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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Motif-module.html">Package Motif</a> ::
Module _Motif
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<h1 class="epydoc">Source Code for <a href="Bio.Motif._Motif-module.html" onclick="show_private();">Module Bio.Motif._Motif</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""Implementation of sequence motifs (PRIVATE).</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Package Bio.SubsMat=Bio.SubsMat-module.html"><a title="Bio.SubsMat" class="py-name" href="#" onclick="return doclink('link-4', 'SubsMat', 'link-4');">SubsMat</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.SubsMat.FreqTable=Bio.SubsMat.FreqTable-module.html,Class Bio.SubsMat.FreqTable.FreqTable=Bio.SubsMat.FreqTable.FreqTable-class.html"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-5', 'FreqTable', 'link-5');">FreqTable</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'Alphabet', 'link-7');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-8', 'IUPAC', 'link-8');">IUPAC</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">math</tt><tt class="py-op">,</tt><tt class="py-name">random</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="Motif"></a><div id="Motif-def"><a name="L12"></a><tt class="py-lineno"> 12</tt> <a class="py-toggle" href="#" id="Motif-toggle" onclick="return toggle('Motif');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html">Motif</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Motif-expanded"><a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> A class representing sequence motifs.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Motif.__init__"></a><div id="Motif.__init__-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="Motif.__init__-toggle" onclick="return toggle('Motif.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">alphabet</tt><tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-9', 'IUPAC', 'link-8');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_dna=Bio.Alphabet.IUPAC-module.html#unambiguous_dna"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-10', 'unambiguous_dna', 'link-10');">unambiguous_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__init__-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds_is_current</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">alphabet</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-11', 'length', 'link-11');">length</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">=</tt><tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-12', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> \ </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-13', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beta</tt><tt class="py-op">=</tt><tt class="py-number">1.0</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">info</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-14');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="Motif._check_length"></a><div id="Motif._check_length-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="Motif._check_length-toggle" onclick="return toggle('Motif._check_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_check_length">_check_length</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">len</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._check_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._check_length-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-15', 'length', 'link-11');">length</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-16', 'length', 'link-11');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-17', 'length', 'link-11');">length</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"len"</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-18', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"You can't change the length of the motif"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="Motif._check_alphabet"></a><div id="Motif._check_alphabet-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="Motif._check_alphabet-toggle" onclick="return toggle('Motif._check_alphabet');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_check_alphabet">_check_alphabet</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._check_alphabet-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._check_alphabet-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">=</tt><tt class="py-name">alphabet</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">!=</tt> <tt class="py-name">alphabet</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Wrong Alphabet"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="Motif.add_instance"></a><div id="Motif.add_instance-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="Motif.add_instance-toggle" onclick="return toggle('Motif.add_instance');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#add_instance">add_instance</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">instance</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.add_instance-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.add_instance-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> adds new instance to the motif</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Motif._Motif.Motif._check_alphabet()=Bio.Motif._Motif.Motif-class.html#_check_alphabet"><a title="Bio.Motif._Motif.Motif._check_alphabet" class="py-name" href="#" onclick="return doclink('link-19', '_check_alphabet', 'link-19');">_check_alphabet</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name" targets="Variable Bio.PopGen.SimCoal.instance=Bio.PopGen.SimCoal-module.html#instance"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-20', 'instance', 'link-20');">instance</a></tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Motif._Motif.Motif._check_length()=Bio.Motif._Motif.Motif-class.html#_check_length"><a title="Bio.Motif._Motif.Motif._check_length" class="py-name" href="#" onclick="return doclink('link-21', '_check_length', 'link-21');">_check_length</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-22', 'instance', 'link-20');">instance</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-23" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-24" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-24', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-25', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">let</tt><tt class="py-op">=</tt><tt id="link-26" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-26', 'instance', 'link-20');">instance</a></tt><tt class="py-op">[</tt><tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">let</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-29', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-30', 'instance', 'link-20');">instance</a></tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds_is_current</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> </tt>
<a name="Motif.set_mask"></a><div id="Motif.set_mask-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="Motif.set_mask-toggle" onclick="return toggle('Motif.set_mask');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#set_mask">set_mask</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">mask</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.set_mask-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.set_mask-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> sets the mask for the motif</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> The mask should be a string containing asterisks in the position of significant columns and spaces in other columns</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Motif._Motif.Motif._check_length" class="py-name" href="#" onclick="return doclink('link-31', '_check_length', 'link-21');">_check_length</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">mask</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">char</tt> <tt class="py-keyword">in</tt> <tt class="py-name">mask</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt><tt class="py-op">==</tt><tt class="py-string">"*"</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">char</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-33', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Mask should contain only '*' or ' ' and not a '%s'"</tt><tt class="py-op">%</tt><tt class="py-name">char</tt><tt class="py-op">)</tt> </tt>
</div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="Motif.pwm"></a><div id="Motif.pwm-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="Motif.pwm-toggle" onclick="return toggle('Motif.pwm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#pwm">pwm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">laplace</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.pwm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.pwm-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> returns the PWM computed for the set of instances</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> if laplace=True (default), pseudocounts equal to self.background multiplied by self.beta are added to all positions.</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment">#we need to compute new pwm</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-34" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-34', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-35', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment">#filling the dict with 0's</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-36', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">laplace</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">beta</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-comment">#taking the raw counts</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-37', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment">#counting the occurences of letters in instances</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-39" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-39', 'seq', 'link-39');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-comment">#dict[seq[i]]=dict[seq[i]]+1</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-40', 'seq', 'link-39');">seq</a></tt><tt class="py-op">[</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-41', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> <tt class="py-comment">#we need to ignore non-alphabet letters</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-42', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-43', 'FreqTable', 'link-5');">FreqTable</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-44', 'FreqTable', 'link-5');">FreqTable</a></tt><tt class="py-op">(</tt><tt class="py-name">dict</tt><tt class="py-op">,</tt><tt id="link-45" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-45', 'FreqTable', 'link-5');">FreqTable</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Variable Bio.SubsMat.FreqTable.COUNT=Bio.SubsMat.FreqTable-module.html#COUNT"><a title="Bio.SubsMat.FreqTable.COUNT" class="py-name" href="#" onclick="return doclink('link-46', 'COUNT', 'link-46');">COUNT</a></tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="Motif.log_odds"></a><div id="Motif.log_odds-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="Motif.log_odds-toggle" onclick="return toggle('Motif.log_odds');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#log_odds">log_odds</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">laplace</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.log_odds-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.log_odds-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> returns the logg odds matrix computed for the set of instances</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds_is_current</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment">#we need to compute new pwm</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt id="link-47" class="py-name" targets="Method Bio.Motif._Motif.Motif.pwm()=Bio.Motif._Motif.Motif-class.html#pwm"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-47', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-48', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-name">laplace</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-50', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-51', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">d</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Variable Bio.Affy.CelFile.log=Bio.Affy.CelFile-module.html#log"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-52', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-53', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-54" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-54', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-55', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds_is_current</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_log_odds</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="Motif.ic"></a><div id="Motif.ic-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Motif.ic-toggle" onclick="return toggle('Motif.ic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#ic">ic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.ic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.ic-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-docstring">"""Method returning the information content of a motif.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-56" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-56', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-57', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-59" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-59', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-60', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-number">2</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-61', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-62" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-62', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-63" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-63', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt id="link-64" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-64', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-65" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-65', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-66', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-67', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="Motif.exp_score"></a><div id="Motif.exp_score-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="Motif.exp_score-toggle" onclick="return toggle('Motif.exp_score');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#exp_score">exp_score</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">st_dev</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.exp_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.exp_score-expanded"><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> Computes expected score of motif's instance and its standard deviation</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">exs</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">var</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt id="link-69" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-69', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-70', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-71" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-71', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-72" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-72', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-73', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">ex1</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">ex2</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-74', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-75" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-75', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-76', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">ex1</tt><tt class="py-op">+=</tt><tt id="link-77" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-77', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-78" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-78', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-79', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-80', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-81" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-81', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-82', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">ex2</tt><tt class="py-op">+=</tt><tt id="link-83" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-83', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-84" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-84', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-85', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt id="link-86" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-86', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-87" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-87', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-88', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">exs</tt><tt class="py-op">+=</tt><tt class="py-name">ex1</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">var</tt><tt class="py-op">+=</tt><tt class="py-name">ex2</tt><tt class="py-op">-</tt><tt class="py-name">ex1</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">st_dev</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">exs</tt><tt class="py-op">,</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Variable Bio.Affy.CelFile.sqrt=Bio.Affy.CelFile-module.html#sqrt,Variable Bio.SVDSuperimposer.SVDSuperimposer'.sqrt=Bio.SVDSuperimposer.SVDSuperimposer%27-module.html#sqrt"><a title="Bio.Affy.CelFile.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt" class="py-name" href="#" onclick="return doclink('link-89', 'sqrt', 'link-89');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">var</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">exs</tt> </tt>
