Sophie: biopython-doc-1.47-2mdv2008.1 x86

biopython-doc-1.47-2mdv2008.1.x86_64.rpm

<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
          "DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
  <title>Bio.MEME.Parser</title>
  <link rel="stylesheet" href="epydoc.css" type="text/css" />
  <script type="text/javascript" src="epydoc.js"></script>
</head>

<body bgcolor="white" text="black" link="blue" vlink="#204080"
      alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

      <th class="navbar" width="100%"></th>
  </tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
  <tr valign="top">
    <td width="100%">
      <span class="breadcrumbs">
        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.MEME-module.html">Package&nbsp;MEME</a> ::
        Module&nbsp;Parser
      </span>
    </td>
    <td>
      <table cellpadding="0" cellspacing="0">
        <!-- hide/show private -->
        <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
    onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
        <tr><td align="right"><span class="options"
            >[<a href="frames.html" target="_top">frames</a
            >]&nbsp;|&nbsp;<a href="Bio.MEME.Parser-pysrc.html"
            target="_top">no&nbsp;frames</a>]</span></td></tr>
      </table>
    </td>
  </tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.MEME.Parser-module.html">Module Bio.MEME.Parser</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 2004 by Jason A. Hackney.  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>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">string</tt> <tt class="py-keyword">import</tt> <tt class="py-name">join</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-2', 'IUPAC', 'link-2');">IUPAC</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-4', 'File', 'link-4');">File</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-5', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-6', 'ParserSupport', 'link-6');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" 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-8', 'Seq', 'link-8');">Seq</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Package Bio.MEME=Bio.MEME-module.html"><a title="Bio.MEME" class="py-name" href="#" onclick="return doclink('link-10', 'MEME', 'link-10');">MEME</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Module Bio.AlignAce.Motif=Bio.AlignAce.Motif-module.html,Class Bio.AlignAce.Motif.Motif=Bio.AlignAce.Motif.Motif-class.html,Module Bio.MEME.Motif=Bio.MEME.Motif-module.html,Class Bio.MEME.Motif.Motif=Bio.MEME.Motif.Motif-class.html,Module Bio.NeuralNetwork.Gene.Motif=Bio.NeuralNetwork.Gene.Motif-module.html"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-11', 'Motif', 'link-11');">Motif</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"> </tt>
<a name="MEMERecord"></a><div id="MEMERecord-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="MEMERecord-toggle" onclick="return toggle('MEMERecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMERecord-class.html">MEMERecord</a><tt class="py-op">:</tt> </tt>
</div><div id="MEMERecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MEMERecord-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-docstring">"""A class for holding the results of a MEME run.</tt> </tt>
<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 MEMERecord is an object that holds the results from running</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">    MEME. It implements no methods of its own.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="MEMERecord.__init__"></a><div id="MEMERecord.__init__-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="MEMERecord.__init__-toggle" onclick="return toggle('MEMERecord.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMERecord-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="MEMERecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MEMERecord.__init__-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-docstring">"""__init__ (self)"""</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">motifs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-12', 'version', 'link-12');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">datafile</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sequence_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">         </tt>
<a name="MEMERecord.get_motif_by_name"></a><div id="MEMERecord.get_motif_by_name-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="MEMERecord.get_motif_by_name-toggle" onclick="return toggle('MEMERecord.get_motif_by_name');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMERecord-class.html#get_motif_by_name">get_motif_by_name</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MEMERecord.get_motif_by_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MEMERecord.get_motif_by_name-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</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">if</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-14', 'name', 'link-14');">name</a></tt> <tt class="py-op">==</tt> <tt id="link-15" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-15', 'name', 'link-14');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">m</tt> </tt>
</div></div><a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"> </tt>
<a name="MEMEParser"></a><div id="MEMEParser-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="MEMEParser-toggle" onclick="return toggle('MEMEParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMEParser-class.html">MEMEParser</a> <tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MEMEParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MEMEParser-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-docstring">"""A parser for the text output of the MEME program.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">    Parses the output into an object of the MEMERecord class.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">    parse (handle): parses the contents of the file handle passed to it.</tt> </tt>
<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">    Example:</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-docstring">    f = open("meme.output.txt")</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    parser = MEMEParser()</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">    meme_record = parser.parse(f)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    for motif in meme_record.motifs:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">        for instance in motif.instances:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">            print instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="MEMEParser.__init__"></a><div id="MEMEParser.__init__-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="MEMEParser.__init__-toggle" onclick="return toggle('MEMEParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMEParser-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="MEMEParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MEMEParser.__init__-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-docstring">"""__init__ (self)"""</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class Bio.MEME.Parser._MEMEScanner=Bio.MEME.Parser._MEMEScanner-class.html"><a title="Bio.MEME.Parser._MEMEScanner" class="py-name" href="#" onclick="return doclink('link-16', '_MEMEScanner', 'link-16');">_MEMEScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Class Bio.MEME.Parser._MEMEConsumer=Bio.MEME.Parser._MEMEConsumer-class.html"><a title="Bio.MEME.Parser._MEMEConsumer" class="py-name" href="#" onclick="return doclink('link-17', '_MEMEConsumer', 'link-17');">_MEMEConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">     </tt>
<a name="MEMEParser.parse"></a><div id="MEMEParser.parse-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="MEMEParser.parse-toggle" onclick="return toggle('MEMEParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MEMEParser-class.html#parse">parse</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MEMEParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MEMEParser.parse-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">        <tt class="py-docstring">"""parse (self, handle)"""</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">_scanner</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-18', 'feed', 'link-18');">feed</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-19', 'handle', 'link-19');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</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">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'data', 'link-20');">data</a></tt> </tt>
</div></div><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">     </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="_MEMEScanner"></a><div id="_MEMEScanner-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="_MEMEScanner-toggle" onclick="return toggle('_MEMEScanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEScanner-class.html">_MEMEScanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEScanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_MEMEScanner-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-docstring">"""Scanner for MEME output. </tt> </tt>
<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">    Methods:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">    feed</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">     </tt>
<a name="_MEMEScanner.feed"></a><div id="_MEMEScanner.feed-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="_MEMEScanner.feed-toggle" onclick="return toggle('_MEMEScanner.feed');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEScanner-class.html#feed">feed</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEScanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEScanner.feed-expanded"><a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-docstring">        Feeds in MEME output for scanning. handle should</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-docstring">        implement the readline method. consumer is </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">        a Consumer object that can receive the salient events.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-21', 'handle', 'link-19');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-22', 'File', 'link-4');">File</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-23', 'UndoHandle', 'link-23');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">            <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-24', 'handle', 'link-19');">handle</a></tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-keyword">else</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">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-25', 'File', 'link-4');">File</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-26', 'UndoHandle', 'link-23');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-27', 'handle', 'link-19');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">         </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 id="link-28" class="py-name" targets="Method Bio.Blast.NCBIStandalone._Scanner._scan_header()=Bio.Blast.NCBIStandalone._Scanner-class.html#_scan_header,Method Bio.Blast.NCBIWWW._Scanner._scan_header()=Bio.Blast.NCBIWWW._Scanner-class.html#_scan_header,Method Bio.MEME.Parser._MASTScanner._scan_header()=Bio.MEME.Parser._MASTScanner-class.html#_scan_header,Method Bio.MEME.Parser._MEMEScanner._scan_header()=Bio.MEME.Parser._MEMEScanner-class.html#_scan_header,Method Bio.SwissProt.KeyWList._Scanner._scan_header()=Bio.SwissProt.KeyWList._Scanner-class.html#_scan_header"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_header
Bio.Blast.NCBIWWW._Scanner._scan_header
Bio.MEME.Parser._MASTScanner._scan_header
Bio.MEME.Parser._MEMEScanner._scan_header
Bio.SwissProt.KeyWList._Scanner._scan_header" class="py-name" href="#" onclick="return doclink('link-28', '_scan_header', 'link-28');">_scan_header</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.MEME.Parser._MEMEScanner._scan_motifs()=Bio.MEME.Parser._MEMEScanner-class.html#_scan_motifs"><a title="Bio.MEME.Parser._MEMEScanner._scan_motifs" class="py-name" href="#" onclick="return doclink('link-29', '_scan_motifs', 'link-29');">_scan_motifs</a></tt>    <tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">     </tt>
<a name="_MEMEScanner._scan_header"></a><div id="_MEMEScanner._scan_header-def"><a name="L86"></a><tt class="py-lineno"> 86</tt> <a class="py-toggle" href="#" id="_MEMEScanner._scan_header-toggle" onclick="return toggle('_MEMEScanner._scan_header');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEScanner-class.html#_scan_header">_scan_header</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEScanner._scan_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEScanner._scan_header-expanded"><a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">            <tt id="link-30" class="py-name" targets="Function Bio.ParserSupport.read_and_call_until()=Bio.ParserSupport-module.html#read_and_call_until"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-30', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.noevent()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#noevent,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#noevent,Method Bio.MEME.Parser._MASTConsumer.noevent()=Bio.MEME.Parser._MASTConsumer-class.html#noevent,Method Bio.MEME.Parser._MEMEConsumer.noevent()=Bio.MEME.Parser._MEMEConsumer-class.html#noevent"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-31', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name" targets="Method Bio.Alphabet.Alphabet.contains()=Bio.Alphabet.Alphabet-class.html#contains,Method Bio.Alphabet.AlphabetEncoder.contains()=Bio.Alphabet.AlphabetEncoder-class.html#contains,Method Bio.Alphabet.Gapped.contains()=Bio.Alphabet.Gapped-class.html#contains,Method Bio.Alphabet.HasStopCodon.contains()=Bio.Alphabet.HasStopCodon-class.html#contains,Method Bio.Pathway.Rep.HashSet.HashSet.contains()=Bio.Pathway.Rep.HashSet.HashSet-class.html#contains,Method Bio.biblio.Biblio.contains()=Bio.biblio.Biblio-class.html#contains"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-32', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MEME version'</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Improper input file. File should contain a line starting MEME version."</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt id="link-33" class="py-name" targets="Function Bio.ParserSupport.read_and_call()=Bio.ParserSupport-module.html#read_and_call"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-33', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord._version()=Bio.MEME.Parser.MASTRecord-class.html#_version,Method Bio.MEME.Parser._MASTConsumer._version()=Bio.MEME.Parser._MASTConsumer-class.html#_version,Method Bio.MEME.Parser._MEMEConsumer._version()=Bio.MEME.Parser._MEMEConsumer-class.html#_version"><a title="Bio.MEME.Parser.MASTRecord._version
Bio.MEME.Parser._MASTConsumer._version
Bio.MEME.Parser._MEMEConsumer._version" class="py-name" href="#" onclick="return doclink('link-34', '_version', 'link-34');">_version</a></tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-35', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MEME version'</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">        <tt id="link-36" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-36', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-37', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-38', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'TRAINING SET'</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt id="link-39" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-39', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-40', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-41', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'TRAINING SET'</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt id="link-42" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-42', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-43', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-44', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'****'</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt id="link-45" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-45', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.MEME.Parser._MEMEConsumer._datafile()=Bio.MEME.Parser._MEMEConsumer-class.html#_datafile"><a title="Bio.MEME.Parser._MEMEConsumer._datafile" class="py-name" href="#" onclick="return doclink('link-46', '_datafile', 'link-46');">_datafile</a></tt><tt class="py-op">,</tt> <tt id="link-47" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-47', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'DATAFILE'</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt id="link-48" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-48', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.MEME.Motif.Motif._alphabet()=Bio.MEME.Motif.Motif-class.html#_alphabet,Method Bio.MEME.Parser.MASTRecord._alphabet()=Bio.MEME.Parser.MASTRecord-class.html#_alphabet,Method Bio.MEME.Parser._MEMEConsumer._alphabet()=Bio.MEME.Parser._MEMEConsumer-class.html#_alphabet"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-49', '_alphabet', 'link-49');">_alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-50" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-50', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'ALPHABET'</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt id="link-51" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-51', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-52', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-53', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Sequence name'</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt id="link-54" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-54', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-55', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-56" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-56', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'----'</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt id="link-57" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-57', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method Bio.MEME.Parser._MEMEConsumer._sequence_name()=Bio.MEME.Parser._MEMEConsumer-class.html#_sequence_name"><a title="Bio.MEME.Parser._MEMEConsumer._sequence_name" class="py-name" href="#" onclick="return doclink('link-58', '_sequence_name', 'link-58');">_sequence_name</a></tt><tt class="py-op">,</tt> <tt id="link-59" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-59', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'***'</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt id="link-60" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-60', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-61', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-62', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'command:'</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt id="link-63" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-63', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.MEME.Parser._MEMEConsumer._commandline()=Bio.MEME.Parser._MEMEConsumer-class.html#_commandline"><a title="Bio.MEME.Parser._MEMEConsumer._commandline" class="py-name" href="#" onclick="return doclink('link-64', '_commandline', 'link-64');">_commandline</a></tt><tt class="py-op">,</tt> <tt id="link-65" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-65', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'command:'</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt id="link-66" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-66', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-67', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-68', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MOTIF  1'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">     </tt>
