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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignAce-module.html">Package AlignAce</a> ::
Module Motif
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<h1 class="epydoc">Source Code for <a href="Bio.AlignAce.Motif-module.html">Module Bio.AlignAce.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 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"></tt><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"></tt><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"></tt><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-comment"></tt><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">Implementation of sequence motifs.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Changes:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">9.2007 (BW) : added the to_faste() and .weblogo() methods allowing to use the Berkeley weblogo server at http://weblogo.berkeley.edu/</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">__future__</tt> <tt class="py-keyword">import</tt> <tt class="py-name">generators</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</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="Package Bio.SubsMat=Bio.SubsMat-module.html"><a title="Bio.SubsMat" class="py-name" href="#" onclick="return doclink('link-1', 'SubsMat', 'link-1');">SubsMat</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" 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-2', 'FreqTable', 'link-2');">FreqTable</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="Motif"></a><div id="Motif-def"><a name="L15"></a><tt class="py-lineno"> 15</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.AlignAce.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="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> A class representing sequence motifs.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Motif.__init__"></a><div id="Motif.__init__-def"><a name="L19"></a><tt class="py-lineno"> 19</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.AlignAce.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-op">:</tt> </tt>
</div><div id="Motif.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__init__-expanded"><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">instances</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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 id="link-3" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-3', 'score', 'link-3');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0.0</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">mask</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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_is_current</tt> <tt class="py-op">=</tt> <tt class="py-number">0</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">_pwm</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</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 id="link-4" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-4', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">=</tt><tt class="py-name">None</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 id="link-5" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-5', 'length', 'link-5');">length</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
</div><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="Motif._check_length"></a><div id="Motif._check_length-def"><a name="L28"></a><tt class="py-lineno"> 28</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.AlignAce.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="L29"></a><tt class="py-lineno"> 29</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-6" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-6', 'length', 'link-5');">length</a></tt><tt class="py-op">==</tt><tt class="py-name">None</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 id="link-7" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-7', 'length', 'link-5');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</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-8" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-8', 'length', 'link-5');">length</a></tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</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>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="Motif._check_alphabet"></a><div id="Motif._check_alphabet-def"><a name="L34"></a><tt class="py-lineno"> 34</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.AlignAce.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="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-9" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-9', 'alphabet', 'link-4');">alphabet</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-10" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-10', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">=</tt><tt id="link-11" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'alphabet', 'link-4');">alphabet</a></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-12" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-12', 'alphabet', 'link-4');">alphabet</a></tt> <tt class="py-op">!=</tt> <tt id="link-13" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-13', 'alphabet', 'link-4');">alphabet</a></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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Wrong Alphabet"</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="Motif.add_instance"></a><div id="Motif.add_instance-def"><a name="L40"></a><tt class="py-lineno"> 40</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.AlignAce.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="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> adds new instance to the motif</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</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.AlignAce.Motif.Motif._check_alphabet()=Bio.AlignAce.Motif.Motif-class.html#_check_alphabet"><a title="Bio.AlignAce.Motif.Motif._check_alphabet" class="py-name" href="#" onclick="return doclink('link-14', '_check_alphabet', 'link-14');">_check_alphabet</a></tt><tt class="py-op">(</tt><tt id="link-15" 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-15', 'instance', 'link-15');">instance</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-16', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.AlignAce.Motif.Motif._check_length()=Bio.AlignAce.Motif.Motif-class.html#_check_length"><a title="Bio.AlignAce.Motif.Motif._check_length" class="py-name" href="#" onclick="return doclink('link-17', '_check_length', 'link-17');">_check_length</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-18', 'instance', 'link-15');">instance</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</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-19" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-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,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-19', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-20', 'instance', 'link-15');">instance</a></tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</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 id="link-21" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-21', 'False', 'link-21');">False</a></tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="Motif.set_mask"></a><div id="Motif.set_mask-def"><a name="L49"></a><tt class="py-lineno"> 49</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.AlignAce.