</div><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="Motif.search_instances"></a><div id="Motif.search_instances-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="Motif.search_instances-toggle" onclick="return toggle('Motif.search_instances');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#search_instances">search_instances</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.search_instances-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.search_instances-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> a generator function, returning found positions of instances of the motif in a given sequence</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">(</tt><tt class="py-string">"This motif has no instances"</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-90" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.Phylo.PhyloXMLIO.Writer.sequence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#sequence"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-90', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-91', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-92" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-92', 'instance', 'link-20');">instance</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-93" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-93', 'instance', 'link-20');">instance</a></tt><tt class="py-op">.</tt><tt id="link-94" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-94', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt id="link-95" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-95', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-name">pos</tt><tt class="py-op">+</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-96', 'length', 'link-11');">length</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-97', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-98" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-98', 'instance', 'link-20');">instance</a></tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> <tt class="py-comment"># no other instance will fit (we don't want to return multiple hits)</tt> </tt>
</div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="Motif.score_hit"></a><div id="Motif.score_hit-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="Motif.score_hit-toggle" onclick="return toggle('Motif.score_hit');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#score_hit">score_hit</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">,</tt><tt class="py-param">normalized</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-param">masked</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.score_hit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.score_hit-expanded"><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> give the pwm score for a given position</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">lo</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name" targets="Method Bio.Motif._Motif.Motif.log_odds()=Bio.Motif._Motif.Motif-class.html#log_odds"><a title="Bio.Motif._Motif.Motif.log_odds" class="py-name" href="#" onclick="return doclink('link-99', 'log_odds', 'link-99');">log_odds</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt id="link-100" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-100', 'score', 'link-100');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-101', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-102', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">position</tt><tt class="py-op">+</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">masked</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt id="link-103" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-103', 'score', 'link-100');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">lo</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-104" class="py-name" targets="Method Bio.PDB.Vector'.Vector.normalized()=Bio.PDB.Vector%27.Vector-class.html#normalized"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-104', 'normalized', 'link-104');">normalized</a></tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">masked</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-105', 'score', 'link-100');">score</a></tt><tt class="py-op">/=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-106', 'length', 'link-11');">length</a></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-107" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-107', 'score', 'link-100');">score</a></tt><tt class="py-op">/=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-108" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-108', 'x', 'link-108');">x</a></tt> <tt class="py-keyword">for</tt> <tt id="link-109" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-109', 'x', 'link-108');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> <tt class="py-keyword">if</tt> <tt id="link-110" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-110', 'x', 'link-108');">x</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-111" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-111', 'score', 'link-100');">score</a></tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="Motif.search_pwm"></a><div id="Motif.search_pwm-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="Motif.search_pwm-toggle" onclick="return toggle('Motif.search_pwm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#search_pwm">search_pwm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">,</tt><tt class="py-param">normalized</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-param">masked</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-param">threshold</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt><tt class="py-param">both</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.search_pwm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.search_pwm-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> a generator function, returning found hits in a given sequence with the pwm score higher than the threshold</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">both</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">rc</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Motif._Motif.Motif.reverse_complement()=Bio.Motif._Motif.Motif-class.html#reverse_complement,Method Bio.Seq.MutableSeq.reverse_complement()=Bio.Seq.MutableSeq-class.html#reverse_complement,Method Bio.Seq.Seq.reverse_complement()=Bio.Seq.Seq-class.html#reverse_complement,Method Bio.Seq.UnknownSeq.reverse_complement()=Bio.Seq.UnknownSeq-class.html#reverse_complement,Function Bio.Seq.reverse_complement()=Bio.Seq-module.html#reverse_complement,Method Bio.SeqRecord.SeqRecord.reverse_complement()=Bio.SeqRecord.SeqRecord-class.html#reverse_complement"><a title="Bio.Motif._Motif.Motif.reverse_complement
Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.UnknownSeq.reverse_complement
Bio.Seq.reverse_complement
Bio.SeqRecord.SeqRecord.reverse_complement" class="py-name" href="#" onclick="return doclink('link-112', 'reverse_complement', 'link-112');">reverse_complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-113', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">=</tt><tt id="link-114" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-114', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-115', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.Seq.Seq.upper()=Bio.Seq.Seq-class.html#upper,Method Bio.Seq.UnknownSeq.upper()=Bio.Seq.UnknownSeq-class.html#upper,Method Bio.SeqRecord.SeqRecord.upper()=Bio.SeqRecord.SeqRecord-class.html#upper"><a title="Bio.Seq.Seq.upper
Bio.Seq.UnknownSeq.upper
Bio.SeqRecord.SeqRecord.upper" class="py-name" href="#" onclick="return doclink('link-116', 'upper', 'link-116');">upper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-117', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-118', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-119', 'score', 'link-100');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method Bio.Motif._Motif.Motif.score_hit()=Bio.Motif._Motif.Motif-class.html#score_hit"><a title="Bio.Motif._Motif.Motif.score_hit" class="py-name" href="#" onclick="return doclink('link-120', 'score_hit', 'link-120');">score_hit</a></tt><tt class="py-op">(</tt><tt id="link-121" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-121', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">,</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-122" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-122', 'normalized', 'link-104');">normalized</a></tt><tt class="py-op">,</tt><tt class="py-name">masked</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-123" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-123', 'score', 'link-100');">score</a></tt> <tt class="py-op">></tt> <tt id="link-124" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.threshold()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#threshold,Method Bio.Compass._Consumer.threshold()=Bio.Compass._Consumer-class.html#threshold"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-124', 'threshold', 'link-124');">threshold</a></tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-125" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-125', 'score', 'link-100');">score</a></tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">both</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">rev_score</tt> <tt class="py-op">=</tt> <tt class="py-name">rc</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Motif._Motif.Motif.score_hit" class="py-name" href="#" onclick="return doclink('link-126', 'score_hit', 'link-120');">score_hit</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-127', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">,</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-128" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-128', 'normalized', 'link-104');">normalized</a></tt><tt class="py-op">,</tt><tt class="py-name">masked</tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rev_score</tt> <tt class="py-op">></tt> <tt id="link-129" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.threshold
Bio.Compass._Consumer.threshold" class="py-name" href="#" onclick="return doclink('link-129', 'threshold', 'link-124');">threshold</a></tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt class="py-name">rev_score</tt><tt class="py-op">)</tt> </tt>
</div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_pearson"></a><div id="Motif.dist_pearson-def"><a name="L217"></a><tt class="py-lineno">217</tt> <a class="py-toggle" href="#" id="Motif.dist_pearson-toggle" onclick="return toggle('Motif.dist_pearson');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_pearson">dist_pearson</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">motif</tt><tt class="py-op">,</tt> <tt class="py-param">masked</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_pearson-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_pearson-expanded"><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> return the similarity score based on pearson correlation for the given motif against self.</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> We use the Pearson's correlation of the respective probabilities.</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">!=</tt> <tt class="py-name">motif</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Cannot compare motifs with different alphabets"</tt><tt class="py-op">)</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">max_p</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">2</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">offset</tt> <tt class="py-keyword">in</tt> <tt id="link-130" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-130', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-131', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-132', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">offset</tt><tt class="py-op"><</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Method Bio.Motif._Motif.Motif.dist_pearson_at()=Bio.Motif._Motif.Motif-class.html#dist_pearson_at"><a title="Bio.Motif._Motif.Motif.dist_pearson_at" class="py-name" href="#" onclick="return doclink('link-133', 'dist_pearson_at', 'link-133');">dist_pearson_at</a></tt><tt class="py-op">(</tt><tt class="py-name">motif</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment">#offset>=0</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="Bio.Motif._Motif.Motif.dist_pearson_at" class="py-name" href="#" onclick="return doclink('link-134', 'dist_pearson_at', 'link-133');">dist_pearson_at</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max_p</tt><tt class="py-op"><</tt><tt class="py-name">p</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">max_p</tt><tt class="py-op">=</tt><tt class="py-name">p</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">max_o</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">max_p</tt><tt class="py-op">,</tt><tt class="py-name">max_o</tt> </tt>
</div><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_pearson_at"></a><div id="Motif.dist_pearson_at-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="Motif.dist_pearson_at-toggle" onclick="return toggle('Motif.dist_pearson_at');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_pearson_at">dist_pearson_at</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">motif</tt><tt class="py-op">,</tt><tt class="py-param">offset</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_pearson_at-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_pearson_at-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">sxx</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># \sum x^2</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">sxy</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># \sum x \cdot y</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">sx</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># \sum x</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">sy</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># \sum y</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">syy</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># \sum x^2</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt id="link-135" class="py-name" targets="Method Bio.PDB.Vector'.Vector.norm()=Bio.PDB.Vector%27.Vector-class.html#norm"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-135', 'norm', 'link-135');">norm</a></tt><tt class="py-op">=</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-136', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">+</tt><tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-137', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt id="link-138" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-138', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-139', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">+</tt><tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-140', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-141', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">xi</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">yi</tt> <tt class="py-op">=</tt> <tt class="py-name">motif</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">sx</tt> <tt class="py-op">=</tt> <tt class="py-name">sx</tt> <tt class="py-op">+</tt> <tt class="py-name">xi</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">sy</tt> <tt class="py-op">=</tt> <tt class="py-name">sy</tt> <tt class="py-op">+</tt> <tt class="py-name">yi</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">sxx</tt> <tt class="py-op">=</tt> <tt class="py-name">sxx</tt> <tt class="py-op">+</tt> <tt class="py-name">xi</tt> <tt class="py-op">*</tt> <tt class="py-name">xi</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">syy</tt> <tt class="py-op">=</tt> <tt class="py-name">syy</tt> <tt class="py-op">+</tt> <tt class="py-name">yi</tt> <tt class="py-op">*</tt> <tt class="py-name">yi</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">sxy</tt> <tt class="py-op">=</tt> <tt class="py-name">sxy</tt> <tt class="py-op">+</tt> <tt class="py-name">xi</tt> <tt class="py-op">*</tt> <tt class="py-name">yi</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt id="link-142" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-142', 'norm', 'link-135');">norm</a></tt> <tt class="py-op">*=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-143', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">s1</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">sxy</tt> <tt class="py-op">-</tt> <tt class="py-name">sx</tt><tt class="py-op">*</tt><tt class="py-name">sy</tt><tt class="py-op">*</tt><tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt id="link-144" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-144', 'norm', 'link-135');">norm</a></tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">s2</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-145" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-145', 'norm', 'link-135');">norm</a></tt><tt class="py-op">*</tt><tt class="py-name">sxx</tt> <tt class="py-op">-</tt> <tt class="py-name">sx</tt><tt class="py-op">*</tt><tt class="py-name">sx</tt><tt class="py-op">*</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-146', 'norm', 'link-135');">norm</a></tt><tt class="py-op">*</tt><tt class="py-name">syy</tt><tt class="py-op">-</tt> <tt class="py-name">sy</tt><tt class="py-op">*</tt><tt class="py-name">sy</tt><tt class="py-op">*</tt><tt class="py-number">1.0</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">s1</tt><tt class="py-op">/</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Affy.CelFile.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt" class="py-name" href="#" onclick="return doclink('link-147', 'sqrt', 'link-89');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">s2</tt><tt class="py-op">)</tt> </tt>