<a name="_MEMEScanner._scan_motifs"></a><div id="_MEMEScanner._scan_motifs-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="_MEMEScanner._scan_motifs-toggle" onclick="return toggle('_MEMEScanner._scan_motifs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEScanner-class.html#_scan_motifs">_scan_motifs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEScanner._scan_motifs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEScanner._scan_motifs-expanded"><a name="L105"></a><tt class="py-lineno">105</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="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">            <tt id="link-69" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-69', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method Bio.MEME.Parser._MEMEConsumer._add_motif_with_info()=Bio.MEME.Parser._MEMEConsumer-class.html#_add_motif_with_info"><a title="Bio.MEME.Parser._MEMEConsumer._add_motif_with_info" class="py-name" href="#" onclick="return doclink('link-70', '_add_motif_with_info', 'link-70');">_add_motif_with_info</a></tt><tt class="py-op">,</tt> <tt id="link-71" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-71', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MOTIF'</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">            <tt id="link-72" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-72', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-73', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-74" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-74', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'sorted by position p-value'</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">            <tt id="link-75" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-75', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Method Bio.MEME.Parser._MEMEConsumer.motif_name()=Bio.MEME.Parser._MEMEConsumer-class.html#motif_name"><a title="Bio.MEME.Parser._MEMEConsumer.motif_name" class="py-name" href="#" onclick="return doclink('link-76', 'motif_name', 'link-76');">motif_name</a></tt><tt class="py-op">,</tt> <tt id="link-77" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-77', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'sorted by position p-value'</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">            <tt id="link-78" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-78', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-79', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-80" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-80', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt id="link-81" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-81', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-82', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-83" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-83', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Sequence name'</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt id="link-84" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-84', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-85', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-86" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-86', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">            <tt id="link-87" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-87', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-88" 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-88', 'add_instance', 'link-88');">add_instance</a></tt><tt class="py-op">,</tt> <tt id="link-89" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-89', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">            <tt id="link-90" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-90', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-91', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-92', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'log-odds matrix'</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">            <tt id="link-93" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-93', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-94', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt id="link-95" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-95', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method Bio.MEME.Motif.MEMEMotif.add_to_logodds()=Bio.MEME.Motif.MEMEMotif-class.html#add_to_logodds,Method Bio.MEME.Parser._MEMEConsumer.add_to_logodds()=Bio.MEME.Parser._MEMEConsumer-class.html#add_to_logodds"><a title="Bio.MEME.Motif.MEMEMotif.add_to_logodds
Bio.MEME.Parser._MEMEConsumer.add_to_logodds" class="py-name" href="#" onclick="return doclink('link-96', 'add_to_logodds', 'link-96');">add_to_logodds</a></tt><tt class="py-op">,</tt> <tt id="link-97" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-97', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">            <tt id="link-98" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-98', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-99', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-100', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'letter-probability matrix'</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt id="link-101" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-101', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-102', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-103" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-103', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'letter-probability matrix'</tt><tt class="py-op">)</tt>     </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt id="link-104" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-104', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Method Bio.MEME.Motif.MEMEMotif.add_to_pssm()=Bio.MEME.Motif.MEMEMotif-class.html#add_to_pssm,Method Bio.MEME.Parser._MEMEConsumer.add_to_pssm()=Bio.MEME.Parser._MEMEConsumer-class.html#add_to_pssm"><a title="Bio.MEME.Motif.MEMEMotif.add_to_pssm
Bio.MEME.Parser._MEMEConsumer.add_to_pssm" class="py-name" href="#" onclick="return doclink('link-105', 'add_to_pssm', 'link-105');">add_to_pssm</a></tt><tt class="py-op">,</tt> <tt id="link-106" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-106', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">            <tt id="link-107" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-107', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-108', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-109" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-109', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Time'</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">            <tt id="link-110" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-110', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-111', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-112" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-112', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Time'</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">            <tt id="link-113" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-113', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-114', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-115" class="py-name" targets="Variable Bio.MetaTool.metatool_format.blank=Bio.MetaTool.metatool_format-module.html#blank"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-115', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">            <tt id="link-116" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-116', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-117', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-118" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-118', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'***'</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">            <tt id="link-119" class="py-name" targets="Function Bio.ParserSupport.read_and_call_while()=Bio.ParserSupport-module.html#read_and_call_while"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-119', 'read_and_call_while', 'link-119');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-120', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-121" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-121', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">            <tt id="link-122" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-122', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-123', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-124', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'***'</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-125" class="py-name" targets="Function Bio.ParserSupport.safe_peekline()=Bio.ParserSupport-module.html#safe_peekline"><a title="Bio.ParserSupport.safe_peekline" class="py-name" href="#" onclick="return doclink('link-125', 'safe_peekline', 'link-125');">safe_peekline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"SUMMARY OF MOTIFS"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">                <tt class="py-keyword">break</tt> </tt>
</div></div><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">     </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>
<a name="_MEMEConsumer"></a><div id="_MEMEConsumer-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="_MEMEConsumer-toggle" onclick="return toggle('_MEMEConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html">_MEMEConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_MEMEConsumer-expanded"><a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring">    Consumer that can receive events from MEME Scanner.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">    This is the Consumer object that should be passed to the </tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring">    MEME Scanner.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.__init__"></a><div id="_MEMEConsumer.__init__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.__init__-toggle" onclick="return toggle('_MEMEConsumer.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-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="_MEMEConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.__init__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sequence_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-126', 'data', 'link-20');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-127" class="py-name" targets="Class Bio.MEME.Parser.MEMERecord=Bio.MEME.Parser.MEMERecord-class.html"><a title="Bio.MEME.Parser.MEMERecord" class="py-name" href="#" onclick="return doclink('link-127', 'MEMERecord', 'link-127');">MEMERecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._version"></a><div id="_MEMEConsumer._version-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._version-toggle" onclick="return toggle('_MEMEConsumer._version');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_version">_version</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._version-expanded"><a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-128" 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-128', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-129', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-130', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-131', 'version', 'link-12');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._datafile"></a><div id="_MEMEConsumer._datafile-def"><a name="L149"></a><tt class="py-lineno">149</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._datafile-toggle" onclick="return toggle('_MEMEConsumer._datafile');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_datafile">_datafile</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._datafile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._datafile-expanded"><a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-132" 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-132', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'DATAFILE= '</tt><tt class="py-op">,</tt><tt class="py-string">''</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">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-133', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">datafile</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._alphabet"></a><div id="_MEMEConsumer._alphabet-def"><a name="L154"></a><tt class="py-lineno">154</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._alphabet-toggle" onclick="return toggle('_MEMEConsumer._alphabet');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_alphabet">_alphabet</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._alphabet-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._alphabet-expanded"><a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-134" 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-134', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'ALPHABET= '</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">'ACGT'</tt><tt class="py-op">:</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">            <tt class="py-name">al</tt> <tt class="py-op">=</tt> <tt id="link-135" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-135', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-136" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_dna=Bio.Alphabet.IUPAC-module.html#unambiguous_dna"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-136', 'unambiguous_dna', 'link-136');">unambiguous_dna</a></tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">            <tt class="py-name">al</tt> <tt class="py-op">=</tt> <tt id="link-137" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-137', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Variable Bio.Alphabet.IUPAC.protein=Bio.Alphabet.IUPAC-module.html#protein"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-138', 'protein', 'link-138');">protein</a></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-139', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-140', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">al</tt> </tt>
</div><a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._sequence_name"></a><div id="_MEMEConsumer._sequence_name-def"><a name="L163"></a><tt class="py-lineno">163</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._sequence_name-toggle" onclick="return toggle('_MEMEConsumer._sequence_name');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_sequence_name">_sequence_name</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._sequence_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._sequence_name-expanded"><a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-141" 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-141', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-142', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-143', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">sequence_names</tt><tt class="py-op">.</tt><tt id="link-144" 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-144', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">6</tt><tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-145', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">sequence_names</tt><tt class="py-op">.</tt><tt id="link-146" 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-146', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._commandline"></a><div id="_MEMEConsumer._commandline-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._commandline-toggle" onclick="return toggle('_MEMEConsumer._commandline');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_commandline">_commandline</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._commandline-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._commandline-expanded"><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-147" 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-147', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'command: '</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-148" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-148', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer._add_motif_with_info"></a><div id="_MEMEConsumer._add_motif_with_info-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_MEMEConsumer._add_motif_with_info-toggle" onclick="return toggle('_MEMEConsumer._add_motif_with_info');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#_add_motif_with_info">_add_motif_with_info</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer._add_motif_with_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer._add_motif_with_info-expanded"><a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-149" 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-149', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-150', 'split', 'link-129');">split</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 id="link-151" 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-151', 'motif', 'link-151');">motif</a></tt> <tt class="py-op">=</tt> <tt id="link-152" class="py-name"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-152', 'Motif', 'link-11');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Class Bio.MEME.Motif.MEMEMotif=Bio.MEME.Motif.MEMEMotif-class.html"><a title="Bio.MEME.Motif.MEMEMotif" class="py-name" href="#" onclick="return doclink('link-153', 'MEMEMotif', 'link-153');">MEMEMotif</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt id="link-154" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-154', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-155" class="py-name" targets="Method Bio.MEME.Motif.Instance._length()=Bio.MEME.Motif.Instance-class.html#_length,Method Bio.MEME.Motif.Motif._length()=Bio.MEME.Motif.Motif-class.html#_length"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-155', '_length', 'link-155');">_length</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">4</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 id="link-156" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-156', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-157" class="py-name" targets="Method Bio.MEME.Motif.Motif._numoccurrences()=Bio.MEME.Motif.Motif-class.html#_numoccurrences"><a title="Bio.MEME.Motif.Motif._numoccurrences" class="py-name" href="#" onclick="return doclink('link-157', '_numoccurrences', 'link-157');">_numoccurrences</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt id="link-158" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-158', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-159" class="py-name" targets="Method Bio.MEME.Motif.MEMEMotif._evalue()=Bio.MEME.Motif.MEMEMotif-class.html#_evalue"><a title="Bio.MEME.Motif.MEMEMotif._evalue" class="py-name" href="#" onclick="return doclink('link-159', '_evalue', 'link-159');">_evalue</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">13</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt id="link-160" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-160', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-161', '_alphabet', 'link-49');">_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-162', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-163" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-163', 'alphabet', 'link-13');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-164', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">.