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="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-docstring"> sets the mask for the motif</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</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="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.AlignAce.Motif.Motif._check_length" class="py-name" href="#" onclick="return doclink('link-22', '_check_length', 'link-17');">_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="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">mask</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</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="L58"></a><tt class="py-lineno"> 58</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="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">mask</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-23', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</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="L61"></a><tt class="py-lineno"> 61</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-24" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-24', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</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="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="Motif.pwm"></a><div id="Motif.pwm-def"><a name="L65"></a><tt class="py-lineno"> 65</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.AlignAce.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-op">:</tt> </tt>
</div><div id="Motif.pwm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.pwm-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> returns the PWM computed for the set of instances</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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="L71"></a><tt class="py-lineno"> 71</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="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment">#we need to compute new pwm</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt> <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="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-25" 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-25', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-26" class="py-name" targets="Method Bio.GFF.Feature.xrange()=Bio.GFF.Feature-class.html#xrange"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-26', 'xrange', 'link-26');">xrange</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">mask</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</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="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment">#filling the dict with 0's</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> <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 id="link-27" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-27', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-28" 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,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-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
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-28', 'letters', 'link-28');">letters</a></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">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</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment">#counting the occurences of letters in instances</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-29" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-29', 'seq', 'link-29');">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="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt id="link-30" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-30', 'seq', 'link-29');">seq</a></tt><tt class="py-op">[</tt><tt id="link-31" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-31', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">dict</tt><tt class="py-op">[</tt><tt id="link-32" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-32', 'seq', 'link-29');">seq</a></tt><tt class="py-op">[</tt><tt id="link-33" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-33', 'i', 'link-25');">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="L82"></a><tt class="py-lineno"> 82</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-34" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-34', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-35', 'FreqTable', 'link-2');">FreqTable</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-36', 'FreqTable', 'link-2');">FreqTable</a></tt><tt class="py-op">(</tt><tt class="py-name">dict</tt><tt class="py-op">,</tt><tt id="link-37" class="py-name"><a title="Bio.SubsMat.FreqTable
Bio.SubsMat.FreqTable.FreqTable" class="py-name" href="#" onclick="return doclink('link-37', 'FreqTable', 'link-2');">FreqTable</a></tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'COUNT', 'link-38');">COUNT</a></tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-39', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</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 id="link-40" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-40', 'True', 'link-40');">True</a></tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</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="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt>