</div><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_product"></a><div id="Motif.dist_product-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="Motif.dist_product-toggle" onclick="return toggle('Motif.dist_product');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_product">dist_product</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_product-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_product-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"> A similarity measure taking into account a product probability of generating overlaping instances of two motifs</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">max_p</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">offset</tt> <tt class="py-keyword">in</tt> <tt id="link-148" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-148', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-149', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt id="link-150" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.other()=Bio.Phylo.PhyloXMLIO.Parser-class.html#other,Method Bio.Phylo.PhyloXMLIO.Writer.other()=Bio.Phylo.PhyloXMLIO.Writer-class.html#other"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-150', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-151', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">offset</tt><tt class="py-op"><</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name" targets="Method Bio.Motif._Motif.Motif.dist_product_at()=Bio.Motif._Motif.Motif-class.html#dist_product_at"><a title="Bio.Motif._Motif.Motif.dist_product_at" class="py-name" href="#" onclick="return doclink('link-152', 'dist_product_at', 'link-152');">dist_product_at</a></tt><tt class="py-op">(</tt><tt id="link-153" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-153', 'other', 'link-150');">other</a></tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment">#offset>=0</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-154" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-154', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Motif._Motif.Motif.dist_product_at" class="py-name" href="#" onclick="return doclink('link-155', 'dist_product_at', 'link-152');">dist_product_at</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max_p</tt><tt class="py-op"><</tt><tt class="py-name">p</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">max_p</tt><tt class="py-op">=</tt><tt class="py-name">p</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">max_o</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt><tt class="py-op">-</tt><tt class="py-name">max_p</tt><tt class="py-op">/</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Motif._Motif.Motif.dist_product_at" class="py-name" href="#" onclick="return doclink('link-156', 'dist_product_at', 'link-152');">dist_product_at</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">max_o</tt> </tt>
</div><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_product_at"></a><div id="Motif.dist_product_at-def"><a name="L277"></a><tt class="py-lineno">277</tt> <a class="py-toggle" href="#" id="Motif.dist_product_at-toggle" onclick="return toggle('Motif.dist_product_at');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_product_at">dist_product_at</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">other</tt><tt class="py-op">,</tt><tt class="py-param">offset</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_product_at-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_product_at-expanded"><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-157" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-157', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-158" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-158', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-159', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">+</tt><tt id="link-160" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-160', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-161', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">f1</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-162" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-162', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">f2</tt><tt class="py-op">=</tt><tt id="link-163" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-163', 'other', 'link-150');">other</a></tt><tt class="py-op">[</tt><tt id="link-164" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-164', 'i', 'link-23');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">]</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name" targets="Method Bio.SeqIO._index._IndexedSeqFileDict.iteritems()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#iteritems,Method BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#iteritems,Method BioSQL.BioSeqDatabase.DBServer.iteritems()=BioSQL.BioSeqDatabase.DBServer-class.html#iteritems"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-165', 'iteritems', 'link-165');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">+=</tt><tt class="py-name">b</tt><tt class="py-op">*</tt><tt class="py-name">f1</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">f2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">s</tt><tt class="py-op">/</tt><tt id="link-166" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-166', 'i', 'link-23');">i</a></tt> </tt>
</div><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_dpq"></a><div id="Motif.dist_dpq-def"><a name="L286"></a><tt class="py-lineno">286</tt> <a class="py-toggle" href="#" id="Motif.dist_dpq-toggle" onclick="return toggle('Motif.dist_dpq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_dpq">dist_dpq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_dpq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_dpq-expanded"><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-docstring">r"""Calculates the DPQ distance measure between motifs.</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"> It is calculated as a maximal value of DPQ formula (shown using LaTeX</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> markup, familiar to mathematicians):</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> \sqrt{\sum_{i=1}^{alignment.len()} \sum_{k=1}^alphabet.len() \</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> \{ m1[i].freq(alphabet[k])*log_2(m1[i].freq(alphabet[k])/m2[i].freq(alphabet[k])) +</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> m2[i].freq(alphabet[k])*log_2(m2[i].freq(alphabet[k])/m1[i].freq(alphabet[k]))</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> }</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> over possible non-spaced alignemts of two motifs. See this reference:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> D. M Endres and J. E Schindelin, "A new metric for probability</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> distributions", IEEE transactions on Information Theory 49, no. 7</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> (July 2003): 1858-1860.</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">min_d</tt><tt class="py-op">=</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-string">"inf"</tt><tt class="py-op">)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">min_o</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">d_s</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">offset</tt> <tt class="py-keyword">in</tt> <tt id="link-167" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-167', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-168', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt id="link-169" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-169', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-170', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-comment">#print "%2.3d"%offset,</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">offset</tt><tt class="py-op"><</tt><tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name" targets="Method Bio.Motif._Motif.Motif.dist_dpq_at()=Bio.Motif._Motif.Motif-class.html#dist_dpq_at"><a title="Bio.Motif._Motif.Motif.dist_dpq_at" class="py-name" href="#" onclick="return doclink('link-171', 'dist_dpq_at', 'link-171');">dist_dpq_at</a></tt><tt class="py-op">(</tt><tt id="link-172" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-172', 'other', 'link-150');">other</a></tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">overlap</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-173', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt class="py-name">offset</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment">#offset>=0</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt id="link-174" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-174', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-175" class="py-name"><a title="Bio.Motif._Motif.Motif.dist_dpq_at" class="py-name" href="#" onclick="return doclink('link-175', 'dist_dpq_at', 'link-171');">dist_dpq_at</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">overlap</tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-176', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-177', 'length', 'link-11');">length</a></tt><tt class="py-op">-</tt><tt class="py-name">offset</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">overlap</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-178', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt id="link-179" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-179', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-180" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-180', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">overlap</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-181', 'length', 'link-11');">length</a></tt><tt class="py-op">+</tt><tt id="link-182" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-182', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-183" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-183', 'length', 'link-11');">length</a></tt><tt class="py-op">-</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">overlap</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-comment">#print d,1.0*(overlap+out)/overlap,d*(overlap+out)/overlap</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-comment">#d = d/(2*overlap)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">out</tt><tt class="py-op">+</tt><tt class="py-name">overlap</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">overlap</tt><tt class="py-op">+</tt><tt class="py-name">out</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt class="py-name">overlap</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment">#print d</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">d_s</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-184', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">offset</tt><tt class="py-op">,</tt><tt class="py-name">d</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">min_d</tt><tt class="py-op">></tt> <tt class="py-name">d</tt><tt class="py-op">:</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-name">min_d</tt><tt class="py-op">=</tt><tt class="py-name">d</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">min_o</tt><tt class="py-op">=</tt><tt class="py-op">-</tt><tt class="py-name">offset</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">min_d</tt><tt class="py-op">,</tt><tt class="py-name">min_o</tt><tt class="py-comment">#,d_s</tt> </tt>
</div><a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> </tt>
<a name="Motif.dist_dpq_at"></a><div id="Motif.dist_dpq_at-def"><a name="L327"></a><tt class="py-lineno">327</tt> <a class="py-toggle" href="#" id="Motif.dist_dpq_at-toggle" onclick="return toggle('Motif.dist_dpq_at');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#dist_dpq_at">dist_dpq_at</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">other</tt><tt class="py-op">,</tt><tt class="py-param">offset</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.dist_dpq_at-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.dist_dpq_at-expanded"><a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-docstring"> calculates the dist_dpq measure with a given offset.</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"> offset should satisfy 0<=offset<=len(self)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">dpq</tt> <tt class="py-op">(</tt><tt class="py-param">f1</tt><tt class="py-op">,</tt><tt class="py-param">f2</tt><tt class="py-op">,</tt><tt class="py-param">alpha</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alpha</tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-185', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">avg</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-name">f1</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">f2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">+=</tt><tt class="py-name">f1</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-186', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">f1</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">avg</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">f2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">*</tt><tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="Bio.Affy.CelFile.log" class="py-name" href="#" onclick="return doclink('link-187', 'log', 'link-52');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">f2</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">avg</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.Affy.CelFile.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt" class="py-name" href="#" onclick="return doclink('link-188', 'sqrt', 'link-89');">sqrt</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
</div><a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-189" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-189', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-190" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-190', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-191', 'length', 'link-11');">length</a></tt><tt class="py-op">,</tt><tt class="py-name">offset</tt><tt class="py-op">+</tt><tt id="link-192" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-192', 'other', 'link-150');">other</a></tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-193', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">f1</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-194" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-194', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">f2</tt><tt class="py-op">=</tt><tt id="link-195" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.other