</tt><tt id="link-165" 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-165', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt id="link-166" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-166', 'motif', 'link-151');">motif</a></tt><tt class="py-op">)</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt> <tt class="py-op">=</tt> <tt id="link-167" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-167', 'motif', 'link-151');">motif</a></tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.motif_name"></a><div id="_MEMEConsumer.motif_name-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.motif_name-toggle" onclick="return toggle('_MEMEConsumer.motif_name');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#motif_name">motif_name</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer.motif_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.motif_name-expanded"><a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-168" 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-168', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-169', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt id="link-170" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-170', 'name', 'link-14');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name" targets="Method Bio.KEGG.Compound.Record._name()=Bio.KEGG.Compound.Record-class.html#_name,Method Bio.KEGG.Enzyme.Record._name()=Bio.KEGG.Enzyme.Record-class.html#_name,Method Bio.MEME.Motif.Motif._name()=Bio.MEME.Motif.Motif-class.html#_name,Variable Bio.Mindy.XPath._name=Bio.Mindy.XPath-module.html#_name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-171', '_name', 'link-171');">_name</a></tt><tt class="py-op">(</tt><tt id="link-172" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-172', 'name', 'link-14');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.add_instance"></a><div id="_MEMEConsumer.add_instance-def"><a name="L192"></a><tt class="py-lineno">192</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.add_instance-toggle" onclick="return toggle('_MEMEConsumer.add_instance');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-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">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer.add_instance-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.add_instance-expanded"><a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-173" 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-173', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-174', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</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-175" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-175', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">command</tt><tt class="py-op">.</tt><tt id="link-176" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-176', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'revcomp'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">            <tt id="link-177" 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-177', 'seq', 'link-177');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-178" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-178', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-179', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">5</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-180" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-180', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-181', 'alphabet', 'link-13');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name" targets="Method Bio.MEME.Motif.MEMEMotif.add_instance_from_values()=Bio.MEME.Motif.MEMEMotif-class.html#add_instance_from_values"><a title="Bio.MEME.Motif.MEMEMotif.add_instance_from_values" class="py-name" href="#" onclick="return doclink('link-182', 'add_instance_from_values', 'link-182');">add_instance_from_values</a></tt><tt class="py-op">(</tt><tt id="link-183" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-183', 'name', 'link-14');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-184" 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-184', 'sequence', 'link-184');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-185" 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-185', 'seq', 'link-177');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-186" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-186', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">pvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-187" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.strand()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#strand,Variable Bio.expressions.blast.ncbiblast.strand=Bio.expressions.blast.ncbiblast-module.html#strand"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-187', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</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="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">            <tt id="link-188" 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-188', 'seq', 'link-177');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-189', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-190', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">4</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-191" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-191', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-192', 'alphabet', 'link-13');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.MEME.Motif.MEMEMotif.add_instance_from_values" class="py-name" href="#" onclick="return doclink('link-193', 'add_instance_from_values', 'link-182');">add_instance_from_values</a></tt><tt class="py-op">(</tt><tt id="link-194" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-194', 'name', 'link-14');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-195" 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-195', 'sequence', 'link-184');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-196" 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-196', 'seq', 'link-177');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-197" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-197', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">pvalue</tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.add_to_pssm"></a><div id="_MEMEConsumer.add_to_pssm-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.add_to_pssm-toggle" onclick="return toggle('_MEMEConsumer.add_to_pssm');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#add_to_pssm">add_to_pssm</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer.add_to_pssm-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.add_to_pssm-expanded"><a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-198" 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-198', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">        <tt class="py-name">sl</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-199', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-name">thisposition</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-200" 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-200', 'i', 'link-200');">i</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-201" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-201', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">sl</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.MEME.Motif.MEMEMotif.add_to_pssm
Bio.MEME.Parser._MEMEConsumer.add_to_pssm" class="py-name" href="#" onclick="return doclink('link-202', 'add_to_pssm', 'link-105');">add_to_pssm</a></tt><tt class="py-op">(</tt><tt class="py-name">thisposition</tt><tt class="py-op">)</tt> </tt>
</div><a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.add_to_logodds"></a><div id="_MEMEConsumer.add_to_logodds-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.add_to_logodds-toggle" onclick="return toggle('_MEMEConsumer.add_to_logodds');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#add_to_logodds">add_to_logodds</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer.add_to_logodds-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.add_to_logodds-expanded"><a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-203" 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-203', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">        <tt class="py-name">sl</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-204', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt class="py-name">thisposition</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-205" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-205', 'i', 'link-200');">i</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-206" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-206', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">sl</tt><tt class="py-op">]</tt><tt class="py-op">)</tt>     </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.MEME.Motif.MEMEMotif.add_to_logodds
Bio.MEME.Parser._MEMEConsumer.add_to_logodds" class="py-name" href="#" onclick="return doclink('link-207', 'add_to_logodds', 'link-96');">add_to_logodds</a></tt><tt class="py-op">(</tt><tt class="py-name">thisposition</tt><tt class="py-op">)</tt> </tt>
</div><a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">     </tt>
<a name="_MEMEConsumer.noevent"></a><div id="_MEMEConsumer.noevent-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="_MEMEConsumer.noevent-toggle" onclick="return toggle('_MEMEConsumer.noevent');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MEMEConsumer-class.html#noevent">noevent</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MEMEConsumer.noevent-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MEMEConsumer.noevent-expanded"><a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div></div><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>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line"> </tt>
<a name="_MASTConsumer"></a><div id="_MASTConsumer-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="_MASTConsumer-toggle" onclick="return toggle('_MASTConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html">_MASTConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_MASTConsumer-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">    Consumer that can receive events from _MASTScanner.</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">    A _MASTConsumer parses lines from a mast text output file.</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line"><tt class="py-docstring">    The motif match diagrams are parsed using line buffering. </tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"><tt class="py-docstring">    Each of the buffering functions have a dummy variable that is</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line"><tt class="py-docstring">    required for testing using the Bio.ParserSupport.TaggingConsumer.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line"><tt class="py-docstring">    If this variable isn't there, the TaggingConsumer barfs. In</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"><tt class="py-docstring">    the _MASTScanner, None is passed in the place of this variable.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="_MASTConsumer.__init__"></a><div id="_MASTConsumer.__init__-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="_MASTConsumer.__init__-toggle" onclick="return toggle('_MASTConsumer.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-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="_MASTConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer.__init__-expanded"><a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-208', 'data', 'link-20');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-209" class="py-name" targets="Class Bio.MEME.Parser.MASTRecord=Bio.MEME.Parser.MASTRecord-class.html"><a title="Bio.MEME.Parser.MASTRecord" class="py-name" href="#" onclick="return doclink('link-209', 'MASTRecord', 'link-209');">MASTRecord</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffered_seq_start</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._version"></a><div id="_MASTConsumer._version-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="_MASTConsumer._version-toggle" onclick="return toggle('_MASTConsumer._version');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_version">_version</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._version-expanded"><a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-210" 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-210', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-211', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-212', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._version
Bio.MEME.Parser._MASTConsumer._version
Bio.MEME.Parser._MEMEConsumer._version" class="py-name" href="#" onclick="return doclink('link-213', '_version', 'link-34');">_version</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._database"></a><div id="_MASTConsumer._database-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="_MASTConsumer._database-toggle" onclick="return toggle('_MASTConsumer._database');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_database">_database</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._database-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._database-expanded"><a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-214" 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-214', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-215', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-216', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-217" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord._database()=Bio.MEME.Parser.MASTRecord-class.html#_database,Method Bio.MEME.Parser._MASTConsumer._database()=Bio.MEME.Parser._MASTConsumer-class.html#_database"><a title="Bio.MEME.Parser.MASTRecord._database
Bio.MEME.Parser._MASTConsumer._database" class="py-name" href="#" onclick="return doclink('link-217', '_database', 'link-217');">_database</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</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="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">        <tt class="py-name">al</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'(nucleotide)'</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">            <tt class="py-name">al</tt> <tt class="py-op">=</tt> <tt id="link-218" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-218', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-219', 'unambiguous_dna', 'link-136');">unambiguous_dna</a></tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-220', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-221', '_alphabet', 'link-49');">_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">al</tt><tt class="py-op">)</tt>         </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">            <tt class="py-name">al</tt> <tt class="py-op">=</tt> <tt id="link-222" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-222', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-223', 'protein', 'link-138');">protein</a></tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-224', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-225" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-225', '_alphabet', 'link-49');">_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">al</tt><tt class="py-op">)</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">         </tt>
<a name="_MASTConsumer._add_motif"></a><div id="_MASTConsumer._add_motif-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_motif-toggle" onclick="return toggle('_MASTConsumer._add_motif');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_motif">_add_motif</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_motif-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_motif-expanded"><a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-226" 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-226', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-227" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-227', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-228" class="py-name"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-228', 'Motif', 'link-11');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.MEME.Motif.MEMEMotif" class="py-name" href="#" onclick="return doclink('link-229', 'MEMEMotif', 'link-153');">MEMEMotif</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">        <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Bio.MEME.Motif.Motif._alphabet
Bio.MEME.Parser.MASTRecord._alphabet