<a name="Motif.search_instances"></a><div id="Motif.search_instances-def"><a name="L86"></a><tt class="py-lineno"> 86</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.AlignAce.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="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 class="py-docstring"> a generator function, returning found positions of instances of the motif in a given sequence</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</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-41" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-41', 'xrange', 'link-26');">xrange</a></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-42" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,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.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-42', 'sequence', 'link-42');">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-43" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-43', 'length', 'link-5');">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="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-44" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-44', 'instance', 'link-15');">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="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-45" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-45', 'instance', 'link-15');">instance</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-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.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-46', 'tostring', 'link-46');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt id="link-47" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-47', 'sequence', 'link-42');">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-48" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-48', 'length', 'link-5');">length</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-49', 'tostring', 'link-46');">tostring</a></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">yield</tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-50" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-50', 'instance', 'link-15');">instance</a></tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</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="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="Motif.score_hit"></a><div id="Motif.score_hit-def"><a name="L96"></a><tt class="py-lineno"> 96</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.AlignAce.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">1</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="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> give the pwm score for a given position</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-51', 'score', 'link-3');">score</a></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">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt id="link-52" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-52', 'xrange', 'link-26');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-53', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</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="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-54', 'score', 'link-3');">score</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.pwm()=Bio.AlignAce.Motif.Motif-class.html#pwm"><a title="Bio.AlignAce.Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-55', 'pwm', 'link-55');">pwm</a></tt><tt class="py-op">(</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-op">[</tt><tt id="link-56" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-56', 'sequence', 'link-42');">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 class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-57" 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-57', 'normalized', 'link-57');">normalized</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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">masked</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt id="link-58" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-58', 'score', 'link-3');">score</a></tt><tt class="py-op">/=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-59', 'length', 'link-5');">length</a></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-60" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-60', 'score', 'link-3');">score</a></tt><tt class="py-op">/=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-61" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-61', 'filter', 'link-61');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-62" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-62', 'x', 'link-62');">x</a></tt><tt class="py-op">:</tt> <tt id="link-63" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-63', 'x', 'link-62');">x</a></tt><tt class="py-op">,</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-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-64" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-64', 'score', 'link-3');">score</a></tt> </tt>
</div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="Motif.search_pwm"></a><div id="Motif.search_pwm-def"><a name="L111"></a><tt class="py-lineno">111</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.AlignAce.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">threshold</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt><tt class="py-op">,</tt><tt class="py-param">normalized</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-param">masked</tt><tt class="py-op">=</tt><tt class="py-number">1</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="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</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="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt>
<a name="L116"></a><tt class="py-lineno">116</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-65" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-65', 'xrange', 'link-26');">xrange</a></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-66" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-66', 'sequence', 'link-42');">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-67" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-67', 'length', 'link-5');">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="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-68" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-68', 'score', 'link-3');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.score_hit()=Bio.AlignAce.Motif.Motif-class.html#score_hit"><a title="Bio.AlignAce.Motif.Motif.score_hit" class="py-name" href="#" onclick="return doclink('link-69', 'score_hit', 'link-69');">score_hit</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-70', 'sequence', 'link-42');">sequence</a></tt><tt class="py-op">,</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt><tt