Bio.Phylo.PhyloXMLIO.Writer.other" class="py-name" href="#" onclick="return doclink('link-195', 'other', 'link-150');">other</a></tt><tt class="py-op">[</tt><tt id="link-196" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-196', 'i', 'link-23');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">offset</tt><tt class="py-op">]</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">s</tt><tt class="py-op">+=</tt><tt class="py-name">dpq</tt><tt class="py-op">(</tt><tt class="py-name">f1</tt><tt class="py-op">,</tt><tt class="py-name">f2</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">s</tt> </tt>
</div><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> </tt>
<a name="Motif._read"></a><div id="Motif._read-def"><a name="L347"></a><tt class="py-lineno">347</tt> <a class="py-toggle" href="#" id="Motif._read-toggle" onclick="return toggle('Motif._read');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_read">_read</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._read-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._read-expanded"><a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-docstring">"""Reads the motif from the stream (in AlignAce format).</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> the self.alphabet variable must be set beforehand.</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-docstring"> If the last line contains asterisks it is used for setting mask</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-name">ln</tt> <tt class="py-op">=</tt> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name" targets="Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-197', 'readline', 'link-197');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"*"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ln</tt><tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name" targets="Method Bio.Motif._Motif.Motif.set_mask()=Bio.Motif._Motif.Motif-class.html#set_mask"><a title="Bio.Motif._Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-198', 'set_mask', 'link-198');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-name">ln</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-199', 'strip', 'link-199');">strip</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n\c"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-200" class="py-name" targets="Method Bio.Motif._Motif.Motif.add_instance()=Bio.Motif._Motif.Motif-class.html#add_instance"><a title="Bio.Motif._Motif.Motif.add_instance" class="py-name" href="#" onclick="return doclink('link-200', 'add_instance', 'link-200');">add_instance</a></tt><tt class="py-op">(</tt><tt id="link-201" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-201', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ln</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-202', 'strip', 'link-199');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> </tt>
<a name="Motif.__str__"></a><div id="Motif.__str__-def"><a name="L361"></a><tt class="py-lineno">361</tt> <a class="py-toggle" href="#" id="Motif.__str__-toggle" onclick="return toggle('Motif.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">masked</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__str__-expanded"><a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-docstring">""" string representation of a motif.</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">inst</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> <tt class="py-op">+</tt> <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-203', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">masked</tt><tt class="py-op">:</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-204" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-204', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-205', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">[</tt><tt id="link-206" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-206', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> <tt class="py-op">+</tt> <tt class="py-string">"*"</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt> </tt>
</div><a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> </tt>
<a name="Motif.__len__"></a><div id="Motif.__len__-def"><a name="L377"></a><tt class="py-lineno">377</tt> <a class="py-toggle" href="#" id="Motif.__len__-toggle" onclick="return toggle('Motif.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__len__-expanded"><a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-docstring">"""return the length of a motif</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-docstring"> Please use this method (i.e. invoke len(m)) instead of refering to the m.length directly.</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-207', 'length', 'link-11');">length</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-208', 'length', 'link-11');">length</a></tt> </tt>
</div><a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="Motif._write"></a><div id="Motif._write-def"><a name="L387"></a><tt class="py-lineno">387</tt> <a class="py-toggle" href="#" id="Motif._write-toggle" onclick="return toggle('Motif._write');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_write">_write</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._write-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._write-expanded"><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"> writes the motif to the stream</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-209', 'write', 'link-209');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name" targets="Method Bio.Align.AlignInfo.PSSM.__str__()=Bio.Align.AlignInfo.PSSM-class.html#__str__,Method Bio.Align.Generic.Alignment.__str__()=Bio.Align.Generic.Alignment-class.html#__str__,Method Bio.Application.AbstractCommandline.__str__()=Bio.Application.AbstractCommandline-class.html#__str__,Method Bio.Application.ApplicationError.__str__()=Bio.Application.ApplicationError-class.html#__str__,Method Bio.Application._AbstractParameter.__str__()=Bio.Application._AbstractParameter-class.html#__str__,Method Bio.Application._Argument.__str__()=Bio.Application._Argument-class.html#__str__,Method Bio.Application._Option.__str__()=Bio.Application._Option-class.html#__str__,Method Bio.Application._Switch.__str__()=Bio.Application._Switch-class.html#__str__,Method Bio.Blast.Record.Alignment.__str__()=Bio.Blast.Record.Alignment-class.html#__str__,Method Bio.Blast.Record.Description.__str__()=Bio.Blast.Record.Description-class.html#__str__,Method Bio.Blast.Record.HSP.__str__()=Bio.Blast.Record.HSP-class.html#__str__,Method Bio.Crystal.Chain.__str__()=Bio.Crystal.Chain-class.html#__str__,Method Bio.Crystal.Crystal.__str__()=Bio.Crystal.Crystal-class.html#__str__,Method Bio.Crystal.Hetero.__str__()=Bio.Crystal.Hetero-class.html#__str__,Method Bio.Data.CodonTable.CodonTable.__str__()=Bio.Data.CodonTable.CodonTable-class.html#__str__,Method Bio.Emboss.PrimerSearch.InputRecord.__str__()=Bio.Emboss.PrimerSearch.InputRecord-class.html#__str__,Method Bio.Entrez.Parser.CorruptedXMLError.__str__()=Bio.Entrez.Parser.CorruptedXMLError-class.html#__str__,Method Bio.Entrez.Parser.NotXMLError.__str__()=Bio.Entrez.Parser.NotXMLError-class.html#__str__,Method Bio.Entrez.Parser.ValidationError.__str__()=Bio.Entrez.Parser.ValidationError-class.html#__str__,Method Bio.ExPASy.Enzyme.Record.__str__()=Bio.ExPASy.Enzyme.Record-class.html#__str__,Method Bio.GA.Organism.Organism.__str__()=Bio.GA.Organism.Organism-class.html#__str__,Method Bio.GenBank.LocationParser.Integer.__str__()=Bio.GenBank.LocationParser.Integer-class.html#__str__,Method Bio.GenBank.LocationParser.Symbol.__str__()=Bio.GenBank.LocationParser.Symbol-class.html#__str__,Method Bio.GenBank.Record.Feature.__str__()=Bio.GenBank.Record.Feature-class.html#__str__,Method Bio.GenBank.Record.Record.__str__()=Bio.GenBank.Record.Record-class.html#__str__,Method Bio.GenBank.Record.Reference.__str__()=Bio.GenBank.Record.Reference-class.html#__str__,Method Bio.Geo.Record.Record.__str__()=Bio.Geo.Record.Record-class.html#__str__,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.__str__()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#__str__,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__str__()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#__str__,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.__str__()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#__str__,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__str__()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#__str__,Method Bio.Graphics.GenomeDiagram._Track.Track.__str__()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#__str__,Method Bio.KEGG.Compound.Record.__str__()=Bio.KEGG.Compound.Record-class.html#__str__,Method Bio.KEGG.Enzyme.Record.__str__()=Bio.KEGG.Enzyme.Record-class.html#__str__,Method Bio.MarkovModel.MarkovModel.__str__()=Bio.MarkovModel.MarkovModel-class.html#__str__,Method Bio.Motif._Motif.Motif.__str__()=Bio.Motif._Motif.Motif-class.html#__str__,Method Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__str__()=Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#__str__,Method Bio.Nexus.Trees.Tree.__str__()=Bio.Nexus.Trees.Tree-class.html#__str__,Method Bio.Pathway.Interaction.__str__()=Bio.Pathway.Interaction-class.html#__str__,Method Bio.Pathway.Network.__str__()=Bio.Pathway.Network-class.html#__str__,Method Bio.Pathway.Reaction.__str__()=Bio.Pathway.Reaction-class.html#__str__,Method Bio.Pathway.Rep.Graph.Graph.__str__()=Bio.Pathway.Rep.Graph.Graph-class.html#__str__,Method Bio.Pathway.Rep.HashSet.HashSet.__str__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__str__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__str__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__str__,Method Bio.Pathway.System.__str__()=Bio.Pathway.System-class.html#__str__,Method Bio.Phylo.BaseTree.Clade.__str__()=Bio.Phylo.BaseTree.Clade-class.html#__str__,Method Bio.Phylo.BaseTree.Tree.__str__()=Bio.Phylo.BaseTree.Tree-class.html#__str__,Method Bio.Phylo.PhyloXML.Accession.__str__()=Bio.Phylo.PhyloXML.Accession-class.html#__str__,Method Bio.Phylo.PhyloXML.BranchColor.__str__()=Bio.Phylo.PhyloXML.BranchColor-class.html#__str__,Method Bio.Phylo.PhyloXML.Date.__str__()=Bio.Phylo.PhyloXML.Date-class.html#__str__,Method Bio.Phylo.PhyloXML.Id.__str__()=Bio.Phylo.PhyloXML.Id-class.html#__str__,Method Bio.Phylo.PhyloXML.MolSeq.__str__()=Bio.Phylo.PhyloXML.MolSeq-class.html#__str__,Method Bio.Phylo.PhyloXML.Phyloxml.__str__()=Bio.Phylo.PhyloXML.Phyloxml-class.html#__str__,Method Bio.Phylo.PhyloXML.Polygon.__str__()=Bio.Phylo.PhyloXML.Polygon-class.html#__str__,Method Bio.Phylo.PhyloXML.Taxonomy.__str__()=Bio.Phylo.PhyloXML.Taxonomy-class.html#__str__,Method Bio.Phylo.PhyloXML.Uri.__str__()=Bio.Phylo.PhyloXML.Uri-class.html#__str__,Method Bio.PopGen.FDist.Record.__str__()=Bio.PopGen.FDist.Record-class.html#__str__,Method Bio.PopGen.GenePop.FileParser.FileRecord.__str__()=Bio.PopGen.GenePop.FileParser.FileRecord-class.html#__str__,Method Bio.PopGen.GenePop.Record.__str__()=Bio.PopGen.GenePop.Record-class.html#__str__,Method Bio.Restriction.Restriction.RestrictionBatch.__str__()=Bio.Restriction.Restriction.RestrictionBatch-class.html#__str__,Method Bio.Restriction.Restriction.RestrictionType.__str__()=Bio.Restriction.Restriction.RestrictionType-class.html#__str__,Method Bio.SCOP.Cla.Record.__str__()=Bio.SCOP.Cla.Record-class.html#__str__,Method Bio.SCOP.Des.Record.__str__()=Bio.SCOP.Des.Record-class.html#__str__,Method Bio.SCOP.Dom.Record.__str__()=Bio.SCOP.Dom.Record-class.html#__str__,Method Bio.SCOP.Domain.__str__()=Bio.SCOP.Domain-class.html#__str__,Method Bio.SCOP.Hie.Record.__str__()=Bio.SCOP.Hie.Record-class.html#__str__,Method Bio.SCOP.Node.__str__()=Bio.SCOP.Node-class.html#__str__,Method Bio.SCOP.Residues'.Residues.__str__()=Bio.SCOP.Residues%27.Residues-class.html#__str__,Method Bio.Seq.MutableSeq.__str__()=Bio.Seq.MutableSeq-class.html#__str__,Method Bio.Seq.Seq.__str__()=Bio.Seq.Seq-class.html#__str__,Method Bio.Seq.UnknownSeq.__str__()=Bio.Seq.UnknownSeq-class.html#__str__,Method Bio.SeqFeature.AfterPosition.__str__()=Bio.SeqFeature.AfterPosition-class.html#__str__,Method Bio.SeqFeature.BeforePosition.__str__()=Bio.SeqFeature.BeforePosition-class.html#__str__,Method Bio.SeqFeature.BetweenPosition.__str__()=Bio.SeqFeature.BetweenPosition-class.html#__str__,Method Bio.SeqFeature.ExactPosition.__str__()=Bio.SeqFeature.ExactPosition-class.html#__str__,Method Bio.SeqFeature.FeatureLocation.__str__()=Bio.SeqFeature.FeatureLocation-class.html#__str__,Method Bio.SeqFeature.OneOfPosition.__str__()=Bio.SeqFeature.OneOfPosition-class.html#__str__,Method Bio.SeqFeature.PositionGap.__str__()=Bio.SeqFeature.PositionGap-class.html#__str__,Method Bio.SeqFeature.Reference.__str__()=Bio.SeqFeature.Reference-class.html#__str__,Method Bio.SeqFeature.SeqFeature.__str__()=Bio.SeqFeature.SeqFeature-class.html#__str__,Method Bio.SeqFeature.WithinPosition.__str__()=Bio.SeqFeature.WithinPosition-class.html#__str__,Method Bio.SeqIO._index._IndexedSeqFileDict.__str__()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#__str__,Method Bio.SeqRecord.SeqRecord.__str__()=Bio.SeqRecord.SeqRecord-class.html#__str__,Method Bio.SubsMat.SeqMat.__str__()=Bio.SubsMat.SeqMat-class.html#__str__,Method Bio.Wise.dnal.Statistics.__str__()=Bio.Wise.dnal.Statistics-class.html#__str__,Method Bio.Wise.psw.ColumnUnit.__str__()=Bio.Wise.psw.ColumnUnit-class.html#__str__,Method BioSQL.BioSeq.DBSeq.__str__()=BioSQL.BioSeq.DBSeq-class.html#__str__"><a title="Bio.Align.AlignInfo.PSSM.__str__
Bio.Align.Generic.Alignment.__str__
Bio.Application.AbstractCommandline.__str__
Bio.Application.ApplicationError.__str__
Bio.Application._AbstractParameter.__str__
Bio.Application._Argument.__str__
Bio.Application._Option.__str__
Bio.Application._Switch.__str__
Bio.Blast.Record.Alignment.__str__
Bio.Blast.Record.Description.__str__
Bio.Blast.Record.HSP.__str__
Bio.Crystal.Chain.__str__
Bio.Crystal.Crystal.__str__
Bio.Crystal.Hetero.__str__
Bio.Data.CodonTable.CodonTable.__str__
Bio.Emboss.PrimerSearch.InputRecord.__str__
Bio.Entrez.Parser.CorruptedXMLError.__str__
Bio.Entrez.Parser.NotXMLError.__str__
Bio.Entrez.Parser.ValidationError.__str__
Bio.ExPASy.Enzyme.Record.__str__
Bio.GA.Organism.Organism.__str__
Bio.GenBank.LocationParser.Integer.__str__
Bio.GenBank.LocationParser.Symbol.__str__
Bio.GenBank.Record.Feature.__str__
Bio.GenBank.Record.Record.__str__
Bio.GenBank.Record.Reference.__str__
Bio.Geo.Record.Record.__str__
Bio.Graphics.GenomeDiagram._Diagram.Diagram.__str__
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.__str__
Bio.Graphics.GenomeDiagram._Graph.GraphData.__str__
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.__str__
Bio.Graphics.GenomeDiagram._Track.Track.__str__
Bio.KEGG.Compound.Record.__str__
Bio.KEGG.Enzyme.Record.__str__
Bio.MarkovModel.MarkovModel.__str__
Bio.Motif._Motif.Motif.__str__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__str__
Bio.Nexus.Trees.Tree.__str__
Bio.Pathway.Interaction.__str__
Bio.Pathway.Network.__str__
Bio.Pathway.Reaction.__str__
Bio.Pathway.Rep.Graph.Graph.__str__
Bio.Pathway.Rep.HashSet.HashSet.__str__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__str__
Bio.Pathway.System.__str__
Bio.Phylo.BaseTree.Clade.__str__
Bio.Phylo.BaseTree.Tree.__str__
Bio.Phylo.PhyloXML.Accession.__str__
Bio.Phylo.PhyloXML.BranchColor.__str__
Bio.Phylo.PhyloXML.Date.__str__
Bio.Phylo.PhyloXML.Id.__str__
Bio.Phylo.PhyloXML.MolSeq.__str__
Bio.Phylo.PhyloXML.Phyloxml.__str__
Bio.Phylo.PhyloXML.Polygon.__str__
Bio.Phylo.PhyloXML.Taxonomy.__str__
Bio.Phylo.PhyloXML.Uri.__str__
Bio.PopGen.FDist.Record.__str__
Bio.PopGen.GenePop.FileParser.FileRecord.__str__
Bio.PopGen.GenePop.Record.__str__
Bio.Restriction.Restriction.RestrictionBatch.__str__
Bio.Restriction.Restriction.RestrictionType.__str__
Bio.SCOP.Cla.Record.__str__
Bio.SCOP.Des.Record.__str__
Bio.SCOP.Dom.Record.__str__
Bio.SCOP.Domain.__str__
Bio.SCOP.Hie.Record.__str__
Bio.SCOP.Node.__str__
Bio.SCOP.Residues'.Residues.__str__
Bio.Seq.MutableSeq.__str__
Bio.Seq.Seq.__str__
Bio.Seq.UnknownSeq.__str__
Bio.SeqFeature.AfterPosition.__str__
Bio.SeqFeature.BeforePosition.__str__
Bio.SeqFeature.BetweenPosition.__str__
Bio.SeqFeature.ExactPosition.__str__
Bio.SeqFeature.FeatureLocation.__str__
Bio.SeqFeature.OneOfPosition.__str__
Bio.SeqFeature.PositionGap.__str__
Bio.SeqFeature.Reference.__str__
Bio.SeqFeature.SeqFeature.__str__
Bio.SeqFeature.WithinPosition.__str__
Bio.SeqIO._index._IndexedSeqFileDict.__str__
Bio.SeqRecord.SeqRecord.__str__
Bio.SubsMat.SeqMat.__str__
Bio.Wise.dnal.Statistics.__str__
Bio.Wise.psw.ColumnUnit.__str__
BioSQL.BioSeq.DBSeq.__str__" class="py-name" href="#" onclick="return doclink('link-210', '__str__', 'link-210');">__str__</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> </tt>