Bio.MEME.Parser._MEMEConsumer._alphabet" class="py-name" href="#" onclick="return doclink('link-230', '_alphabet', 'link-49');">_alphabet</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-231" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-231', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-232', 'alphabet', 'link-13');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-233', '_length', 'link-155');">_length</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</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="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">        <tt id="link-234" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-234', 'name', 'link-14');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">        <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-235', '_name', 'link-171');">_name</a></tt><tt class="py-op">(</tt><tt id="link-236" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-236', 'name', 'link-14');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">        <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name" targets="Method Bio.MEME.Motif.Motif._consensus()=Bio.MEME.Motif.Motif-class.html#_consensus"><a title="Bio.MEME.Motif.Motif._consensus" class="py-name" href="#" onclick="return doclink('link-237', '_consensus', 'link-237');">_consensus</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-238', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-239" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord._add_motif()=Bio.MEME.Parser.MASTRecord-class.html#_add_motif,Method Bio.MEME.Parser._MASTConsumer._add_motif()=Bio.MEME.Parser._MASTConsumer-class.html#_add_motif,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder._add_motif()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#_add_motif"><a title="Bio.MEME.Parser.MASTRecord._add_motif
Bio.MEME.Parser._MASTConsumer._add_motif
Bio.NeuralNetwork.Gene.Motif.MotifFinder._add_motif" class="py-name" href="#" onclick="return doclink('link-239', '_add_motif', 'link-239');">_add_motif</a></tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">)</tt> </tt>
</div><a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._add_match_diagram"></a><div id="_MASTConsumer._add_match_diagram-def"><a name="L265"></a><tt class="py-lineno">265</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_match_diagram-toggle" onclick="return toggle('_MASTConsumer._add_match_diagram');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_match_diagram">_add_match_diagram</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_match_diagram-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_match_diagram-expanded"><a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-240" 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-240', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-241', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-242', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-243" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord._add_diagram_for_sequence()=Bio.MEME.Parser.MASTRecord-class.html#_add_diagram_for_sequence"><a title="Bio.MEME.Parser.MASTRecord._add_diagram_for_sequence" class="py-name" href="#" onclick="return doclink('link-243', '_add_diagram_for_sequence', 'link-243');">_add_diagram_for_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt id="link-244" class="py-name" targets="Method Bio.Sequencing.Ace._RecordConsumer.ds()=Bio.Sequencing.Ace._RecordConsumer-class.html#ds,Class Bio.Sequencing.Ace.ds=Bio.Sequencing.Ace.ds-class.html"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-244', 'ds', 'link-244');">ds</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-245', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'_'</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt id="link-246" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-246', 'i', 'link-200');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt id="link-247" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-247', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-248" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-248', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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-249" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-249', 'ds', 'link-244');">ds</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-250" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-250', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-251" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-251', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-252', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'['</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt id="link-253" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-253', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-254" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-254', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-255', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'&lt;'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</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">inst</tt> <tt class="py-op">=</tt> <tt id="link-256" class="py-name"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-256', 'Motif', 'link-11');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-257" class="py-name" targets="Class Bio.MEME.Motif.Instance=Bio.MEME.Motif.Instance-class.html"><a title="Bio.MEME.Motif.Instance" class="py-name" href="#" onclick="return doclink('link-257', 'Instance', 'link-257');">Instance</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name" targets="Method Bio.MEME.Motif.Instance._seqname()=Bio.MEME.Motif.Instance-class.html#_seqname"><a title="Bio.MEME.Motif.Instance._seqname" class="py-name" href="#" onclick="return doclink('link-258', '_seqname', 'link-258');">_seqname</a></tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name" targets="Method Bio.MEME.Motif.Instance._start()=Bio.MEME.Motif.Instance-class.html#_start"><a title="Bio.MEME.Motif.Instance._start" class="py-name" href="#" onclick="return doclink('link-259', '_start', 'link-259');">_start</a></tt> <tt class="py-op">(</tt><tt id="link-260" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-260', 'start', 'link-35');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line">                <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-261', 'compile', 'link-261');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">'\d+'</tt><tt class="py-op">)</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">                <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt id="link-262" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-262', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-263" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-263', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-264" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-264', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-265" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-265', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-266" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-266', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-267', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-268', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'+'</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">                <tt id="link-269" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-269', 'motif', 'link-151');">motif</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-270', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-271" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord.get_motif_by_name()=Bio.MEME.Parser.MASTRecord-class.html#get_motif_by_name,Method Bio.MEME.Parser.MEMERecord.get_motif_by_name()=Bio.MEME.Parser.MEMERecord-class.html#get_motif_by_name"><a title="Bio.MEME.Parser.MASTRecord.get_motif_by_name
Bio.MEME.Parser.MEMERecord.get_motif_by_name" class="py-name" href="#" onclick="return doclink('link-271', 'get_motif_by_name', 'link-271');">get_motif_by_name</a></tt><tt class="py-op">(</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">                <tt id="link-272" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-272', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><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-273', 'add_instance', 'link-88');">add_instance</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">                <tt id="link-274" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-274', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt id="link-275" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-275', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-276" 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-276', 'length', 'link-276');">length</a></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">                <tt id="link-277" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-277', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-278" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-278', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-279" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-279', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt>             </tt>
</div><a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._add_sequence_match_with_diagram"></a><div id="_MASTConsumer._add_sequence_match_with_diagram-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_sequence_match_with_diagram-toggle" onclick="return toggle('_MASTConsumer._add_sequence_match_with_diagram');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_sequence_match_with_diagram">_add_sequence_match_with_diagram</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_sequence_match_with_diagram-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_sequence_match_with_diagram-expanded"><a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-280" 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-280', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-281', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-282', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-283" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord._add_sequence()=Bio.MEME.Parser.MASTRecord-class.html#_add_sequence"><a title="Bio.MEME.Parser.MASTRecord._add_sequence" class="py-name" href="#" onclick="return doclink('link-283', '_add_sequence', 'link-283');">_add_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-284', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._add_diagram_for_sequence" class="py-name" href="#" onclick="return doclink('link-285', '_add_diagram_for_sequence', 'link-243');">_add_diagram_for_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">        <tt id="link-286" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-286', 'ds', 'link-244');">ds</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-287', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'_'</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">        <tt id="link-288" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-288', 'i', 'link-200');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">        <tt id="link-289" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-289', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-290" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-290', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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-291" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-291', 'ds', 'link-244');">ds</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-292" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-292', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-293" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-293', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-294', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'+'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt id="link-295" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-295', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-296" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-296', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-297', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">                <tt class="py-name">inst</tt> <tt class="py-op">=</tt> <tt id="link-298" class="py-name"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-298', 'Motif', 'link-11');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.MEME.Motif.Instance" class="py-name" href="#" onclick="return doclink('link-299', 'Instance', 'link-257');">Instance</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.MEME.Motif.Instance._seqname" class="py-name" href="#" onclick="return doclink('link-300', '_seqname', 'link-258');">_seqname</a></tt> <tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-301" class="py-name"><a title="Bio.MEME.Motif.Instance._start" class="py-name" href="#" onclick="return doclink('link-301', '_start', 'link-259');">_start</a></tt> <tt class="py-op">(</tt><tt id="link-302" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-302', 'start', 'link-35');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">                <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-303" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-303', 'compile', 'link-261');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">'\d+'</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">                <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt id="link-304" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-304', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-305" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-305', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-306" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-306', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-307" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-307', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-308', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-309" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-309', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-310', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'+'</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">                <tt id="link-311" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-311', 'motif', 'link-151');">motif</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-312', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-313" class="py-name"><a title="Bio.MEME.Parser.MASTRecord.get_motif_by_name
Bio.MEME.Parser.MEMERecord.get_motif_by_name" class="py-name" href="#" onclick="return doclink('link-313', 'get_motif_by_name', 'link-271');">get_motif_by_name</a></tt><tt class="py-op">(</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">                <tt id="link-314" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-314', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><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-315', 'add_instance', 'link-88');">add_instance</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line">                <tt id="link-316" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-316', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt id="link-317" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-317', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-318" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-318', 'length', 'link-276');">length</a></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">                <tt id="link-319" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-319', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-320" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-320', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-321" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-321', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt>             </tt>
</div><a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._add_diagram_from_buffer"></a><div id="_MASTConsumer._add_diagram_from_buffer-def"><a name="L314"></a><tt class="py-lineno">314</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_diagram_from_buffer-toggle" onclick="return toggle('_MASTConsumer._add_diagram_from_buffer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_diagram_from_buffer">_add_diagram_from_buffer</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dummy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_diagram_from_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_diagram_from_buffer-expanded"><a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">            <tt class="py-name">line</tt> <tt class="py-op">+=</tt> <tt class="py-name">l</tt><tt class="py-op">.</tt><tt id="link-322" 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-322', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt class="py-name">ls</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-323" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-323', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-324" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-324', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-325" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._add_diagram_for_sequence" class="py-name" href="#" onclick="return doclink('link-325', '_add_diagram_for_sequence', 'link-243');">_add_diagram_for_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">        <tt id="link-326" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-326', 'ds', 'link-244');">ds</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ls</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-327" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-327', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'_'</tt><tt class="py-op">)</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt id="link-328" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-328', 'i', 'link-200');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">        <tt id="link-329" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-329', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt id="link-330" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-330', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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-331" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-331', 'ds', 'link-244');">ds</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-332" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-332', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-333" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-333', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-334', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'['</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt id="link-335" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-335', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-336" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-336', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-337" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-337', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'&lt;'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line">                <tt class="py-name">inst</tt> <tt class="py-op">=</tt> <tt id="link-338" class="py-name"><a title="Bio.AlignAce.Motif