id="link-71" class="py-name"><a title="Bio.PDB.Vector'.Vector.normalized" class="py-name" href="#" onclick="return doclink('link-71', 'normalized', 'link-57');">normalized</a></tt><tt class="py-op">,</tt><tt class="py-name">masked</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-72" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-72', 'score', 'link-3');">score</a></tt> <tt class="py-op">></tt> <tt id="link-73" 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-73', 'threshold', 'link-73');">threshold</a></tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</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-74" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-74', 'score', 'link-3');">score</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="Motif.sim"></a><div id="Motif.sim-def"><a name="L122"></a><tt class="py-lineno">122</tt> <a class="py-toggle" href="#" id="Motif.sim-toggle" onclick="return toggle('Motif.sim');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Motif.Motif-class.html#sim">sim</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.sim-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.sim-expanded"><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> return the similarity score for the given motif against self.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> We use the Pearson's correlation of the respective probabilities.</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> If the motifs have different length or mask raise the ValueError.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt id="link-75" class="py-name" targets="Variable Bio.Affy.CelFile.sqrt=Bio.Affy.CelFile-module.html#sqrt,Variable Bio.LogisticRegression.sqrt=Bio.LogisticRegression-module.html#sqrt,Variable Bio.MarkovModel.sqrt=Bio.MarkovModel-module.html#sqrt,Variable Bio.MaxEntropy.sqrt=Bio.MaxEntropy-module.html#sqrt,Variable Bio.NaiveBayes.sqrt=Bio.NaiveBayes-module.html#sqrt,Variable Bio.PDB.ResidueDepth'.sqrt=Bio.PDB.ResidueDepth%27-module.html#sqrt,Variable Bio.PDB.Vector'.sqrt=Bio.PDB.Vector%27-module.html#sqrt,Variable Bio.SVDSuperimposer.SVDSuperimposer'.sqrt=Bio.SVDSuperimposer.SVDSuperimposer%27-module.html#sqrt,Variable Bio.SVDSuperimposer.sqrt=Bio.SVDSuperimposer-module.html#sqrt,Variable Bio.Statistics.lowess.sqrt=Bio.Statistics.lowess-module.html#sqrt,Variable Bio.distance.sqrt=Bio.distance-module.html#sqrt,Variable Bio.kNN.sqrt=Bio.kNN-module.html#sqrt"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-75', 'sqrt', 'link-75');">sqrt</a></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="L132"></a><tt class="py-lineno">132</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-76" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-76', 'alphabet', 'link-4');">alphabet</a></tt> <tt class="py-op">!=</tt> <tt id="link-77" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.motif()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-77', 'motif', 'link-77');">motif</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-78', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</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>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</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-79" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-79', 'length', 'link-5');">length</a></tt> <tt class="py-op">!=</tt> <tt id="link-80" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-80', 'motif', 'link-77');">motif</a></tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-81', 'length', 'link-5');">length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</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 length"</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">masked</tt> <tt class="py-keyword">and</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-82" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-82', 'motif', 'link-77');">motif</a></tt><tt class="py-op">.</tt><tt class="py-name">mask</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</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 mask"</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</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="L142"></a><tt class="py-lineno">142</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="L143"></a><tt class="py-lineno">143</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="L144"></a><tt class="py-lineno">144</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="L145"></a><tt class="py-lineno">145</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="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</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-83" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-83', 'xrange', 'link-26');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-84', 'length', 'link-5');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</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>
<a name="L149"></a><tt class="py-lineno">149</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 id="link-85" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-85', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-86" 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
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-86', 'letters', 'link-28');">letters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</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 id="link-87" class="py-name"><a title="Bio.AlignAce.Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-87', 'pwm', 'link-55');">pwm</a></tt><tt class="py-op">(</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-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">yi</tt> <tt class="py-op">=</tt> <tt id="link-88" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-88', 'motif', 'link-77');">motif</a></tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.AlignAce.Motif.Motif.pwm" class="py-name" href="#" onclick="return doclink('link-89', 'pwm', 'link-55');">pwm</a></tt><tt class="py-op">(</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-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</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="L153"></a><tt class="py-lineno">153</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="L154"></a><tt class="py-lineno">154</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="L155"></a><tt class="py-lineno">155</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="L156"></a><tt class="py-lineno">156</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="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</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="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-90" 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-90', 'norm', 'link-90');">norm</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-91" class="py-name"><a title="Bio.FSSP.FSSPTools.filter