<a name="Motif._to_fasta"></a><div id="Motif._to_fasta-def"><a name="L396"></a><tt class="py-lineno">396</tt> <a class="py-toggle" href="#" id="Motif._to_fasta-toggle" onclick="return toggle('Motif._to_fasta');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_to_fasta">_to_fasta</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._to_fasta-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._to_fasta-expanded"><a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-docstring"> FASTA representation of motif</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name" targets="Method Bio.Motif._Motif.Motif.make_instances_from_counts()=Bio.Motif._Motif.Motif-class.html#make_instances_from_counts"><a title="Bio.Motif._Motif.Motif.make_instances_from_counts" class="py-name" href="#" onclick="return doclink('link-211', 'make_instances_from_counts', 'link-211');">make_instances_from_counts</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-212" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-212', 'i', 'link-23');">i</a></tt><tt class="py-op">,</tt><tt class="py-name">inst</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> <tt class="py-op">+</tt> <tt class="py-string">">instance%d\n"</tt><tt class="py-op">%</tt><tt id="link-213" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-213', 'i', 'link-23');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-214', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt> </tt>
</div><a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> </tt>
<a name="Motif.reverse_complement"></a><div id="Motif.reverse_complement-def"><a name="L408"></a><tt class="py-lineno">408</tt> <a class="py-toggle" href="#" id="Motif.reverse_complement-toggle" onclick="return toggle('Motif.reverse_complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#reverse_complement">reverse_complement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.reverse_complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.reverse_complement-expanded"><a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"> Gives the reverse complement of the motif</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt id="link-215" class="py-name" targets="Package Bio.Motif=Bio.Motif-module.html,Class Bio.Motif._Motif.Motif=Bio.Motif._Motif.Motif-class.html,Module Bio.NeuralNetwork.Gene.Motif=Bio.NeuralNetwork.Gene.Motif-module.html"><a title="Bio.Motif
Bio.Motif._Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-215', 'Motif', 'link-215');">Motif</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-216" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-216', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.Motif._Motif.Motif.add_instance" class="py-name" href="#" onclick="return doclink('link-217', 'add_instance', 'link-200');">add_instance</a></tt><tt class="py-op">(</tt><tt id="link-218" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-218', 'i', 'link-23');">i</a></tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Bio.Motif._Motif.Motif.reverse_complement
Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.UnknownSeq.reverse_complement
Bio.Seq.reverse_complement
Bio.SeqRecord.SeqRecord.reverse_complement" class="py-name" href="#" onclick="return doclink('link-219', 'reverse_complement', 'link-112');">reverse_complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># has counts</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"T"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"T"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"G"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"G"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name" targets="Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-220', 'reverse', 'link-220');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-221', 'reverse', 'link-220');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"G"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-222" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-222', 'reverse', 'link-220');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-string">"T"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-223', 'reverse', 'link-220');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-224', 'length', 'link-11');">length</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-225', 'length', 'link-11');">length</a></tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">mask</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> </tt>
<a name="Motif._from_jaspar_pfm"></a><div id="Motif._from_jaspar_pfm-def"><a name="L431"></a><tt class="py-lineno">431</tt> <a class="py-toggle" href="#" id="Motif._from_jaspar_pfm-toggle" onclick="return toggle('Motif._from_jaspar_pfm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_pfm">_from_jaspar_pfm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt><tt class="py-param">make_instances</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._from_jaspar_pfm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._from_jaspar_pfm-expanded"><a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-docstring"> reads the motif from Jaspar .pfm file</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-docstring"> The instances are fake, but the pwm is accurate.</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-226" class="py-name" targets="Method Bio.Motif._Motif.Motif._from_horiz_matrix()=Bio.Motif._Motif.Motif-class.html#_from_horiz_matrix"><a title="Bio.Motif._Motif.Motif._from_horiz_matrix" class="py-name" href="#" onclick="return doclink('link-226', '_from_horiz_matrix', 'link-226');">_from_horiz_matrix</a></tt><tt class="py-op">(</tt><tt class="py-name">stream</tt><tt class="py-op">,</tt><tt id="link-227" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-227', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-string">"ACGT"</tt><tt class="py-op">,</tt><tt class="py-name">make_instances</tt><tt class="py-op">=</tt><tt class="py-name">make_instances</tt><tt class="py-op">)</tt> </tt>
</div><a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> </tt>
<a name="Motif._from_vert_matrix"></a><div id="Motif._from_vert_matrix-def"><a name="L439"></a><tt class="py-lineno">439</tt> <a class="py-toggle" href="#" id="Motif._from_vert_matrix-toggle" onclick="return toggle('Motif._from_vert_matrix');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_from_vert_matrix">_from_vert_matrix</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt><tt class="py-param">letters</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">make_instances</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._from_vert_matrix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._from_vert_matrix-expanded"><a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-docstring">"""reads a vertical count matrix from stream and fill in the counts.</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-228" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-228', 'letters', 'link-12');">letters</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt id="link-229" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-229', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-230', 'letters', 'link-12');">letters</a></tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-231', 'length', 'link-11');">length</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-232" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-232', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-233" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-233', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt id="link-234" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-234', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ln</tt> <tt class="py-keyword">in</tt> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-235" class="py-name" targets="Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines"><a title="Bio.File.UndoHandle.readlines" class="py-name" href="#" onclick="return doclink('link-235', 'readlines', 'link-235');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-name">rec</tt><tt class="py-op">=</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt><tt class="py-name">ln</tt><tt class="py-op">.</tt><tt id="link-236" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-236', 'strip', 'link-199');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-237', 'split', 'link-237');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt id="link-238" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-238', 'letters', 'link-12');">letters</a></tt><tt class="py-op">,</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-239', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-240', 'length', 'link-11');">length</a></tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.Motif._Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-241', 'set_mask', 'link-198');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-string">"*"</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-242', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">make_instances</tt><tt class="py-op">==</tt><tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.Motif._Motif.Motif.make_instances_from_counts" class="py-name" href="#" onclick="return doclink('link-243', 'make_instances_from_counts', 'link-211');">make_instances_from_counts</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> </tt>
<a name="Motif._from_horiz_matrix"></a><div id="Motif._from_horiz_matrix-def"><a name="L460"></a><tt class="py-lineno">460</tt> <a class="py-toggle" href="#" id="Motif._from_horiz_matrix-toggle" onclick="return toggle('Motif._from_horiz_matrix');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_from_horiz_matrix">_from_horiz_matrix</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">,</tt><tt class="py-param">letters</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">make_instances</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._from_horiz_matrix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._from_horiz_matrix-expanded"><a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-docstring">"""reads a horizontal count matrix from stream and fill in the counts.</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-244" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-244', 'letters', 'link-12');">letters</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt id="link-245" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-245', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-246', 'letters', 'link-12');">letters</a></tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-247" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-247', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-248" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-248', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">ln</tt> <tt class="py-op">=</tt> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-249', 'readline', 'link-197');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-250', 'strip', 'link-199');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-251" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-251', 'split', 'link-237');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-comment">#if there is a letter in the beginning, ignore it</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ln</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt id="link-252" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-252', 'i', 'link-23');">i</a></tt><tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">ln</tt><tt class="py-op">=</tt><tt class="py-name">ln</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-comment">#print ln</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt id="link-253" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-253', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt><tt class="py-name">ln</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> <tt class="py-comment">#not integers</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt id="link-254" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-254', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">,</tt><tt class="py-name">ln</tt><tt class="py-op">)</tt> <tt class="py-comment">#map(lambda s: int(100*float(s)),ln)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-comment">#print counts[i]</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt id="link-255" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Method Bio.SubsMat.SeqMat.sum()=Bio.SubsMat.SeqMat-class.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-255', 'sum', 'link-255');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">nuc</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">nuc</tt> <tt class="py-keyword">in</tt> <tt id="link-256" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-256', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt id="link-257" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-257', 'letters', 'link-12');">letters</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-258', 'length', 'link-11');">length</a></tt><tt class="py-op">=</tt><tt class="py-name">l</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="Bio.Motif._Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-259', 'set_mask', 'link-198');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-string">"*"</tt><tt class="py-op">*</tt><tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">make_instances</tt><tt class="py-op">==</tt><tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.Motif._Motif.Motif.make_instances_from_counts" class="py-name" href="#" onclick="return doclink('link-260', 'make_instances_from_counts', 'link-211');">make_instances_from_counts</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> </tt>
<a name="Motif.make_instances_from_counts"></a><div id="Motif.make_instances_from_counts-def"><a name="L489"></a><tt class="py-lineno">489</tt> <a class="py-toggle" href="#" id="Motif.make_instances_from_counts-toggle" onclick="return toggle('Motif.make_instances_from_counts');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#make_instances_from_counts">make_instances_from_counts</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.make_instances_from_counts-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.make_instances_from_counts-expanded"><a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-docstring">"""Creates "fake" instances for a motif created from a count matrix.</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"><tt class="py-docstring"> In case the sums of counts are different for different columnes, the</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-docstring"> shorter columns are padded with background.</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">alpha</tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-261', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-comment">#col[i] is a column taken from aligned motif instances</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-name">col</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_instances</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt id="link-262" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.SubsMat.SeqMat.sum" class="py-name" href="#" onclick="return doclink('link-262', 'sum', 'link-255');">sum</a></tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">nuc</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">nuc</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-263', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-264" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-264', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-265" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-265', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-266" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-266', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-name">col</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-267', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-268', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-269" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-269', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-270" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-270', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-271" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-271', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-272" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-272', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op"><</tt><tt class="py-name">s</tt><tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"WARNING, column too short"</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-273" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-273', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">s</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-274" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-274', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">*</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">col</tt><tt class="py-op">[</tt><tt id="link-275" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-275', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-comment">#print i,col[i]</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-comment">#iterate over instances</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-276" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-276', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-277" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-277', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> <tt class="py-comment">#start with empty seq</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt id="link-278" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-278', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-279', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment">#iterate over positions</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">+=</tt><tt class="py-name">col</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-280" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-280', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-comment">#print i,inst</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">=</tt><tt id="link-281" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-281', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Bio.Motif._Motif.Motif.add_instance" class="py-name" href="#" onclick="return doclink('link-282', 'add_instance', 'link-200');">add_instance</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt> </tt>