Bio.AlignAce.Motif.Motif
Bio.MEME.Motif
Bio.MEME.Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-338', 'Motif', 'link-11');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-339" class="py-name"><a title="Bio.MEME.Motif.Instance" class="py-name" href="#" onclick="return doclink('link-339', 'Instance', 'link-257');">Instance</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-340" class="py-name"><a title="Bio.MEME.Motif.Instance._seqname" class="py-name" href="#" onclick="return doclink('link-340', '_seqname', 'link-258');">_seqname</a></tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-341" class="py-name"><a title="Bio.MEME.Motif.Instance._start" class="py-name" href="#" onclick="return doclink('link-341', '_start', 'link-259');">_start</a></tt> <tt class="py-op">(</tt><tt id="link-342" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-342', 'start', 'link-35');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">                <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-343" class="py-name"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-343', 'compile', 'link-261');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">'\d+'</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">                <tt class="py-name">mn</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt id="link-344" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-344', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-345" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-345', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-346" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-346', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-347" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-347', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-348" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-348', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'-'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-349" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-349', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-350" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-350', 'strand', 'link-187');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'+'</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">                <tt id="link-351" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-351', 'motif', 'link-151');">motif</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-352" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-352', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-353" class="py-name"><a title="Bio.MEME.Parser.MASTRecord.get_motif_by_name
Bio.MEME.Parser.MEMERecord.get_motif_by_name" class="py-name" href="#" onclick="return doclink('link-353', 'get_motif_by_name', 'link-271');">get_motif_by_name</a></tt><tt class="py-op">(</tt><tt class="py-name">mn</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">                <tt id="link-354" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-354', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-355" class="py-name"><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-355', 'add_instance', 'link-88');">add_instance</a></tt><tt class="py-op">(</tt><tt class="py-name">inst</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">                <tt id="link-356" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-356', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt id="link-357" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-357', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-358" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-358', 'length', 'link-276');">length</a></tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">                <tt id="link-359" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-359', 'start', 'link-35');">start</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-360" class="py-name"><a title="Bio.Sequencing.Ace._RecordConsumer.ds
Bio.Sequencing.Ace.ds" class="py-name" href="#" onclick="return doclink('link-360', 'ds', 'link-244');">ds</a></tt><tt class="py-op">[</tt><tt id="link-361" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-361', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt>             </tt>
</div><a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._set_current_seq"></a><div id="_MASTConsumer._set_current_seq-def"><a name="L340"></a><tt class="py-lineno">340</tt> <a class="py-toggle" href="#" id="_MASTConsumer._set_current_seq-toggle" onclick="return toggle('_MASTConsumer._set_current_seq');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_set_current_seq">_set_current_seq</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._set_current_seq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._set_current_seq-expanded"><a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-362" 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-362', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-363" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-363', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-364" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequences()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequences"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-364', 'sequences', 'link-364');">sequences</a></tt><tt class="py-op">.</tt><tt id="link-365" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-365', 'count', 'link-365');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-366" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-366', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-367" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-367', 'sequences', 'link-364');">sequences</a></tt><tt class="py-op">.</tt><tt id="link-368" 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-368', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._add_line_to_buffer"></a><div id="_MASTConsumer._add_line_to_buffer-def"><a name="L346"></a><tt class="py-lineno">346</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_line_to_buffer-toggle" onclick="return toggle('_MASTConsumer._add_line_to_buffer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_line_to_buffer">_add_line_to_buffer</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_line_to_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_line_to_buffer-expanded"><a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-369" 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-369', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'*****'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">.</tt><tt id="link-370" 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-370', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
</div><a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._parse_buffer"></a><div id="_MASTConsumer._parse_buffer-def"><a name="L353"></a><tt class="py-lineno">353</tt> <a class="py-toggle" href="#" id="_MASTConsumer._parse_buffer-toggle" onclick="return toggle('_MASTConsumer._parse_buffer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_parse_buffer">_parse_buffer</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dummy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._parse_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._parse_buffer-expanded"><a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">        <tt class="py-docstring">"""Parses the line buffer to get e-values for each instance of a motif.</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line"><tt class="py-docstring">        This buffer parser is the most likely point of failure for the </tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line"><tt class="py-docstring">        MASTParser.</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">        <tt class="py-name">insts</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-371" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-371', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-372" class="py-name" targets="Method Bio.MEME.Parser.MASTRecord.get_motif_matches_for_sequence()=Bio.MEME.Parser.MASTRecord-class.html#get_motif_matches_for_sequence"><a title="Bio.MEME.Parser.MASTRecord.get_motif_matches_for_sequence" class="py-name" href="#" onclick="return doclink('link-372', 'get_motif_matches_for_sequence', 'link-372');">get_motif_matches_for_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">)</tt>     </tt>
<a name="L359"></a><tt class="py-lineno">359</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">insts</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">             </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">            <tt class="py-name">fullSeq</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">            <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-373" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-373', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">            <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">            <tt class="py-name">lpval</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pvals</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">p</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">lpval</tt><tt class="py-op">:</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-374" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-374', 'count', 'link-365');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'e'</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">                <tt class="py-comment">#Break blocks up by e and parse into valid floats. This only </tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line"><tt class="py-comment"></tt>                <tt class="py-comment">#works if there are no e-values greater than 1e-5.</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line"><tt class="py-comment"></tt>                    <tt class="py-name">pvs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">                    <tt class="py-name">spe</tt> <tt class="py-op">=</tt> <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-375" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-375', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'e'</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">                    <tt class="py-name">spe</tt><tt class="py-op">.</tt><tt id="link-376" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-376', 'reverse', 'link-376');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">                    <tt class="py-name">dotind</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-377" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-377', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">dotind</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">                        <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">                        <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">dotind</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">                    <tt class="py-name">pvs</tt><tt class="py-op">.</tt><tt id="link-378" 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-378', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">thispval</tt><tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">                    <tt class="py-keyword">for</tt> <tt class="py-name">spi</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">spe</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">                        <tt class="py-name">dotind</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-379', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">                        <tt class="py-name">prevdotind</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-380" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-380', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">                        <tt class="py-keyword">if</tt> <tt class="py-name">dotind</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">                            <tt class="py-keyword">if</tt> <tt class="py-name">prevdotind</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">                                <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">dotind</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">                            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">                                <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">dotind</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">prevdotind</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">                        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">                            <tt class="py-keyword">if</tt> <tt class="py-name">prevdotind</tt> <tt class="py-op">==</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">                                <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">                            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">                                <tt class="py-name">thispval</tt> <tt class="py-op">=</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">'e'</tt> <tt class="py-op">+</tt> <tt class="py-name">spe</tt><tt class="py-op">[</tt><tt class="py-name">spi</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">prevdotind</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">                        <tt class="py-name">pvs</tt><tt class="py-op">.</tt><tt id="link-381" 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-381', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">thispval</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">                    <tt class="py-name">pvs</tt><tt class="py-op">.</tt><tt id="link-382" class="py-name"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-382', 'reverse', 'link-376');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">                    <tt class="py-keyword">if</tt> <tt class="py-name">p</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">                        <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">pvs</tt> <tt class="py-op">+</tt> <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-name">p</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="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line">                    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line">                        <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-name">pvs</tt> <tt class="py-op">+</tt> <tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt class="py-name">p</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="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line">                    <tt class="py-name">lpval</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pvals</tt><tt class="py-op">)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">                <tt class="py-name">p</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">            <tt id="link-383" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-383', 'i', 'link-200');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">pvals</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">insts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line">                <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt id="link-384" 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
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-384', 'write', 'link-384');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"Failure to parse p-values for "</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt> <tt class="py-op">+</tt>  <tt class="py-string">":  "</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">" to: "</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">pvals</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">                <tt class="py-name">pvals</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line"><tt class="py-comment">#            else:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#                sys.stderr.write('These are just fine' + self._current_seq + ': ' + self._line_buffer[1] + " to: " + str(pvals) + "\n")</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">for</tt> <tt id="link-385" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-385', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</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 class="py-name">insts</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">                <tt class="py-name">inst</tt> <tt class="py-op">=</tt> <tt class="py-name">insts</tt><tt class="py-op">[</tt><tt id="link-386" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-386', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line">                <tt id="link-387" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-387', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-388" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-388', 'start', 'link-35');">start</a></tt> <tt class="py-op">-</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffered_seq_start</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line">                <tt class="py-name">thisSeq</tt> <tt class="py-op">=</tt> <tt class="py-name">fullSeq</tt><tt class="py-op">[</tt><tt id="link-389" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-389', 'start', 'link-35');">start</a></tt><tt class="py-op">:</tt><tt id="link-390" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-390', 'start', 'link-35');">start</a></tt><tt class="py-op">+</tt><tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-391" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-391', 'length', 'link-276');">length</a></tt><tt class="py-op">]</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">                <tt class="py-name">thisSeq</tt> <tt class="py-op">=</tt> <tt id="link-392" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-392', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">.</tt><tt id="link-393" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-393', 'Seq', 'link-8');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">thisSeq</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-394" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-394', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-395" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-395', 'alphabet', 'link-13');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">                <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-396" class="py-name" targets="Method Bio.MEME.Motif.Instance._sequence()=Bio.MEME.Motif.Instance-class.html#_sequence"><a title="Bio.MEME.Motif.Instance._sequence" class="py-name" href="#" onclick="return doclink('link-396', '_sequence', 'link-396');">_sequence</a></tt><tt class="py-op">(</tt><tt class="py-name">thisSeq</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">pvals</tt><tt class="py-op">:</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">                    <tt class="py-name">inst</tt><tt class="py-op">.</tt><tt id="link-397" class="py-name" targets="Method Bio.MEME.Motif.Instance._pvalue()=Bio.MEME.Motif.Instance-class.html#_pvalue"><a title="Bio.MEME.Motif.Instance._pvalue" class="py-name" href="#" onclick="return doclink('link-397', '_pvalue', 'link-397');">_pvalue</a></tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">pvals</tt><tt class="py-op">[</tt><tt id="link-398" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-398', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L413"></a><tt class="py-lineno">413</tt>  <tt class="py-line"> </tt>
