">source code</a></span>
</td>
</tr></table>
<p>return the length of a motif</p>
<p>Please use this method (i.e. invoke len(m)) instead of refering to the
m.length directly.</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">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">masked</span>=<span class="sig-default">False</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.__str__">source code</a></span>
</td>
</tr></table>
<p>string representation of a motif.</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
<a name="_from_jaspar_pfm"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_from_jaspar_pfm</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">stream</span>,
<span class="sig-arg">make_instances</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif._from_jaspar_pfm">source code</a></span>
</td>
</tr></table>
<p>reads the motif from Jaspar .pfm file</p>
<p>The instances are fake, but the pwm is accurate.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_from_jaspar_sites"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_from_jaspar_sites</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.Motif._Motif-pysrc.html#Motif._from_jaspar_sites">source code</a></span>
</td>
</tr></table>
<p>reads the motif from Jaspar .sites file</p>
<p>The instances and pwm are OK.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_read"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<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.Motif._Motif-pysrc.html#Motif._read">source code</a></span>
</td>
</tr></table>
<p>Reads the motif from the stream (in AlignAce format).</p>
<p>the self.alphabet variable must be set beforehand. If the last line
contains asterisks it is used for setting mask</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="dist_dpq"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">dist_dpq</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_dpq">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Calculates the DPQ distance measure between motifs.
It is calculated as a maximal value of DPQ formula (shown using LaTeX
markup, familiar to mathematicians):
\sqrt{\sum_{i=1}^{alignment.len()} \sum_{k=1}^alphabet.len() \
\{ m1[i].freq(alphabet[k])*log_2(m1[i].freq(alphabet[k])/m2[i].freq(alphabet[k])) +
m2[i].freq(alphabet[k])*log_2(m2[i].freq(alphabet[k])/m1[i].freq(alphabet[k]))
}
over possible non-spaced alignemts of two motifs. See this reference:
D. M Endres and J. E Schindelin, "A new metric for probability
distributions", IEEE transactions on Information Theory 49, no. 7
(July 2003): 1858-1860.
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="dist_dpq_at"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">dist_dpq_at</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">other</span>,
<span class="sig-arg">offset</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.dist_dpq_at">source code</a></span>
</td>
</tr></table>
<p>calculates the dist_dpq measure with a given offset.</p>
<p>offset should satisfy 0<=offset<=len(self)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="dist_pearson"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">dist_pearson</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.Motif._Motif-pysrc.html#Motif.dist_pearson">source code</a></span>
</td>
</tr></table>
<p>return the similarity score based on pearson correlation for the given
motif against self.</p>
<p>We use the Pearson's correlation of the respective probabilities.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="format"></a>
<div>
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">format</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">format</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.format">source code</a></span>
</td>
</tr></table>
<p>Returns a string representation of the Motif in a given format</p>
<p>Currently supported fromats:</p>
<ul>
<li>
jaspar-pfm : JASPAR Position Frequency Matrix
</li>
<li>
transfac : TRANSFAC like files
</li>
<li>
fasta : FASTA file with instances
</li>
</ul>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="make_instances_from_counts"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">make_instances_from_counts</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.make_instances_from_counts">source code</a></span>
</td>
</tr></table>
<p>Creates "fake" instances for a motif created from a count
matrix.</p>
<p>In case the sums of counts are different for different columnes, the
shorter columns are padded with background.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="max_score"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">max_score</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.max_score">source code</a></span>
</td>
</tr></table>
<p>Maximal possible score for this motif.</p>
<p>returns the score computed for the consensus sequence.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="min_score"></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">min_score</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.min_score">source code</a></span>
</td>
</tr></table>
<p>Minimal possible score for this motif.</p>
<p>returns the score computed for the anticonsensus sequence.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="pwm"></a>
<div>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">pwm</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">laplace</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.pwm">source code</a></span>
</td>
</tr></table>
<p>returns the PWM computed for the set of instances</p>
<p>if laplace=True (default), pseudocounts equal to self.background
multiplied by self.beta are added to all positions.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="scanPWM"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">scanPWM</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">seq</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Motif._Motif-pysrc.html#Motif.scanPWM">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Matrix of log-odds scores for a nucleotide sequence.
scans a nucleotide sequence and returns the matrix of log-odds
scores for all positions.
- the result is a one-dimensional list or numpy array
- the sequence can only be a DNA sequence
- the search is performed only on one strand
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="set_mask"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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.Motif._Motif-pysrc.html#Motif.set_mask">source code</a></span>
</td>
</tr></table>
<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="weblogo"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<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.Motif._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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