</div><a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> </tt>
<a name="Motif.make_counts_from_instances"></a><div id="Motif.make_counts_from_instances-def"><a name="L519"></a><tt class="py-lineno">519</tt> <a class="py-toggle" href="#" id="Motif.make_counts_from_instances-toggle" onclick="return toggle('Motif.make_counts_from_instances');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#make_counts_from_instances">make_counts_from_instances</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.make_counts_from_instances-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.make_counts_from_instances-expanded"><a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-docstring">"""Creates the count matrix for a motif with instances.</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-comment">#make strings for "columns" of motifs</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-comment">#col[i] is a column taken from aligned motif instances</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">counts</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-283', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">=</tt><tt class="py-name">True</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-284" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-284', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-285" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-285', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-286', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-name">ci</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-287', 'letters', 'link-12');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">inst</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">ci</tt><tt class="py-op">[</tt><tt class="py-name">inst</tt><tt class="py-op">[</tt><tt id="link-288" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-288', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-289', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-290" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-290', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ci</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">=</tt><tt class="py-name">counts</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">counts</tt> </tt>
</div><a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> </tt>
<a name="Motif._from_jaspar_sites"></a><div id="Motif._from_jaspar_sites-def"><a name="L539"></a><tt class="py-lineno">539</tt> <a class="py-toggle" href="#" id="Motif._from_jaspar_sites-toggle" onclick="return toggle('Motif._from_jaspar_sites');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_from_jaspar_sites">_from_jaspar_sites</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">stream</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._from_jaspar_sites-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._from_jaspar_sites-expanded"><a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"><tt class="py-docstring"> reads the motif from Jaspar .sites file</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"><tt class="py-docstring"> The instances and pwm are OK.</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-name">ln</tt> <tt class="py-op">=</tt> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-291', 'readline', 'link-197');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-comment"># read the header "$>...."</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ln</tt><tt class="py-op">==</tt><tt class="py-string">""</tt> <tt class="py-keyword">or</tt> <tt class="py-name">ln</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">!=</tt><tt class="py-string">">"</tt><tt class="py-op">:</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">ln</tt><tt class="py-op">=</tt><tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="Bio.File.UndoHandle.readline" class="py-name" href="#" onclick="return doclink('link-292', 'readline', 'link-197');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-293', 'strip', 'link-199');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-comment">#read the actual sequence</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt id="link-294" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-294', 'i', 'link-23');">i</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">ln</tt><tt class="py-op">[</tt><tt id="link-295" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-295', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-name">ln</tt><tt class="py-op">[</tt><tt id="link-296" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-296', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name" targets="Method Bio.Seq.Seq.lower()=Bio.Seq.Seq-class.html#lower,Method Bio.Seq.UnknownSeq.lower()=Bio.Seq.UnknownSeq-class.html#lower,Method Bio.SeqRecord.SeqRecord.lower()=Bio.SeqRecord.SeqRecord-class.html#lower"><a title="Bio.Seq.Seq.lower
Bio.Seq.UnknownSeq.lower
Bio.SeqRecord.SeqRecord.lower" class="py-name" href="#" onclick="return doclink('link-297', 'lower', 'link-297');">lower</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt id="link-298" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-298', 'i', 'link-23');">i</a></tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-299" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-299', 'i', 'link-23');">i</a></tt><tt class="py-op"><</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ln</tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">ln</tt><tt class="py-op">[</tt><tt id="link-300" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-300', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-name">ln</tt><tt class="py-op">[</tt><tt id="link-301" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-301', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-302" class="py-name"><a title="Bio.Seq.Seq.upper
Bio.Seq.UnknownSeq.upper
Bio.SeqRecord.SeqRecord.upper" class="py-name" href="#" onclick="return doclink('link-302', 'upper', 'link-116');">upper</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">+=</tt><tt class="py-name">ln</tt><tt class="py-op">[</tt><tt id="link-303" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-303', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt id="link-304" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-304', 'i', 'link-23');">i</a></tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-name">inst</tt><tt class="py-op">=</tt><tt id="link-305" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-305', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-306" class="py-name"><a title="Bio.Motif._Motif.Motif.add_instance" class="py-name" href="#" onclick="return doclink('link-306', 'add_instance', 'link-200');">add_instance</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-307" class="py-name"><a title="Bio.Motif._Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-307', 'set_mask', 'link-198');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-string">"*"</tt><tt class="py-op">*</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> </tt>
<a name="Motif.__getitem__"></a><div id="Motif.__getitem__-def"><a name="L566"></a><tt class="py-lineno">566</tt> <a class="py-toggle" href="#" id="Motif.__getitem__-toggle" onclick="return toggle('Motif.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__getitem__-expanded"><a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the probability distribution over symbols at a given position, padding with background.</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"><tt class="py-docstring"> If the requested index is out of bounds, the returned distribution comes from background.</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-308" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index,Function Bio.SeqIO.index()=Bio.SeqIO-module.html#index"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-308', 'index', 'link-308');">index</a></tt> <tt class="py-keyword">in</tt> <tt id="link-309" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-309', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-310', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-311" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-311', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt id="link-312" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-312', 'index', 'link-308');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">background</tt> </tt>
</div><a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> </tt>
<a name="Motif.consensus"></a><div id="Motif.consensus-def"><a name="L576"></a><tt class="py-lineno">576</tt> <a class="py-toggle" href="#" id="Motif.consensus-toggle" onclick="return toggle('Motif.consensus');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#consensus">consensus</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.consensus-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.consensus-expanded"><a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the consensus sequence of a motif.</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-313" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-313', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-314" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-314', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-315', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-name">max_f</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-name">max_n</tt><tt class="py-op">=</tt><tt class="py-string">"X"</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-316" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-316', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-317" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-317', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op">></tt><tt class="py-name">max_f</tt><tt class="py-op">:</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-name">max_f</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-318" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-318', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">max_n</tt><tt class="py-op">=</tt><tt class="py-name">n</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-name">max_n</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-319" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-319', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
</div><a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> </tt>
<a name="Motif.anticonsensus"></a><div id="Motif.anticonsensus-def"><a name="L590"></a><tt class="py-lineno">590</tt> <a class="py-toggle" href="#" id="Motif.anticonsensus-toggle" onclick="return toggle('Motif.anticonsensus');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#anticonsensus">anticonsensus</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.anticonsensus-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.anticonsensus-expanded"><a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-docstring">"""returns the least probable pattern to be generated from this motif.</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-320" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-320', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-321" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-321', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-322" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-322', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-name">min_f</tt><tt class="py-op">=</tt><tt class="py-number">10.0</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-name">min_n</tt><tt class="py-op">=</tt><tt class="py-string">"X"</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-323" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-323', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-324" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-324', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt><tt class="py-op"><</tt><tt class="py-name">min_f</tt><tt class="py-op">:</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-name">min_f</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-325" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-325', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">n</tt><tt class="py-op">]</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-name">min_n</tt><tt class="py-op">=</tt><tt class="py-name">n</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-name">min_n</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-326" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-326', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">res</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">)</tt> </tt>
</div><a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> </tt>
<a name="Motif.max_score"></a><div id="Motif.max_score-def"><a name="L604"></a><tt class="py-lineno">604</tt> <a class="py-toggle" href="#" id="Motif.max_score-toggle" onclick="return toggle('Motif.max_score');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#max_score">max_score</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.max_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.max_score-expanded"><a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-docstring">"""Maximal possible score for this motif.</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"><tt class="py-docstring"> returns the score computed for the consensus sequence.</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-327" class="py-name"><a title="Bio.Motif._Motif.Motif.score_hit" class="py-name" href="#" onclick="return doclink('link-327', 'score_hit', 'link-120');">score_hit</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name" targets="Method Bio.Motif._Motif.Motif.consensus()=Bio.Motif._Motif.Motif-class.html#consensus,Function Bio.Nexus.Trees.consensus()=Bio.Nexus.Trees-module.html#consensus"><a title="Bio.Motif._Motif.Motif.consensus
Bio.Nexus.Trees.consensus" class="py-name" href="#" onclick="return doclink('link-328', 'consensus', 'link-328');">consensus</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> </tt>
<a name="Motif.min_score"></a><div id="Motif.min_score-def"><a name="L611"></a><tt class="py-lineno">611</tt> <a class="py-toggle" href="#" id="Motif.min_score-toggle" onclick="return toggle('Motif.min_score');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#min_score">min_score</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.min_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.min_score-expanded"><a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-docstring">"""Minimal possible score for this motif.</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"><tt class="py-docstring"> returns the score computed for the anticonsensus sequence.</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="Bio.Motif._Motif.Motif.score_hit" class="py-name" href="#" onclick="return doclink('link-329', 'score_hit', 'link-120');">score_hit</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name" targets="Method Bio.Motif._Motif.Motif.anticonsensus()=Bio.Motif._Motif.Motif-class.html#anticonsensus"><a title="Bio.Motif._Motif.Motif.anticonsensus" class="py-name" href="#" onclick="return doclink('link-330', 'anticonsensus', 'link-330');">anticonsensus</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> </tt>