<a name="_MASTConsumer._blank_buffer"></a><div id="_MASTConsumer._blank_buffer-def"><a name="L414"></a><tt class="py-lineno">414</tt> <a class="py-toggle" href="#" id="_MASTConsumer._blank_buffer-toggle" onclick="return toggle('_MASTConsumer._blank_buffer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_blank_buffer">_blank_buffer</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dummy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._blank_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._blank_buffer-expanded"><a name="L415"></a><tt class="py-lineno">415</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._collapse_buffer"></a><div id="_MASTConsumer._collapse_buffer-def"><a name="L418"></a><tt class="py-lineno">418</tt> <a class="py-toggle" href="#" id="_MASTConsumer._collapse_buffer-toggle" onclick="return toggle('_MASTConsumer._collapse_buffer');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_collapse_buffer">_collapse_buffer</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dummy</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._collapse_buffer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._collapse_buffer-expanded"><a name="L419"></a><tt class="py-lineno">419</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">_buffer_size</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</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">_line_buffer</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt>  <tt class="py-line">                <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-399" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-399', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffered_seq_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">            <tt id="link-400" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-400', 'i', 'link-200');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-401" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-401', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</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">_line_buffer</tt><tt class="py-op">)</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="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">                    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt id="link-402" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-402', 'i', 'link-200');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt id="link-403" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-403', 'i', 'link-200');">i</a></tt><tt class="py-op">-</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt id="link-404" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-404', 'i', 'link-200');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-405" 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-405', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">            <tt class="py-name">ll</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</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">_line_buffer</tt><tt class="py-op">)</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-406" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-406', 'split', 'link-129');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffered_seq_start</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">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">                <tt class="py-name">differ</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffered_seq_start</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">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-string">"N"</tt><tt class="py-op">*</tt><tt class="py-name">differ</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">ll</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_line_buffer</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt><tt class="py-op">]</tt> </tt>
</div><a name="L437"></a><tt class="py-lineno">437</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer._add_motif_match"></a><div id="_MASTConsumer._add_motif_match-def"><a name="L438"></a><tt class="py-lineno">438</tt> <a class="py-toggle" href="#" id="_MASTConsumer._add_motif_match-toggle" onclick="return toggle('_MASTConsumer._add_motif_match');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#_add_motif_match">_add_motif_match</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer._add_motif_match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer._add_motif_match-expanded"><a name="L439"></a><tt class="py-lineno">439</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-407" 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-407', 'strip', 'link-128');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-408" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-408', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'['</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-409" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-409', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'&lt;'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-410" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-410', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'e'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-411" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-411', 'find', 'link-176');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'+'</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
</div><a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">     </tt>
<a name="_MASTConsumer.noevent"></a><div id="_MASTConsumer.noevent-def"><a name="L447"></a><tt class="py-lineno">447</tt> <a class="py-toggle" href="#" id="_MASTConsumer.noevent-toggle" onclick="return toggle('_MASTConsumer.noevent');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTConsumer-class.html#noevent">noevent</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTConsumer.noevent-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTConsumer.noevent-expanded"><a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line">     </tt>
<a name="L450"></a><tt class="py-lineno">450</tt>  <tt class="py-line"> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt>  <tt class="py-line"> </tt>
<a name="MASTParser"></a><div id="MASTParser-def"><a name="L452"></a><tt class="py-lineno">452</tt> <a class="py-toggle" href="#" id="MASTParser-toggle" onclick="return toggle('MASTParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTParser-class.html">MASTParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MASTParser-expanded"><a name="L453"></a><tt class="py-lineno">453</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt>  <tt class="py-line"><tt class="py-docstring">    Parser for MAST text output. HTML output cannot be parsed, yet. Returns a MASTRecord</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt>  <tt class="py-line"><tt class="py-docstring">    A MASTParser takes a file handle for a MAST text output file and </tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt>  <tt class="py-line"><tt class="py-docstring">    returns a MASTRecord, containing the hits between motifs and </tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt>  <tt class="py-line"><tt class="py-docstring">    sequences. The parser does some unusual line buffering to parse out </tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt>  <tt class="py-line"><tt class="py-docstring">    match diagrams. Really complex diagrams often lead to an error message </tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt>  <tt class="py-line"><tt class="py-docstring">    and p-values not being parsed for a given line.</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt>  <tt class="py-line"><tt class="py-docstring">    parse (handle): parses the data from the file handle passed to it.</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt>  <tt class="py-line"><tt class="py-docstring">    Example:</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt>  <tt class="py-line"><tt class="py-docstring">    f = open("mast_file.txt")</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt>  <tt class="py-line"><tt class="py-docstring">    parser = MASTParser()</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt>  <tt class="py-line"><tt class="py-docstring">    mast_record = parser.parse(f)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt>  <tt class="py-line"><tt class="py-docstring">    for motif in mast_record.motifs:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt>  <tt class="py-line"><tt class="py-docstring">        for instance in motif.instances:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt>  <tt class="py-line"><tt class="py-docstring">            print instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="MASTParser.__init__"></a><div id="MASTParser.__init__-def"><a name="L474"></a><tt class="py-lineno">474</tt> <a class="py-toggle" href="#" id="MASTParser.__init__-toggle" onclick="return toggle('MASTParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTParser-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="MASTParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTParser.__init__-expanded"><a name="L475"></a><tt class="py-lineno">475</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-412" class="py-name" targets="Class Bio.MEME.Parser._MASTConsumer=Bio.MEME.Parser._MASTConsumer-class.html"><a title="Bio.MEME.Parser._MASTConsumer" class="py-name" href="#" onclick="return doclink('link-412', '_MASTConsumer', 'link-412');">_MASTConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-413" class="py-name" targets="Class Bio.MEME.Parser._MASTScanner=Bio.MEME.Parser._MASTScanner-class.html"><a title="Bio.MEME.Parser._MASTScanner" class="py-name" href="#" onclick="return doclink('link-413', '_MASTScanner', 'link-413');">_MASTScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L477"></a><tt class="py-lineno">477</tt>  <tt class="py-line">     </tt>
<a name="MASTParser.parse"></a><div id="MASTParser.parse-def"><a name="L478"></a><tt class="py-lineno">478</tt> <a class="py-toggle" href="#" id="MASTParser.parse-toggle" onclick="return toggle('MASTParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTParser-class.html#parse">parse</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTParser.parse-expanded"><a name="L479"></a><tt class="py-lineno">479</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-414" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-414', 'feed', 'link-18');">feed</a></tt><tt class="py-op">(</tt><tt id="link-415" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-415', 'handle', 'link-19');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</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">_consumer</tt><tt class="py-op">.</tt><tt id="link-416" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-416', 'data', 'link-20');">data</a></tt> </tt>
</div></div><a name="L481"></a><tt class="py-lineno">481</tt>  <tt class="py-line">     </tt>
<a name="L482"></a><tt class="py-lineno">482</tt>  <tt class="py-line"> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt>  <tt class="py-line"> </tt>
<a name="_MASTScanner"></a><div id="_MASTScanner-def"><a name="L484"></a><tt class="py-lineno">484</tt> <a class="py-toggle" href="#" id="_MASTScanner-toggle" onclick="return toggle('_MASTScanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTScanner-class.html">_MASTScanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_MASTScanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_MASTScanner-expanded"><a name="L485"></a><tt class="py-lineno">485</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt>  <tt class="py-line"><tt class="py-docstring">    Scanner for MAST text output. </tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt>  <tt class="py-line"><tt class="py-docstring">        </tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="_MASTScanner.feed"></a><div id="_MASTScanner.feed-def"><a name="L489"></a><tt class="py-lineno">489</tt> <a class="py-toggle" href="#" id="_MASTScanner.feed-toggle" onclick="return toggle('_MASTScanner.feed');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTScanner-class.html#feed">feed</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTScanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTScanner.feed-expanded"><a name="L490"></a><tt class="py-lineno">490</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-417" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-417', 'handle', 'link-19');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-418" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-418', 'File', 'link-4');">File</a></tt><tt class="py-op">.</tt><tt id="link-419" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-419', 'UndoHandle', 'link-23');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt>  <tt class="py-line">            <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-420" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-420', 'handle', 'link-19');">handle</a></tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt>  <tt class="py-line">            <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-421" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-421', 'File', 'link-4');">File</a></tt><tt class="py-op">.</tt><tt id="link-422" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-422', 'UndoHandle', 'link-23');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-423" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-423', 'handle', 'link-19');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt>  <tt class="py-line">             </tt>
<a name="L495"></a><tt class="py-lineno">495</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-424" class="py-name"><a title="Bio.Blast.NCBIStandalone._Scanner._scan_header
Bio.Blast.NCBIWWW._Scanner._scan_header
Bio.MEME.Parser._MASTScanner._scan_header
Bio.MEME.Parser._MEMEScanner._scan_header
Bio.SwissProt.KeyWList._Scanner._scan_header" class="py-name" href="#" onclick="return doclink('link-424', '_scan_header', 'link-28');">_scan_header</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-425" class="py-name" targets="Method Bio.MEME.Parser._MASTScanner._scan_matches()=Bio.MEME.Parser._MASTScanner-class.html#_scan_matches"><a title="Bio.MEME.Parser._MASTScanner._scan_matches" class="py-name" href="#" onclick="return doclink('link-425', '_scan_matches', 'link-425');">_scan_matches</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-426" class="py-name" targets="Method Bio.MEME.Parser._MASTScanner._scan_annotated_matches()=Bio.MEME.Parser._MASTScanner-class.html#_scan_annotated_matches"><a title="Bio.MEME.Parser._MASTScanner._scan_annotated_matches" class="py-name" href="#" onclick="return doclink('link-426', '_scan_annotated_matches', 'link-426');">_scan_annotated_matches</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L498"></a><tt class="py-lineno">498</tt>  <tt class="py-line">     </tt>
<a name="_MASTScanner._scan_header"></a><div id="_MASTScanner._scan_header-def"><a name="L499"></a><tt class="py-lineno">499</tt> <a class="py-toggle" href="#" id="_MASTScanner._scan_header-toggle" onclick="return toggle('_MASTScanner._scan_header');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTScanner-class.html#_scan_header">_scan_header</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTScanner._scan_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTScanner._scan_header-expanded"><a name="L500"></a><tt class="py-lineno">500</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt>  <tt class="py-line">            <tt id="link-427" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-427', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-428" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-428', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-429" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-429', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"MAST version"</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Improper input file. Does not begin with a line with 'MAST version'"</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt>  <tt class="py-line">        <tt id="link-430" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-430', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-431" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._version
Bio.MEME.Parser._MASTConsumer._version
Bio.MEME.Parser._MEMEConsumer._version" class="py-name" href="#" onclick="return doclink('link-431', '_version', 'link-34');">_version</a></tt><tt class="py-op">,</tt> <tt id="link-432" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-432', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MAST version'</tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt>  <tt class="py-line">        <tt id="link-433" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-433', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-434" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-434', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-435" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-435', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'DATABASE AND MOTIFS'</tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt>  <tt class="py-line">        <tt id="link-436" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-436', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-437" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-437', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-438" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-438', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'DATABASE'</tt><tt class="py-op">)</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt>  <tt class="py-line">        <tt id="link-439" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-439', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-440" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-440', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-441" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-441', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'****'</tt><tt class="py-op">)</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt>  <tt class="py-line">        <tt id="link-442" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-442', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-443" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._database