Bio.FilteredReader.FilteredReader.filter
Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-91', 'filter', 'link-61');">filter</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-92" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-92', 'x', 'link-62');">x</a></tt><tt class="py-op">:</tt> <tt id="link-93" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-93', 'x', 'link-62');">x</a></tt><tt class="py-op">,</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-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-94" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-94', 'norm', 'link-90');">norm</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-95', 'length', 'link-5');">length</a></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-96', 'norm', 'link-90');">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 id="link-97" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-97', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-98" 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
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-98', 'letters', 'link-28');">letters</a></tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt id="link-99" class="py-name" targets="Variable Martel.test.test_swissprot38.s1=Martel.test.test_swissprot38-module.html#s1"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-99', 's1', 'link-99');">s1</a></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-100" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-100', 'norm', 'link-90');">norm</a></tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt id="link-101" class="py-name" targets="Variable Martel.test.test_swissprot38.s2=Martel.test.test_swissprot38-module.html#s2"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-101', 's2', 'link-101');">s2</a></tt> <tt class="py-op">=</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 id="link-102" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-102', 'norm', 'link-90');">norm</a></tt><tt class="py-op">)</tt><tt class="py-op">*</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 id="link-103" class="py-name"><a title="Bio.PDB.Vector'.Vector.norm" class="py-name" href="#" onclick="return doclink('link-103', 'norm', 'link-90');">norm</a></tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-104" class="py-name"><a title="Martel.test.test_swissprot38.s1" class="py-name" href="#" onclick="return doclink('link-104', 's1', 'link-99');">s1</a></tt><tt class="py-op">/</tt><tt id="link-105" class="py-name"><a title="Bio.Affy.CelFile.sqrt
Bio.LogisticRegression.sqrt
Bio.MarkovModel.sqrt
Bio.MaxEntropy.sqrt
Bio.NaiveBayes.sqrt
Bio.PDB.ResidueDepth'.sqrt
Bio.PDB.Vector'.sqrt
Bio.SVDSuperimposer.SVDSuperimposer'.sqrt
Bio.SVDSuperimposer.sqrt
Bio.Statistics.lowess.sqrt
Bio.distance.sqrt
Bio.kNN.sqrt" class="py-name" href="#" onclick="return doclink('link-105', 'sqrt', 'link-75');">sqrt</a></tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="Martel.test.test_swissprot38.s2" class="py-name" href="#" onclick="return doclink('link-106', 's2', 'link-101');">s2</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="Motif.read"></a><div id="Motif.read-def"><a name="L169"></a><tt class="py-lineno">169</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.AlignAce.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="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> reads the motif from the stream</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> the self.alphabet variable must be set before</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-107" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-107', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-108', 'Seq', 'link-108');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-109" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-109', 'Seq', 'link-108');">Seq</a></tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</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="L177"></a><tt class="py-lineno">177</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-110" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-110', 'readline', 'link-110');">readline</a></tt><tt class="py-op">(</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">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="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.set_mask()=Bio.AlignAce.Motif.Motif-class.html#set_mask"><a title="Bio.AlignAce.Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-111', 'set_mask', 'link-111');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-name">ln</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-112', 'strip', 'link-112');">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="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.add_instance()=Bio.AlignAce.Motif.Motif-class.html#add_instance,Method Bio.MEME.Motif.Motif.add_instance()=Bio.MEME.Motif.Motif-class.html#add_instance,Method Bio.MEME.Parser._MEMEConsumer.add_instance()=Bio.MEME.Parser._MEMEConsumer-class.html#add_instance"><a title="Bio.AlignAce.Motif.Motif.add_instance
Bio.MEME.Motif.Motif.add_instance
Bio.MEME.Parser._MEMEConsumer.add_instance" class="py-name" href="#" onclick="return doclink('link-113', 'add_instance', 'link-113');">add_instance</a></tt><tt class="py-op">(</tt><tt id="link-114" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-114', 'Seq', 'link-108');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ln</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-115', 'strip', 'link-112');">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 id="link-116" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-116', 'alphabet', 'link-4');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="Motif.__str__"></a><div id="Motif.__str__-def"><a name="L183"></a><tt class="py-lineno">183</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.AlignAce.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-op">:</tt> </tt>