<a name="Motif.weblogo"></a><div id="Motif.weblogo-def"><a name="L618"></a><tt class="py-lineno">618</tt> <a class="py-toggle" href="#" id="Motif.weblogo-toggle" onclick="return toggle('Motif.weblogo');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#weblogo">weblogo</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">fname</tt><tt class="py-op">,</tt><tt class="py-param">format</tt><tt class="py-op">=</tt><tt class="py-string">"PNG"</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">kwds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.weblogo-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.weblogo-expanded"><a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"><tt class="py-docstring"> uses the Berkeley weblogo service to download and save a weblogo of itself</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"><tt class="py-docstring"> requires an internet connection.</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"><tt class="py-docstring"> The parameters from **kwds are passed directly to the weblogo server.</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib2</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-name">al</tt><tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-331" class="py-name" targets="Method Bio.Motif._Motif.Motif._to_fasta()=Bio.Motif._Motif.Motif-class.html#_to_fasta"><a title="Bio.Motif._Motif.Motif._to_fasta" class="py-name" href="#" onclick="return doclink('link-331', '_to_fasta', 'link-331');">_to_fasta</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-name">url</tt> <tt class="py-op">=</tt> <tt class="py-string">'http://weblogo.berkeley.edu/logo.cgi'</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt id="link-332" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-332', 'values', 'link-332');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'sequence'</tt> <tt class="py-op">:</tt> <tt class="py-name">al</tt><tt class="py-op">,</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-string">'format'</tt> <tt class="py-op">:</tt> <tt id="link-333" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-333', 'format', 'link-333');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-string">'logowidth'</tt> <tt class="py-op">:</tt> <tt class="py-string">'18'</tt><tt class="py-op">,</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-string">'logoheight'</tt> <tt class="py-op">:</tt> <tt class="py-string">'5'</tt><tt class="py-op">,</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-string">'logounits'</tt> <tt class="py-op">:</tt> <tt class="py-string">'cm'</tt><tt class="py-op">,</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-string">'kind'</tt> <tt class="py-op">:</tt> <tt class="py-string">'AUTO'</tt><tt class="py-op">,</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-string">'firstnum'</tt> <tt class="py-op">:</tt> <tt class="py-string">"1"</tt><tt class="py-op">,</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-string">'command'</tt> <tt class="py-op">:</tt> <tt class="py-string">'Create Logo'</tt><tt class="py-op">,</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-string">'smallsamplecorrection'</tt> <tt class="py-op">:</tt> <tt class="py-string">"on"</tt><tt class="py-op">,</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt class="py-string">'symbolsperline'</tt> <tt class="py-op">:</tt> <tt class="py-number">32</tt><tt class="py-op">,</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-string">'res'</tt> <tt class="py-op">:</tt> <tt class="py-string">'96'</tt><tt class="py-op">,</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-string">'res_units'</tt> <tt class="py-op">:</tt> <tt class="py-string">'ppi'</tt><tt class="py-op">,</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-string">'antialias'</tt> <tt class="py-op">:</tt> <tt class="py-string">'on'</tt><tt class="py-op">,</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-string">'title'</tt> <tt class="py-op">:</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-string">'barbits'</tt> <tt class="py-op">:</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-string">'xaxis'</tt><tt class="py-op">:</tt> <tt class="py-string">'on'</tt><tt class="py-op">,</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-string">'xaxis_label'</tt> <tt class="py-op">:</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-string">'yaxis'</tt><tt class="py-op">:</tt> <tt class="py-string">'on'</tt><tt class="py-op">,</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-string">'yaxis_label'</tt> <tt class="py-op">:</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-string">'showends'</tt> <tt class="py-op">:</tt> <tt class="py-string">'on'</tt><tt class="py-op">,</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-string">'shrink'</tt> <tt class="py-op">:</tt> <tt class="py-string">'0.5'</tt><tt class="py-op">,</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-string">'fineprint'</tt> <tt class="py-op">:</tt> <tt class="py-string">'on'</tt><tt class="py-op">,</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-string">'ticbits'</tt> <tt class="py-op">:</tt> <tt class="py-string">'1'</tt><tt class="py-op">,</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-string">'colorscheme'</tt> <tt class="py-op">:</tt> <tt class="py-string">'DEFAULT'</tt><tt class="py-op">,</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-string">'color1'</tt> <tt class="py-op">:</tt> <tt class="py-string">'green'</tt><tt class="py-op">,</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-string">'color2'</tt> <tt class="py-op">:</tt> <tt class="py-string">'blue'</tt><tt class="py-op">,</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-string">'color3'</tt> <tt class="py-op">:</tt> <tt class="py-string">'red'</tt><tt class="py-op">,</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-string">'color4'</tt> <tt class="py-op">:</tt> <tt class="py-string">'black'</tt><tt class="py-op">,</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> <tt class="py-string">'color5'</tt> <tt class="py-op">:</tt> <tt class="py-string">'purple'</tt><tt class="py-op">,</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt class="py-string">'color6'</tt> <tt class="py-op">:</tt> <tt class="py-string">'orange'</tt><tt class="py-op">,</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt class="py-string">'color1'</tt> <tt class="py-op">:</tt> <tt class="py-string">'black'</tt><tt class="py-op">,</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt class="py-name">v</tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwds</tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="Bio.SeqIO._index._IndexedSeqFileDict.iteritems
BioSQL.BioSeqDatabase.BioSeqDatabase.iteritems
BioSQL.BioSeqDatabase.DBServer.iteritems" class="py-name" href="#" onclick="return doclink('link-334', 'iteritems', 'link-165');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt id="link-335" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-335', 'values', 'link-332');">values</a></tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">v</tt><tt class="py-op">)</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt id="link-336" class="py-name" targets="Variable Bio.Seq.Seq.data=Bio.Seq.Seq-class.html#data,Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-336', 'data', 'link-336');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">urllib</tt><tt class="py-op">.</tt><tt class="py-name">urlencode</tt><tt class="py-op">(</tt><tt id="link-337" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-337', 'values', 'link-332');">values</a></tt><tt class="py-op">)</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-name">req</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">Request</tt><tt class="py-op">(</tt><tt class="py-name">url</tt><tt class="py-op">,</tt> <tt id="link-338" class="py-name"><a title="Bio.Seq.Seq.data
BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-338', 'data', 'link-336');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-name">response</tt> <tt class="py-op">=</tt> <tt class="py-name">urllib2</tt><tt class="py-op">.</tt><tt class="py-name">urlopen</tt><tt class="py-op">(</tt><tt class="py-name">req</tt><tt class="py-op">)</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-name">fname</tt><tt class="py-op">,</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-name">im</tt><tt class="py-op">=</tt><tt class="py-name">response</tt><tt class="py-op">.</tt><tt id="link-339" class="py-name" targets="Function Bio.Affy.CelFile.read()=Bio.Affy.CelFile-module.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Blast.NCBIXML.read()=Bio.Blast.NCBIXML-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Function Bio.Compass.read()=Bio.Compass-module.html#read,Function Bio.Emboss.Primer3.read()=Bio.Emboss.Primer3-module.html#read,Function Bio.Emboss.PrimerSearch.read()=Bio.Emboss.PrimerSearch-module.html#read,Method Bio.Entrez.Parser.DataHandler.read()=Bio.Entrez.Parser.DataHandler-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Function Bio.ExPASy.Enzyme.read()=Bio.ExPASy.Enzyme-module.html#read,Function Bio.ExPASy.Prodoc.read()=Bio.ExPASy.Prodoc-module.html#read,Function Bio.ExPASy.Prosite.read()=Bio.ExPASy.Prosite-module.html#read,Function Bio.ExPASy.ScanProsite.read()=Bio.ExPASy.ScanProsite-module.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Function Bio.Medline.read()=Bio.Medline-module.html#read,Function Bio.Motif.Parsers.AlignAce.read()=Bio.Motif.Parsers.AlignAce-module.html#read,Function Bio.Motif.Parsers.MAST.read()=Bio.Motif.Parsers.MAST-module.html#read,Function Bio.Motif.Parsers.MEME.read()=Bio.Motif.Parsers.MEME-module.html#read,Function Bio.Motif.read()=Bio.Motif-module.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Phylo.PAML.baseml.read()=Bio.Phylo.PAML.baseml-module.html#read,Function Bio.Phylo.PAML.codeml.read()=Bio.Phylo.PAML.codeml-module.html#read,Function Bio.Phylo.PAML.yn00.read()=Bio.Phylo.PAML.yn00-module.html#read,Method Bio.Phylo.PhyloXMLIO.Parser.read()=Bio.Phylo.PhyloXMLIO.Parser-class.html#read,Function Bio.Phylo.PhyloXMLIO.read()=Bio.Phylo.PhyloXMLIO-module.html#read,Function Bio.Phylo._io.read()=Bio.Phylo._io-module.html#read,Function Bio.PopGen.GenePop.FileParser.read()=Bio.PopGen.GenePop.FileParser-module.html#read,Function Bio.PopGen.GenePop.LargeFileParser.read()=Bio.PopGen.GenePop.LargeFileParser-module.html#read,Function Bio.PopGen.GenePop.read()=Bio.PopGen.GenePop-module.html#read,Method Bio.SeqIO.SffIO._AddTellHandle.read()=Bio.SeqIO.SffIO._AddTellHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.Sequencing.Ace.read()=Bio.Sequencing.Ace-module.html#read,Function Bio.Sequencing.Phd.read()=Bio.Sequencing.Phd-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read,Function Bio.UniGene.read()=Bio.UniGene-module.html#read"><a title="Bio.Affy.CelFile.read
Bio.AlignIO.read
Bio.Blast.NCBIXML.read
Bio.Cluster.read
Bio.Compass.read
Bio.Emboss.Primer3.read
Bio.Emboss.PrimerSearch.read
Bio.Entrez.Parser.DataHandler.read
Bio.Entrez.read
Bio.ExPASy.Enzyme.read
Bio.ExPASy.Prodoc.read
Bio.ExPASy.Prosite.read
Bio.ExPASy.ScanProsite.read
Bio.File.UndoHandle.read
Bio.Medline.read
Bio.Motif.Parsers.AlignAce.read
Bio.Motif.Parsers.MAST.read
Bio.Motif.Parsers.MEME.read
Bio.Motif.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Phylo.PAML.baseml.read
Bio.Phylo.PAML.codeml.read
Bio.Phylo.PAML.yn00.read
Bio.Phylo.PhyloXMLIO.Parser.read
Bio.Phylo.PhyloXMLIO.read
Bio.Phylo._io.read
Bio.PopGen.GenePop.FileParser.read
Bio.PopGen.GenePop.LargeFileParser.read
Bio.PopGen.GenePop.read
Bio.SeqIO.SffIO._AddTellHandle.read
Bio.SeqIO.read
Bio.Sequencing.Ace.read
Bio.Sequencing.Phd.read
Bio.SwissProt.read
Bio.UniGene.read" class="py-name" href="#" onclick="return doclink('link-339', 'read', 'link-339');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-340" class="py-name"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-340', 'write', 'link-209');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">im</tt><tt class="py-op">)</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-341" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-341', 'close', 'link-341');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> </tt>
<a name="Motif._to_transfac"></a><div id="Motif._to_transfac-def"><a name="L674"></a><tt class="py-lineno">674</tt> <a class="py-toggle" href="#" id="Motif._to_transfac-toggle" onclick="return toggle('Motif._to_transfac');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_to_transfac">_to_transfac</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._to_transfac-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._to_transfac-expanded"><a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-docstring">"""Write the representation of a motif in TRANSFAC format</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-string">"XX\nTY Motif\n"</tt> <tt class="py-comment">#header</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"ID %s\n"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-342" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-342', 'name', 'link-14');">name</a></tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"BF undef\nP0"</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-343" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-343', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">" %s"</tt><tt class="py-op">%</tt><tt class="py-name">a</tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\n"</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-344" class="py-name" targets="Method Bio.Motif._Motif.Motif.make_counts_from_instances()=Bio.Motif._Motif.Motif-class.html#make_counts_from_instances"><a title="Bio.Motif._Motif.Motif.make_counts_from_instances" class="py-name" href="#" onclick="return doclink('link-344', 'make_counts_from_instances', 'link-344');">make_counts_from_instances</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-345" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-345', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-346" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-346', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-347" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-347', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-348" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-348', 'i', 'link-23');">i</a></tt><tt class="py-op"><</tt><tt class="py-number">9</tt><tt class="py-op">:</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"0%d"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-349" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-349', 'i', 'link-23');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"%d"</tt><tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-350" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-350', 'i', 'link-23');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-351', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">" %d"</tt><tt class="py-op">%</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-352" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-352', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\n"</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"XX\n"</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"> </tt>
<a name="Motif._to_vertical_matrix"></a><div id="Motif._to_vertical_matrix-def"><a name="L699"></a><tt class="py-lineno">699</tt> <a class="py-toggle" href="#" id="Motif._to_vertical_matrix-toggle" onclick="return toggle('Motif._to_vertical_matrix');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_to_vertical_matrix">_to_vertical_matrix</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">letters</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._to_vertical_matrix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._to_vertical_matrix-expanded"><a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"> <tt class="py-docstring">"""Return string representation of the motif as a matrix.</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-353" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-353', 'letters', 'link-12');">letters</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt id="link-354" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-354', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-355" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-355', 'letters', 'link-12');">letters</a></tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt id="link-356" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-356', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-357" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-357', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-name">laplace</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-358" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-358', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-359" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-359', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-360" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-360', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-361" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-361', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">[</tt><tt id="link-362" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-362', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-363" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-363', 'letters', 'link-12');">letters</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\n"</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> </tt>