Bio.MEME.Parser._MASTConsumer._database" class="py-name" href="#" onclick="return doclink('link-443', '_database', 'link-217');">_database</a></tt><tt class="py-op">,</tt> <tt id="link-444" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-444', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'DATABASE'</tt><tt class="py-op">)</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt>  <tt class="py-line">        <tt id="link-445" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-445', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-446" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-446', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-447" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-447', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MOTIF WIDTH'</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt>  <tt class="py-line">        <tt id="link-448" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-448', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-449" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-449', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-450" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-450', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'MOTIF'</tt><tt class="py-op">)</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt>  <tt class="py-line">        <tt id="link-451" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-451', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-452" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-452', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-453" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-453', 'contains', 'link-32');">contains</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'----'</tt><tt class="py-op">)</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt>  <tt class="py-line">        <tt id="link-454" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-454', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-455" class="py-name"><a title="Bio.MEME.Parser.MASTRecord._add_motif
Bio.MEME.Parser._MASTConsumer._add_motif
Bio.NeuralNetwork.Gene.Motif.MotifFinder._add_motif" class="py-name" href="#" onclick="return doclink('link-455', '_add_motif', 'link-239');">_add_motif</a></tt><tt class="py-op">,</tt> <tt id="link-456" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-456', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt>  <tt class="py-line">        <tt id="link-457" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-457', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-458" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-458', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-459" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-459', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SECTION II:'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L514"></a><tt class="py-lineno">514</tt>  <tt class="py-line">     </tt>
<a name="_MASTScanner._scan_matches"></a><div id="_MASTScanner._scan_matches-def"><a name="L515"></a><tt class="py-lineno">515</tt> <a class="py-toggle" href="#" id="_MASTScanner._scan_matches-toggle" onclick="return toggle('_MASTScanner._scan_matches');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTScanner-class.html#_scan_matches">_scan_matches</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTScanner._scan_matches-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTScanner._scan_matches-expanded"><a name="L516"></a><tt class="py-lineno">516</tt>  <tt class="py-line">        <tt id="link-460" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-460', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-461" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-461', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-462" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-462', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SEQUENCE NAME'</tt><tt class="py-op">)</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt>  <tt class="py-line">        <tt id="link-463" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-463', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-464" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-464', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-465" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-465', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SEQUENCE NAME'</tt><tt class="py-op">)</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt>  <tt class="py-line">        <tt id="link-466" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-466', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-467" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-467', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-468" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-468', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'---'</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt>  <tt class="py-line"><tt class="py-comment">#        read_and_call_until(uhandle, consumer._add_sequence_match_with_diagram, blank = 1)</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt id="link-469" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-469', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-470" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-470', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-471" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-471', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt>  <tt class="py-line">        <tt id="link-472" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-472', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-473" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-473', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-474" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-474', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L522"></a><tt class="py-lineno">522</tt>  <tt class="py-line">     </tt>
<a name="_MASTScanner._scan_annotated_matches"></a><div id="_MASTScanner._scan_annotated_matches-def"><a name="L523"></a><tt class="py-lineno">523</tt> <a class="py-toggle" href="#" id="_MASTScanner._scan_annotated_matches-toggle" onclick="return toggle('_MASTScanner._scan_annotated_matches');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser._MASTScanner-class.html#_scan_annotated_matches">_scan_annotated_matches</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_MASTScanner._scan_annotated_matches-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_MASTScanner._scan_annotated_matches-expanded"><a name="L524"></a><tt class="py-lineno">524</tt>  <tt class="py-line">        <tt id="link-475" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-475', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-476" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-476', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-477" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-477', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SECTION III:'</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt>  <tt class="py-line">        <tt id="link-478" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-478', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-479" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-479', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-480" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-480', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'SECTION III:'</tt><tt class="py-op">)</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt>  <tt class="py-line">        <tt id="link-481" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-481', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-482" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-482', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-483" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-483', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'****'</tt><tt class="py-op">)</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt>  <tt class="py-line">        <tt id="link-484" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-484', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-485" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-485', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-486" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-486', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'****'</tt><tt class="py-op">)</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt>  <tt class="py-line">        <tt id="link-487" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-487', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-488" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-488', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-489" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-489', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'*****'</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt>  <tt class="py-line">        <tt id="link-490" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-490', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-491" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-491', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt>  <tt class="py-line">        <tt id="link-492" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-492', 'read_and_call_while', 'link-119');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-493" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-493', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-494" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-494', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt>  <tt class="py-line">        <tt class="py-name">readMatches</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">readMatches</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">_current_seq</tt><tt class="py-op">:</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt class="py-name">_buffer_size</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt>  <tt class="py-line">                    <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-495" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._parse_buffer()=Bio.MEME.Parser._MASTConsumer-class.html#_parse_buffer"><a title="Bio.MEME.Parser._MASTConsumer._parse_buffer" class="py-name" href="#" onclick="return doclink('link-495', '_parse_buffer', 'link-495');">_parse_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt>  <tt class="py-line">                <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-496" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._blank_buffer()=Bio.MEME.Parser._MASTConsumer-class.html#_blank_buffer"><a title="Bio.MEME.Parser._MASTConsumer._blank_buffer" class="py-name" href="#" onclick="return doclink('link-496', '_blank_buffer', 'link-496');">_blank_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt>  <tt class="py-line">            <tt id="link-497" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-497', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-498" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._set_current_seq()=Bio.MEME.Parser._MASTConsumer-class.html#_set_current_seq"><a title="Bio.MEME.Parser._MASTConsumer._set_current_seq" class="py-name" href="#" onclick="return doclink('link-498', '_set_current_seq', 'link-498');">_set_current_seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt>  <tt class="py-line">            <tt id="link-499" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-499', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-500" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-500', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-501" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-501', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'  DIAGRAM'</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt>  <tt class="py-line">            <tt id="link-502" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-502', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-503" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._add_line_to_buffer()=Bio.MEME.Parser._MASTConsumer-class.html#_add_line_to_buffer"><a title="Bio.MEME.Parser._MASTConsumer._add_line_to_buffer" class="py-name" href="#" onclick="return doclink('link-503', '_add_line_to_buffer', 'link-503');">_add_line_to_buffer</a></tt><tt class="py-op">,</tt> <tt id="link-504" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-504', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt>  <tt class="py-line">            <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-505" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._add_diagram_from_buffer()=Bio.MEME.Parser._MASTConsumer-class.html#_add_diagram_from_buffer"><a title="Bio.MEME.Parser._MASTConsumer._add_diagram_from_buffer" class="py-name" href="#" onclick="return doclink('link-505', '_add_diagram_from_buffer', 'link-505');">_add_diagram_from_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt>  <tt class="py-line">            <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-506" class="py-name"><a title="Bio.MEME.Parser._MASTConsumer._blank_buffer" class="py-name" href="#" onclick="return doclink('link-506', '_blank_buffer', 'link-496');">_blank_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt>  <tt class="py-line">            <tt id="link-507" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-507', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-508" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-508', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-509" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-509', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</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="L544"></a><tt class="py-lineno">544</tt>  <tt class="py-line">                <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-510" class="py-name"><a title="Bio.ParserSupport.safe_peekline" class="py-name" href="#" onclick="return doclink('link-510', 'safe_peekline', 'link-125');">safe_peekline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'****'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt>  <tt class="py-line">                    <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-511" class="py-name"><a title="Bio.MEME.Parser._MASTConsumer._parse_buffer" class="py-name" href="#" onclick="return doclink('link-511', '_parse_buffer', 'link-495');">_parse_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt>  <tt class="py-line">                    <tt class="py-name">readMatches</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt>  <tt class="py-line">                <tt id="link-512" class="py-name"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-512', 'read_and_call_until', 'link-30');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-513" class="py-name"><a title="Bio.MEME.Parser._MASTConsumer._add_line_to_buffer" class="py-name" href="#" onclick="return doclink('link-513', '_add_line_to_buffer', 'link-503');">_add_line_to_buffer</a></tt><tt class="py-op">,</tt> <tt id="link-514" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-514', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt>  <tt class="py-line">                <tt id="link-515" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-515', 'read_and_call', 'link-33');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-516" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-516', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-517" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-517', 'blank', 'link-115');">blank</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt>  <tt class="py-line">                <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-518" class="py-name" targets="Method Bio.MEME.Parser._MASTConsumer._collapse_buffer()=Bio.MEME.Parser._MASTConsumer-class.html#_collapse_buffer"><a title="Bio.MEME.Parser._MASTConsumer._collapse_buffer" class="py-name" href="#" onclick="return doclink('link-518', '_collapse_buffer', 'link-518');">_collapse_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-519" class="py-name" targets="Function Bio.ParserSupport.attempt_read_and_call()=Bio.ParserSupport-module.html#attempt_read_and_call"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-519', 'attempt_read_and_call', 'link-519');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-520" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-520', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-521" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-521', 'blank', 'link-115');">blank</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="L553"></a><tt class="py-lineno">553</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt>  <tt class="py-line">                <tt class="py-keyword">elif</tt> <tt id="link-522" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-522', 'attempt_read_and_call', 'link-519');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-523" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-523', 'noevent', 'link-31');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-524" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-524', 'start', 'link-35');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'*****'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt>  <tt class="py-line">                    <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-525" class="py-name"><a title="Bio.MEME.Parser._MASTConsumer._parse_buffer" class="py-name" href="#" onclick="return doclink('link-525', '_parse_buffer', 'link-495');">_parse_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt>  <tt class="py-line">                    <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-526" class="py-name"><a title="Bio.MEME.Parser._MASTConsumer._blank_buffer" class="py-name" href="#" onclick="return doclink('link-526', '_blank_buffer', 'link-496');">_blank_buffer</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt>  <tt class="py-line">                    <tt class="py-name">readMatches</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt>  <tt class="py-line">                    <tt class="py-keyword">break</tt> </tt>