</div><div id="Motif.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Motif.__str__-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> string representation of motif</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</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="L189"></a><tt class="py-lineno">189</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-117" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-117', 'tostring', 'link-46');">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="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-118" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-118', 'i', 'link-25');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-119" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-119', 'xrange', 'link-26');">xrange</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"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-120', 'length', 'link-5');">length</a></tt><tt class="py-op">)</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">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-121" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-121', 'i', 'link-25');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</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="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</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="L196"></a><tt class="py-lineno">196</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="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="Motif.write"></a><div id="Motif.write-def"><a name="L200"></a><tt class="py-lineno">200</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.AlignAce.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="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"> writes the motif to the stream</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>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">stream</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
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Bio.LocusLink.web_parse.Url.__str__
Bio.MarkovModel.MarkovModel.__str__
Bio.MetaTool.Record.Metabolite.__str__
Bio.MetaTool.Record.MetaboliteRole.__str__
Bio.MetaTool.Record.PathwayTransform.__str__
Bio.MetaTool.Record.Record.__str__
Bio.Mindy.Location.Location.__str__
Bio.NBRF.Record.Record.__str__
Bio.Ndb.Record.__str__
Bio.NetCatch.ExtractUrls.__str__
Bio.NetCatch.NetCatch.__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.PopGen.FDist.Record.__str__
Bio.PopGen.GenePop.Record.__str__
Bio.Prosite.Pattern.Prosite.__str__
Bio.Prosite.Pattern.PrositeMatch.__str__
Bio.Prosite.Pattern.PrositeTerm.__str__
Bio.Prosite.PatternHit.__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.Saf.Record.Record.__str__
Bio.Seq.MutableSeq.__str__
Bio.Seq.Seq.__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.SeqRecord.SeqRecord.__str__
Bio.StdHandler.Feature.__str__
Bio.SubsMat.BadMatrix.__str__
Bio.Translate.Translator.__str__
Bio.Wise.dnal.Statistics.__str__
Bio.Wise.psw.ColumnUnit.__str__
Bio.config.Registry.Registry.__str__
BioSQL.BioSeq.DBSeq.__str__
Martel.Expression.Alt.__str__
Martel.Expression.Any.__str__
Martel.Expression.AnyEol.__str__
Martel.Expression.Assert.__str__
Martel.Expression.AtBeginning.__str__
Martel.Expression.AtEnd.__str__
Martel.Expression.Debug.__str__
Martel.Expression.Dot.__str__
Martel.Expression.Expression.__str__
Martel.Expression.Group.__str__
Martel.Expression.GroupRef.__str__
Martel.Expression.Literal.__str__
Martel.Expression.MaxRepeat.__str__
Martel.Expression.NullOp.__str__
Martel.Expression.PassThrough.__str__
Martel.Expression.Seq.__str__
Martel.Expression.Str.__str__
Martel.Parser.HeaderFooterParser.__str__
Martel.Parser.MartelAttributeList.__str__
Martel.Parser.Parser.__str__
Martel.Parser.RecordParser.__str__" class="py-name" href="#" onclick="return doclink('link-123', '__str__', 'link-123');">__str__</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><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>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="Motif.to_fasta"></a><div id="Motif.to_fasta-def"><a name="L209"></a><tt class="py-lineno">209</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.AlignAce.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="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> FASTA representation of motif</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-124" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-124', 'i', 'link-25');">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="L215"></a><tt class="py-lineno">215</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-125" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-125', 'i', 'link-25');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-126', 'tostring', 'link-46');">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="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="Motif.weblogo"></a><div id="Motif.weblogo-def"><a name="L219"></a><tt class="py-lineno">219</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.AlignAce.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="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"> uses the Berkeley weblogo service to download and save a weblogo of itself</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 class="py-docstring"> requires an internet connection.</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> The parameters from **kwds are passed directly to the weblogo server.</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">urllib2</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment">#import Image</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"></tt> <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-127" class="py-name" targets="Method Bio.Align.FormatConvert.FormatConverter.to_fasta()=Bio.Align.FormatConvert.FormatConverter-class.html#to_fasta,Method Bio.AlignAce.Motif.Motif.to_fasta()=Bio.AlignAce.Motif.Motif-class.html#to_fasta"><a title="Bio.Align.FormatConvert.FormatConverter.to_fasta
Bio.AlignAce.Motif.Motif.to_fasta" class="py-name" href="#" onclick="return doclink('link-127', 'to_fasta', 'link-127');">to_fasta</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> </tt>
