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        <a href="Bio.AlignAce-module.html">Package&nbsp;AlignAce</a> ::
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<h1 class="epydoc">Source Code for <a href="Bio.AlignAce.Parser-module.html">Module Bio.AlignAce.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 2003 by Bartek Wilczynski.  All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license.  Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">Classes for pparsing AlignAce and CompareACE files</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-1', 'ParserSupport', 'link-1');">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-2" class="py-name" targets="Module Bio.AlignAce.Scanner=Bio.AlignAce.Scanner-module.html,Module Bio.GenBank.Scanner=Bio.GenBank.Scanner-module.html"><a title="Bio.AlignAce.Scanner
Bio.GenBank.Scanner" class="py-name" href="#" onclick="return doclink('link-2', 'Scanner', 'link-2');">Scanner</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.AlignAce.Scanner.AlignAceScanner=Bio.AlignAce.Scanner.AlignAceScanner-class.html"><a title="Bio.AlignAce.Scanner.AlignAceScanner" class="py-name" href="#" onclick="return doclink('link-3', 'AlignAceScanner', 'link-3');">AlignAceScanner</a></tt><tt class="py-op">,</tt><tt id="link-4" class="py-name" targets="Class Bio.AlignAce.Scanner.CompareAceScanner=Bio.AlignAce.Scanner.CompareAceScanner-class.html"><a title="Bio.AlignAce.Scanner.CompareAceScanner" class="py-name" href="#" onclick="return doclink('link-4', 'CompareAceScanner', 'link-4');">CompareAceScanner</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-5" 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-5', 'Motif', 'link-5');">Motif</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" 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-6', 'Motif', 'link-5');">Motif</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</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-op">.</tt><tt id="link-8" 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-8', 'Alphabet', 'link-8');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" 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-9', 'IUPAC', 'link-9');">IUPAC</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'Seq', 'link-11');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-12', 'Seq', 'link-11');">Seq</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="AlignAceConsumer"></a><div id="AlignAceConsumer-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="AlignAceConsumer-toggle" onclick="return toggle('AlignAceConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html">AlignAceConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="AlignAceConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignAceConsumer-expanded"><a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    The general purpose consumer for the AlignAceScanner.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">    Should be passed as the consumer to the feed method of the AlignAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="AlignAceConsumer.__init__"></a><div id="AlignAceConsumer.__init__-def"><a name="L21"></a><tt class="py-lineno"> 21</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.__init__-toggle" onclick="return toggle('AlignAceConsumer.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-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="AlignAceConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.__init__-expanded"><a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_dict</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">     </tt>
<a name="AlignAceConsumer.parameters"></a><div id="AlignAceConsumer.parameters-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.parameters-toggle" onclick="return toggle('AlignAceConsumer.parameters');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#parameters">parameters</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="AlignAceConsumer.parameters-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.parameters-expanded"><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 class="py-name">param_dict</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"> </tt>
<a name="AlignAceConsumer.parameter"></a><div id="AlignAceConsumer.parameter-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.parameter-toggle" onclick="return toggle('AlignAceConsumer.parameter');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#parameter">parameter</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="AlignAceConsumer.parameter-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.parameter-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">        <tt class="py-name">par_name</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'split', 'link-13');">split</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-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'strip', 'link-14');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-name">par_value</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-15', 'split', 'link-13');">split</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-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'strip', 'link-14');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_dict</tt><tt class="py-op">[</tt><tt class="py-name">par_name</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">par_value</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.sequences"></a><div id="AlignAceConsumer.sequences-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.sequences-toggle" onclick="return toggle('AlignAceConsumer.sequences');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequences">sequences</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="AlignAceConsumer.sequences-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.sequences-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_dict</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.sequence"></a><div id="AlignAceConsumer.sequence-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.sequence-toggle" onclick="return toggle('AlignAceConsumer.sequence');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence">sequence</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="AlignAceConsumer.sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.sequence-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">        <tt class="py-name">seq_name</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-17', 'split', 'link-13');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_dict</tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.motif"></a><div id="AlignAceConsumer.motif-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.motif-toggle" onclick="return