</div></div><a name="L559"></a><tt class="py-lineno">559</tt>  <tt class="py-line">     </tt>
<a name="L560"></a><tt class="py-lineno">560</tt>  <tt class="py-line"> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt>  <tt class="py-line"> </tt>
<a name="MASTRecord"></a><div id="MASTRecord-def"><a name="L562"></a><tt class="py-lineno">562</tt> <a class="py-toggle" href="#" id="MASTRecord-toggle" onclick="return toggle('MASTRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html">MASTRecord</a><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MASTRecord-expanded"><a name="L563"></a><tt class="py-lineno">563</tt>  <tt class="py-line">    <tt class="py-docstring">"""The class for holding the results from a MAST run.</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt>  <tt class="py-line"><tt class="py-docstring">    A MASTRecord holds data about matches between motifs and sequences.</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt>  <tt class="py-line"><tt class="py-docstring">    The motifs held by the MASTRecord are objects of the class MEMEMotif.</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt>  <tt class="py-line"><tt class="py-docstring">    Methods:</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt>  <tt class="py-line"><tt class="py-docstring">    get_motif_matches_for_sequence(sequence_name): returns all of the</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt>  <tt class="py-line"><tt class="py-docstring">        motif matches within a given sequence. The matches are objects of</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt>  <tt class="py-line"><tt class="py-docstring">        the class MEME.Motif.Instance</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt>  <tt class="py-line"><tt class="py-docstring">    get_motif_matches (motif_name): returns all of the matches for a motif</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt>  <tt class="py-line"><tt class="py-docstring">        in the sequences searched. The matches returned are of class </tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt>  <tt class="py-line"><tt class="py-docstring">        MEME.Motif.Instance</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt>  <tt class="py-line"><tt class="py-docstring">    get_motif_by_name (motif_name): returns a MEMEMotif with the given</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt>  <tt class="py-line"><tt class="py-docstring">        name.</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="MASTRecord.__init__"></a><div id="MASTRecord.__init__-def"><a name="L578"></a><tt class="py-lineno">578</tt> <a class="py-toggle" href="#" id="MASTRecord.__init__-toggle" onclick="return toggle('MASTRecord.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-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="MASTRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord.__init__-expanded"><a name="L579"></a><tt class="py-lineno">579</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-527" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-527', 'sequences', 'link-364');">sequences</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-528" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-528', 'version', 'link-12');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-529" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database()=Bio.Blast.NCBIStandalone._DatabaseReportConsumer-class.html#database"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-529', 'database', 'link-529');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">diagrams</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-530" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-530', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L586"></a><tt class="py-lineno">586</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._version"></a><div id="MASTRecord._version-def"><a name="L587"></a><tt class="py-lineno">587</tt> <a class="py-toggle" href="#" id="MASTRecord._version-toggle" onclick="return toggle('MASTRecord._version');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_version">_version</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">version</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord._version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._version-expanded"><a name="L588"></a><tt class="py-lineno">588</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-531" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-531', 'version', 'link-12');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-532" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-532', 'version', 'link-12');">version</a></tt> </tt>
</div><a name="L589"></a><tt class="py-lineno">589</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._alphabet"></a><div id="MASTRecord._alphabet-def"><a name="L590"></a><tt class="py-lineno">590</tt> <a class="py-toggle" href="#" id="MASTRecord._alphabet-toggle" onclick="return toggle('MASTRecord._alphabet');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_alphabet">_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="MASTRecord._alphabet-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._alphabet-expanded"><a name="L591"></a><tt class="py-lineno">591</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-533" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-533', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">==</tt> <tt id="link-534" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-534', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-535" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-535', 'protein', 'link-138');">protein</a></tt> <tt class="py-keyword">or</tt> <tt id="link-536" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-536', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">==</tt> <tt id="link-537" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-537', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-538" class="py-name" targets="Variable Bio.Alphabet.IUPAC.ambiguous_dna=Bio.Alphabet.IUPAC-module.html#ambiguous_dna"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-538', 'ambiguous_dna', 'link-538');">ambiguous_dna</a></tt> <tt class="py-keyword">or</tt> <tt id="link-539" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-539', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">==</tt> <tt id="link-540" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-540', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-541" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-541', 'unambiguous_dna', 'link-136');">unambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-542" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-542', 'alphabet', 'link-13');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-543" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-543', 'alphabet', 'link-13');">alphabet</a></tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
</div><a name="L595"></a><tt class="py-lineno">595</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._database"></a><div id="MASTRecord._database-def"><a name="L596"></a><tt class="py-lineno">596</tt> <a class="py-toggle" href="#" id="MASTRecord._database-toggle" onclick="return toggle('MASTRecord._database');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_database">_database</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">database</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord._database-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._database-expanded"><a name="L597"></a><tt class="py-lineno">597</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-544" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-544', 'database', 'link-529');">database</a></tt> <tt class="py-op">=</tt> <tt id="link-545" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-545', 'database', 'link-529');">database</a></tt> </tt>
</div><a name="L598"></a><tt class="py-lineno">598</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord.get_motif_matches_for_sequence"></a><div id="MASTRecord.get_motif_matches_for_sequence-def"><a name="L599"></a><tt class="py-lineno">599</tt> <a class="py-toggle" href="#" id="MASTRecord.get_motif_matches_for_sequence-toggle" onclick="return toggle('MASTRecord.get_motif_matches_for_sequence');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#get_motif_matches_for_sequence">get_motif_matches_for_sequence</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord.get_motif_matches_for_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord.get_motif_matches_for_sequence-expanded"><a name="L600"></a><tt class="py-lineno">600</tt>  <tt class="py-line">        <tt class="py-name">insts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">:</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-546" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-546', 'i', 'link-200');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt><tt class="py-op">:</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt id="link-547" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-547', 'i', 'link-200');">i</a></tt><tt class="py-op">.</tt><tt id="link-548" class="py-name" targets="Method Bio.NBRF._RecordConsumer.sequence_name()=Bio.NBRF._RecordConsumer-class.html#sequence_name"><a title="Bio.NBRF._RecordConsumer.sequence_name" class="py-name" href="#" onclick="return doclink('link-548', 'sequence_name', 'link-548');">sequence_name</a></tt> <tt class="py-op">==</tt> <tt id="link-549" 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-549', 'seq', 'link-177');">seq</a></tt><tt class="py-op">:</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt>  <tt class="py-line">                    <tt class="py-name">insts</tt><tt class="py-op">.</tt><tt id="link-550" 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-550', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt id="link-551" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-551', 'i', 'link-200');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt>  <tt class="py-line">        <tt class="py-name">insts</tt><tt class="py-op">.</tt><tt id="link-552" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-552', 'sort', 'link-552');">sort</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-553" 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-553', 'x', 'link-553');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-554" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-554', 'x', 'link-553');">x</a></tt><tt class="py-op">.</tt><tt id="link-555" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-555', 'start', 'link-35');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">.</tt><tt id="link-556" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-556', 'start', 'link-35');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">insts</tt> </tt>
</div><a name="L607"></a><tt class="py-lineno">607</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord.get_motif_matches"></a><div id="MASTRecord.get_motif_matches-def"><a name="L608"></a><tt class="py-lineno">608</tt> <a class="py-toggle" href="#" id="MASTRecord.get_motif_matches-toggle" onclick="return toggle('MASTRecord.get_motif_matches');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#get_motif_matches">get_motif_matches</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-op">:</tt> </tt>
</div><div id="MASTRecord.get_motif_matches-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord.get_motif_matches-expanded"><a name="L609"></a><tt class="py-lineno">609</tt>  <tt class="py-line">        <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-557" class="py-name"><a title="Bio.MEME.Parser.MASTRecord.get_motif_by_name
Bio.MEME.Parser.MEMERecord.get_motif_by_name" class="py-name" href="#" onclick="return doclink('link-557', 'get_motif_by_name', 'link-271');">get_motif_by_name</a></tt> <tt class="py-op">(</tt><tt id="link-558" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-558', 'motif', 'link-151');">motif</a></tt><tt class="py-op">.</tt><tt id="link-559" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-559', 'name', 'link-14');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt class="py-name">instances</tt> </tt>
</div><a name="L611"></a><tt class="py-lineno">611</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._add_diagram_for_sequence"></a><div id="MASTRecord._add_diagram_for_sequence-def"><a name="L612"></a><tt class="py-lineno">612</tt> <a class="py-toggle" href="#" id="MASTRecord._add_diagram_for_sequence-toggle" onclick="return toggle('MASTRecord._add_diagram_for_sequence');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_add_diagram_for_sequence">_add_diagram_for_sequence</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">diagram</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord._add_diagram_for_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._add_diagram_for_sequence-expanded"><a name="L613"></a><tt class="py-lineno">613</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">diagrams</tt><tt class="py-op">[</tt><tt id="link-560" 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-560', 'seq', 'link-177');">seq</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">diagram</tt> </tt>
</div><a name="L614"></a><tt class="py-lineno">614</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._add_match"></a><div id="MASTRecord._add_match-def"><a name="L615"></a><tt class="py-lineno">615</tt> <a class="py-toggle" href="#" id="MASTRecord._add_match-toggle" onclick="return toggle('MASTRecord._add_match');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_add_match">_add_match</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">match</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord._add_match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._add_match-expanded"><a name="L616"></a><tt class="py-lineno">616</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">matches</tt><tt class="py-op">.</tt><tt id="link-561" 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-561', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt id="link-562" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-562', 'match', 'link-562');">match</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L617"></a><tt class="py-lineno">617</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._add_sequence"></a><div id="MASTRecord._add_sequence-def"><a name="L618"></a><tt class="py-lineno">618</tt> <a class="py-toggle" href="#" id="MASTRecord._add_sequence-toggle" onclick="return toggle('MASTRecord._add_sequence');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_add_sequence">_add_sequence</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="MASTRecord._add_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._add_sequence-expanded"><a name="L619"></a><tt class="py-lineno">619</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-563" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-563', 'sequences', 'link-364');">sequences</a></tt><tt class="py-op">.</tt><tt id="link-564" 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-564', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt id="link-565" 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-565', 'sequence', 'link-184');">sequence</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L620"></a><tt class="py-lineno">620</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord._add_motif"></a><div id="MASTRecord._add_motif-def"><a name="L621"></a><tt class="py-lineno">621</tt> <a class="py-toggle" href="#" id="MASTRecord._add_motif-toggle" onclick="return toggle('MASTRecord._add_motif');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#_add_motif">_add_motif</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-op">:</tt> </tt>
</div><div id="MASTRecord._add_motif-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord._add_motif-expanded"><a name="L622"></a><tt class="py-lineno">622</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">.</tt><tt id="link-566" 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-566', 'append', 'link-144');">append</a></tt><tt class="py-op">(</tt><tt id="link-567" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.motif" class="py-name" href="#" onclick="return doclink('link-567', 'motif', 'link-151');">motif</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L623"></a><tt class="py-lineno">623</tt>  <tt class="py-line">     </tt>
<a name="MASTRecord.get_motif_by_name"></a><div id="MASTRecord.get_motif_by_name-def"><a name="L624"></a><tt class="py-lineno">624</tt> <a class="py-toggle" href="#" id="MASTRecord.get_motif_by_name-toggle" onclick="return toggle('MASTRecord.get_motif_by_name');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.MEME.Parser.MASTRecord-class.html#get_motif_by_name">get_motif_by_name</a> <tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MASTRecord.get_motif_by_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MASTRecord.get_motif_by_name-expanded"><a name="L625"></a><tt class="py-lineno">625</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">:</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-568" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-568', 'name', 'link-14');">name</a></tt> <tt class="py-op">==</tt> <tt id="link-569" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-569', 'name', 'link-14');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt>  <tt class="py-line">                <tt class="py-keyword">return</tt> <tt class="py-name">m</tt> </tt>
</div></div><a name="L628"></a><tt class="py-lineno">628</tt>  <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
       bgcolor="#a0c0ff" cellspacing="0">
  <tr valign="middle">

  <!-- Tree link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Index link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>

  <!-- Help link -->
      <th>&nbsp;&nbsp;&nbsp;<a
        href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>

      <th class="navbar" width="100%"></th>
  </tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
  <tr>
    <td align="left" class="footer">
    Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:49 2008
    </td>
    <td align="right" class="footer">
      <a target="mainFrame" href="http://epydoc.sourceforge.net"
        >http://epydoc.sourceforge.net</a>
    </td>
  </tr>
</table>

<script type="text/javascript">
  <!--
  // Private objects are initially displayed (because if
  // javascript is turned off then we want them to be
  // visible); but by default, we want to hide them.  So hide
  // them unless we have a cookie that says to show them.
  checkCookie();
  // -->
</script>
</body>
</html>