<a name="L231"></a><tt class="py-lineno">231</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="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt id="link-128" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-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,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-128', 'values', 'link-128');">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="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-string">'format'</tt> <tt class="py-op">:</tt> <tt id="link-129" class="py-name" targets="Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Variable Bio.expressions.blast.ncbiblast.format=Bio.expressions.blast.ncbiblast-module.html#format,Variable Bio.expressions.blast.wublast.format=Bio.expressions.blast.wublast-module.html#format,Variable Bio.expressions.blocks.format=Bio.expressions.blocks-module.html#format,Variable Bio.expressions.embl.embl65.format=Bio.expressions.embl.embl65-module.html#format,Variable Bio.expressions.fasta.format=Bio.expressions.fasta-module.html#format,Variable Bio.expressions.genbank.format=Bio.expressions.genbank-module.html#format,Variable Bio.expressions.hmmpfam.format=Bio.expressions.hmmpfam-module.html#format,Variable Bio.expressions.swissprot.ipi.format=Bio.expressions.swissprot.ipi-module.html#format,Variable Bio.expressions.swissprot.speclist.format=Bio.expressions.swissprot.speclist-module.html#format,Variable Bio.expressions.swissprot.sprot38.format=Bio.expressions.swissprot.sprot38-module.html#format,Variable Bio.expressions.swissprot.sprot40.format=Bio.expressions.swissprot.sprot40-module.html#format,Variable Bio.expressions.transfac.format=Bio.expressions.transfac-module.html#format,Variable Martel.test.test_swissprot38.format=Martel.test.test_swissprot38-module.html#format,Variable Martel.test.testformats.swissprot38.format=Martel.test.testformats.swissprot38-module.html#format"><a title="Bio.Restriction.Restriction.RestrictionBatch.format
Bio.expressions.blast.ncbiblast.format
Bio.expressions.blast.wublast.format
Bio.expressions.blocks.format
Bio.expressions.embl.embl65.format
Bio.expressions.fasta.format
Bio.expressions.genbank.format
Bio.expressions.hmmpfam.format
Bio.expressions.swissprot.ipi.format
Bio.expressions.swissprot.speclist.format
Bio.expressions.swissprot.sprot38.format
Bio.expressions.swissprot.sprot40.format
Bio.expressions.transfac.format
Martel.test.test_swissprot38.format
Martel.test.testformats.swissprot38.format" class="py-name" href="#" onclick="return doclink('link-129', 'format', 'link-129');">format</a></tt><tt class="py-op">,</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</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="L235"></a><tt class="py-lineno">235</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="L236"></a><tt class="py-lineno">236</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="L237"></a><tt class="py-lineno">237</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="L238"></a><tt class="py-lineno">238</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="L239"></a><tt class="py-lineno">239</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="L240"></a><tt class="py-lineno">240</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="L241"></a><tt class="py-lineno">241</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="L242"></a><tt class="py-lineno">242</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="L243"></a><tt class="py-lineno">243</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="L244"></a><tt class="py-lineno">244</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="L245"></a><tt class="py-lineno">245</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="L246"></a><tt class="py-lineno">246</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="L247"></a><tt class="py-lineno">247</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="L248"></a><tt class="py-lineno">248</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="L249"></a><tt class="py-lineno">249</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="L250"></a><tt class="py-lineno">250</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="L251"></a><tt class="py-lineno">251</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="L252"></a><tt class="py-lineno">252</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="L253"></a><tt class="py-lineno">253</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="L254"></a><tt class="py-lineno">254</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="L255"></a><tt class="py-lineno">255</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="L256"></a><tt class="py-lineno">256</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="L257"></a><tt class="py-lineno">257</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="L258"></a><tt class="py-lineno">258</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="L259"></a><tt class="py-lineno">259</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="L260"></a><tt class="py-lineno">260</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="L261"></a><tt class="py-lineno">261</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="L262"></a><tt class="py-lineno">262</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="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt id="link-130" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-130', 'v', 'link-130');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">kwds</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-131', 'items', 'link-131');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-132', 'values', 'link-128');">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 id="link-133" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-133', 'v', 'link-130');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt id="link-134" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-134', 'data', 'link-134');">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-135" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-135', 'values', 'link-128');">values</a></tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</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-136" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-136', 'data', 'link-134');">data</a></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">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="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">=</tt><tt id="link-137" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-137', 'open', 'link-137');">open</a></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="L271"></a><tt class="py-lineno">271</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-138" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.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.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-138', 'read', 'link-138');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-139', 'write', 'link-122');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">im</tt><tt class="py-op">)</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-140', 'close', 'link-140');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt><script type="text/javascript">
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