<a name="Motif._to_horizontal_matrix"></a><div id="Motif._to_horizontal_matrix-def"><a name="L713"></a><tt class="py-lineno">713</tt> <a class="py-toggle" href="#" id="Motif._to_horizontal_matrix-toggle" onclick="return toggle('Motif._to_horizontal_matrix');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_to_horizontal_matrix">_to_horizontal_matrix</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">letters</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">normalized</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._to_horizontal_matrix-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._to_horizontal_matrix-expanded"><a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-docstring">"""Return string representation of the motif as a matrix.</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-364" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-364', 'letters', 'link-12');">letters</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt id="link-365" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-365', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">.</tt><tt id="link-366" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-366', 'letters', 'link-12');">letters</a></tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">=</tt><tt class="py-string">""</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-367" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-367', 'normalized', 'link-104');">normalized</a></tt><tt class="py-op">:</tt> <tt class="py-comment">#output PWM</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pwm_is_current</tt><tt class="py-op">=</tt><tt class="py-name">False</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-name">mat</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-368" class="py-name"><a title="Bio.Motif._Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-368', 'pwm', 'link-47');">pwm</a></tt><tt class="py-op">(</tt><tt class="py-name">laplace</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-369" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-369', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mat</tt><tt class="py-op">[</tt><tt id="link-370" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-370', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-371" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-371', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-372" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-372', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-373" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-373', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\n"</tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment">#output counts</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">has_counts</tt><tt class="py-op">:</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-374" class="py-name"><a title="Bio.Motif._Motif.Motif.make_counts_from_instances" class="py-name" href="#" onclick="return doclink('link-374', 'make_counts_from_instances', 'link-344');">make_counts_from_instances</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-name">mat</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">counts</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-375" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-375', 'letters', 'link-12');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\t"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mat</tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-376" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-376', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-377" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-377', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-378" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-378', 'range', 'link-24');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-379', 'length', 'link-11');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-name">res</tt><tt class="py-op">+=</tt><tt class="py-string">"\n"</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> </tt>
<a name="Motif._to_jaspar_pfm"></a><div id="Motif._to_jaspar_pfm-def"><a name="L735"></a><tt class="py-lineno">735</tt> <a class="py-toggle" href="#" id="Motif._to_jaspar_pfm-toggle" onclick="return toggle('Motif._to_jaspar_pfm');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_to_jaspar_pfm">_to_jaspar_pfm</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._to_jaspar_pfm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._to_jaspar_pfm-expanded"><a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the pfm representation of the motif</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-380" class="py-name" targets="Method Bio.Motif._Motif.Motif._to_horizontal_matrix()=Bio.Motif._Motif.Motif-class.html#_to_horizontal_matrix"><a title="Bio.Motif._Motif.Motif._to_horizontal_matrix" class="py-name" href="#" onclick="return doclink('link-380', '_to_horizontal_matrix', 'link-380');">_to_horizontal_matrix</a></tt><tt class="py-op">(</tt><tt id="link-381" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-381', 'normalized', 'link-104');">normalized</a></tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt><tt id="link-382" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters" class="py-name" href="#" onclick="return doclink('link-382', 'letters', 'link-12');">letters</a></tt><tt class="py-op">=</tt><tt class="py-string">"ACGT"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> </tt>
<a name="Motif.format"></a><div id="Motif.format-def"><a name="L740"></a><tt class="py-lineno">740</tt> <a class="py-toggle" href="#" id="Motif.format-toggle" onclick="return toggle('Motif.format');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#format">format</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.format-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.format-expanded"><a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string representation of the Motif in a given format</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"><tt class="py-docstring"> Currently supported fromats:</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"><tt class="py-docstring"> - jaspar-pfm : JASPAR Position Frequency Matrix</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"><tt class="py-docstring"> - transfac : TRANSFAC like files</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-docstring"> - fasta : FASTA file with instances</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-name">formatters</tt><tt class="py-op">=</tt><tt class="py-op">{</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt class="py-string">"jaspar-pfm"</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-383" class="py-name" targets="Method Bio.Motif._Motif.Motif._to_jaspar_pfm()=Bio.Motif._Motif.Motif-class.html#_to_jaspar_pfm"><a title="Bio.Motif._Motif.Motif._to_jaspar_pfm" class="py-name" href="#" onclick="return doclink('link-383', '_to_jaspar_pfm', 'link-383');">_to_jaspar_pfm</a></tt><tt class="py-op">,</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt class="py-string">"transfac"</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-384" class="py-name" targets="Method Bio.Motif._Motif.Motif._to_transfac()=Bio.Motif._Motif.Motif-class.html#_to_transfac"><a title="Bio.Motif._Motif.Motif._to_transfac" class="py-name" href="#" onclick="return doclink('link-384', '_to_transfac', 'link-384');">_to_transfac</a></tt><tt class="py-op">,</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-string">"fasta"</tt> <tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-385" class="py-name"><a title="Bio.Motif._Motif.Motif._to_fasta" class="py-name" href="#" onclick="return doclink('link-385', '_to_fasta', 'link-331');">_to_fasta</a></tt><tt class="py-op">,</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">formatters</tt><tt class="py-op">[</tt><tt id="link-386" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-386', 'format', 'link-333');">format</a></tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Wrong format type"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> </tt>
<a name="Motif.scanPWM"></a><div id="Motif.scanPWM-def"><a name="L760"></a><tt class="py-lineno">760</tt> <a class="py-toggle" href="#" id="Motif.scanPWM-toggle" onclick="return toggle('Motif.scanPWM');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#scanPWM">scanPWM</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif.scanPWM-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.scanPWM-expanded"><a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-docstring">"""Matrix of log-odds scores for a nucleotide sequence.</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"><tt class="py-docstring"> scans a nucleotide sequence and returns the matrix of log-odds</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"><tt class="py-docstring"> scores for all positions.</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"><tt class="py-docstring"> - the result is a one-dimensional list or numpy array</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"><tt class="py-docstring"> - the sequence can only be a DNA sequence</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"><tt class="py-docstring"> - the search is performed only on one strand</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">!=</tt><tt id="link-387" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-387', 'IUPAC', 'link-8');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-388" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-388', 'unambiguous_dna', 'link-10');">unambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Wrong alphabet! Use only with DNA motifs"</tt><tt class="py-op">)</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-389" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-389', 'seq', 'link-39');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt><tt class="py-op">!=</tt><tt id="link-390" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-390', 'IUPAC', 'link-8');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-391" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-391', 'unambiguous_dna', 'link-10');">unambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Wrong alphabet! Use only with DNA sequences"</tt><tt class="py-op">)</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt id="link-392" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-392', 'seq', 'link-39');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-393" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-393', 'seq', 'link-39');">seq</a></tt><tt class="py-op">.</tt><tt id="link-394" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-394', 'tostring', 'link-94');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-comment"># check if the fast C code can be used</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">_pwm</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-comment"># use the slower Python code otherwise</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-395" class="py-name" targets="Method Bio.Motif._Motif.Motif._pwm_calculate()=Bio.Motif._Motif.Motif-class.html#_pwm_calculate"><a title="Bio.Motif._Motif.Motif._pwm_calculate" class="py-name" href="#" onclick="return doclink('link-395', '_pwm_calculate', 'link-395');">_pwm_calculate</a></tt><tt class="py-op">(</tt><tt id="link-396" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-396', 'seq', 'link-39');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-comment"># get the log-odds matrix into a proper shape</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-comment"># (each row contains sorted (ACGT) log-odds values)</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-name">logodds</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">y</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sorted</tt><tt class="py-op">(</tt><tt id="link-397" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-397', 'x', 'link-108');">x</a></tt><tt class="py-op">.</tt><tt id="link-398" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.Phylo.PhyloXML.Events.items()=Bio.Phylo.PhyloXML.Events-class.html#items,Method Bio.SeqIO._index._IndexedSeqFileDict.items()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.Phylo.PhyloXML.Events.items
Bio.SeqIO._index._IndexedSeqFileDict.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items" class="py-name" href="#" onclick="return doclink('link-398', 'items', 'link-398');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-399" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-399', 'x', 'link-108');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-400" class="py-name"><a title="Bio.Motif._Motif.Motif.log_odds" class="py-name" href="#" onclick="return doclink('link-400', 'log_odds', 'link-99');">log_odds</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">_pwm</tt><tt class="py-op">.</tt><tt id="link-401" class="py-name" targets="Function Bio.LogisticRegression.calculate()=Bio.LogisticRegression-module.html#calculate,Function Bio.MaxEntropy.calculate()=Bio.MaxEntropy-module.html#calculate,Function Bio.NaiveBayes.calculate()=Bio.NaiveBayes-module.html#calculate,Function Bio.kNN.calculate()=Bio.kNN-module.html#calculate"><a title="Bio.LogisticRegression.calculate
Bio.MaxEntropy.calculate
Bio.NaiveBayes.calculate
Bio.kNN.calculate" class="py-name" href="#" onclick="return doclink('link-401', 'calculate', 'link-401');">calculate</a></tt><tt class="py-op">(</tt><tt id="link-402" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-402', 'seq', 'link-39');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">logodds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> </tt>
<a name="Motif._pwm_calculate"></a><div id="Motif._pwm_calculate-def"><a name="L789"></a><tt class="py-lineno">789</tt> <a class="py-toggle" href="#" id="Motif._pwm_calculate-toggle" onclick="return toggle('Motif._pwm_calculate');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif._Motif.Motif-class.html#_pwm_calculate">_pwm_calculate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Motif._pwm_calculate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif._pwm_calculate-expanded"><a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt class="py-name">logodds</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-403" class="py-name"><a title="Bio.Motif._Motif.Motif.log_odds" class="py-name" href="#" onclick="return doclink('link-403', 'log_odds', 'link-99');">log_odds</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">logodds</tt><tt class="py-op">)</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-404" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-404', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">s</tt> <tt class="py-op">-</tt> <tt class="py-name">m</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> <tt class="py-op">*</tt> <tt class="py-name">n</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-405" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-405', 'i', 'link-23');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt id="link-406" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-406', 'score', 'link-100');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</tt> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt id="link-407" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-407', 'sequence', 'link-90');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-408" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-408', 'i', 'link-23');">i</a></tt><tt class="py-op">+</tt><tt class="py-name">j</tt><tt class="py-op">]</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-name">temp</tt> <tt class="py-op">=</tt> <tt class="py-name">logodds</tt><tt class="py-op">[</tt><tt class="py-name">j</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-409" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-409', 'get', 'link-409');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">temp</tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> <tt id="link-410" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-410', 'score', 'link-100');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">temp</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> <tt class="py-name">result</tt><tt class="py-op">[</tt><tt id="link-411" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-411', 'i', 'link-23');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-412" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score" class="py-name" href="#" onclick="return doclink('link-412', 'score', 'link-100');">score</a></tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div></div><a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> </tt><script type="text/javascript">
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