toggle('AlignAceConsumer.motif');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif">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="AlignAceConsumer.motif-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.motif-expanded"><a name="L42"></a><tt class="py-lineno"> 42</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-19" 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-19', 'Motif', 'link-5');">Motif</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'alphabet', 'link-21');">alphabet</a></tt><tt class="py-op">=</tt><tt id="link-22" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-22', 'IUPAC', 'link-9');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-23" 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-23', 'unambiguous_dna', 'link-23');">unambiguous_dna</a></tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.motif_hit"></a><div id="AlignAceConsumer.motif_hit-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.motif_hit-toggle" onclick="return toggle('AlignAceConsumer.motif_hit');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif_hit">motif_hit</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="AlignAceConsumer.motif_hit-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.motif_hit-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">        <tt id="link-24" 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-24', 'seq', 'link-24');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-25', 'Seq', 'link-11');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-26', 'split', 'link-13');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt id="link-27" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-27', 'IUPAC', 'link-9');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-28', 'unambiguous_dna', 'link-23');">unambiguous_dna</a></tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</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-29" 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-29', 'add_instance', 'link-29');">add_instance</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-30', 'seq', 'link-24');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.motif_score"></a><div id="AlignAceConsumer.motif_score-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.motif_score-toggle" onclick="return toggle('AlignAceConsumer.motif_score');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif_score">motif_score</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="AlignAceConsumer.motif_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.motif_score-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">current_motif</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.score()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#score,Variable Bio.expressions.blast.ncbiblast.score=Bio.expressions.blast.ncbiblast-module.html#score"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.score
Bio.expressions.blast.ncbiblast.score" class="py-name" href="#" onclick="return doclink('link-31', 'score', 'link-31');">score</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-32', 'split', 'link-13');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.motif_mask"></a><div id="AlignAceConsumer.motif_mask-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.motif_mask-toggle" onclick="return toggle('AlignAceConsumer.motif_mask');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#motif_mask">motif_mask</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="AlignAceConsumer.motif_mask-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.motif_mask-expanded"><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">current_motif</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.set_mask()=Bio.AlignAce.Motif.Motif-class.html#set_mask"><a title="Bio.AlignAce.Motif.Motif.set_mask" class="py-name" href="#" onclick="return doclink('link-33', 'set_mask', 'link-33');">set_mask</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'strip', 'link-14');">strip</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n\c"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"> </tt>
<a name="AlignAceConsumer.noevent"></a><div id="AlignAceConsumer.noevent-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.noevent-toggle" onclick="return toggle('AlignAceConsumer.noevent');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-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="AlignAceConsumer.noevent-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.noevent-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.version"></a><div id="AlignAceConsumer.version-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.version-toggle" onclick="return toggle('AlignAceConsumer.version');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-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="AlignAceConsumer.version-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.version-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ver</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">         </tt>
<a name="AlignAceConsumer.command_line"></a><div id="AlignAceConsumer.command_line-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="AlignAceConsumer.command_line-toggle" onclick="return toggle('AlignAceConsumer.command_line');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceConsumer-class.html#command_line">command_line</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="AlignAceConsumer.command_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceConsumer.command_line-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cmd_line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
</div></div><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">     </tt>
<a name="AlignAceParser"></a><div id="AlignAceParser-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="AlignAceParser-toggle" onclick="return toggle('AlignAceParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceParser-class.html">AlignAceParser</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="AlignAceParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignAceParser-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parses AlignAce data into a sequence of Motifs.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="AlignAceParser.__init__"></a><div id="AlignAceParser.__init__-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="AlignAceParser.__init__-toggle" onclick="return toggle('AlignAceParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceParser-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="AlignAceParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceParser.__init__-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-docstring">"""__init__(self)"""</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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-35" class="py-name"><a title="Bio.AlignAce.Scanner.AlignAceScanner" class="py-name" href="#" onclick="return doclink('link-35', 'AlignAceScanner', 'link-3');">AlignAceScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</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-36" class="py-name" targets="Class Bio.AlignAce.Parser.AlignAceConsumer=Bio.AlignAce.Parser.AlignAceConsumer-class.html"><a title="Bio.AlignAce.Parser.AlignAceConsumer" class="py-name" href="#" onclick="return doclink('link-36', 'AlignAceConsumer', 'link-36');">AlignAceConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="AlignAceParser.parse"></a><div id="AlignAceParser.parse-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="AlignAceParser.parse-toggle" onclick="return toggle('AlignAceParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.AlignAceParser-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="AlignAceParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignAceParser.parse-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-docstring">"""parse(self, handle)"""</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</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-37" 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-37', 'feed', 'link-37');">feed</a></tt><tt class="py-op">(</tt><tt id="link-38" 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-38', 'handle', 'link-38');">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="L76"></a><tt class="py-lineno"> 76</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 class="py-name">motifs</tt> </tt>
</div></div><a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"> </tt>
<a name="CompareAceConsumer"></a><div id="CompareAceConsumer-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="CompareAceConsumer-toggle" onclick="return toggle('CompareAceConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceConsumer-class.html">CompareAceConsumer</a><tt class="py-op">:</tt> </tt>
</div><div id="CompareAceConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CompareAceConsumer-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">    The general purpose consumer for the CompareAceScanner.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">    Should be passed as the consumer to the feed method of the CompareAceScanner. After 'consuming' the file, it has the list of motifs in the motifs property.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="CompareAceConsumer.__init__"></a><div id="CompareAceConsumer.__init__-def"><a name="L85"></a><tt class="py-lineno"> 85</tt> <a class="py-toggle" href="#" id="CompareAceConsumer.__init__-toggle" onclick="return toggle('CompareAceConsumer.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceConsumer-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="CompareAceConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompareAceConsumer.__init__-expanded"><a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-keyword">pass</tt> </tt>
</div><a name="CompareAceConsumer.motif_score"></a><div id="CompareAceConsumer.motif_score-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="CompareAceConsumer.motif_score-toggle" onclick="return toggle('CompareAceConsumer.motif_score');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceConsumer-class.html#motif_score">motif_score</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="CompareAceConsumer.motif_score-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompareAceConsumer.motif_score-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" 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-39', 'data', 'link-39');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">atof</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-40', 'split', 'link-13');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">     </tt>
<a name="CompareAceParser"></a><div id="CompareAceParser-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="CompareAceParser-toggle" onclick="return toggle('CompareAceParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceParser-class.html">CompareAceParser</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="CompareAceParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CompareAceParser-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parses CompareAce output to usable form</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">    ### so far only in a very limited way</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="CompareAceParser.__init__"></a><div id="CompareAceParser.__init__-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="CompareAceParser.__init__-toggle" onclick="return toggle('CompareAceParser.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceParser-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="CompareAceParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompareAceParser.__init__-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-docstring">"""__init__(self)"""</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</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-41" class="py-name"><a title="Bio.AlignAce.Scanner.CompareAceScanner" class="py-name" href="#" onclick="return doclink('link-41', 'CompareAceScanner', 'link-4');">CompareAceScanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name" targets="Class Bio.AlignAce.Parser.CompareAceConsumer=Bio.AlignAce.Parser.CompareAceConsumer-class.html"><a title="Bio.AlignAce.Parser.CompareAceConsumer" class="py-name" href="#" onclick="return doclink('link-42', 'CompareAceConsumer', 'link-42');">CompareAceConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"> </tt>
<a name="CompareAceParser.parse"></a><div id="CompareAceParser.parse-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="CompareAceParser.parse-toggle" onclick="return toggle('CompareAceParser.parse');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.Parser.CompareAceParser-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="CompareAceParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompareAceParser.parse-expanded"><a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-docstring">"""parse(self, handle)"""</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</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-43" 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-43', 'feed', 'link-37');">feed</a></tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-44', 'handle', 'link-38');">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="L103"></a><tt class="py-lineno">103</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-45" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-45', 'data', 'link-39');">data</a></tt> </tt>
</div></div><a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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