<?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.Motif.Parsers.MAST</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> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </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 Bio</a> ::
<a href="Bio.Motif-module.html">Package Motif</a> ::
<a href="Bio.Motif.Parsers-module.html">Package Parsers</a> ::
Module MAST
</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 private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.Motif.Parsers.MAST-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Motif.Parsers.MAST-module.html">Module Bio.Motif.Parsers.MAST</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 2008 by Bartek Wilczynski.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Adapted from Bio.MEME.Parser by Jason A. Hackney. All rights reserved.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </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-op">.</tt><tt id="link-4" class="py-name" targets="Package Bio.Motif=Bio.Motif-module.html,Class Bio.Motif._Motif.Motif=Bio.Motif._Motif.Motif-class.html,Module Bio.NeuralNetwork.Gene.Motif=Bio.NeuralNetwork.Gene.Motif-module.html"><a title="Bio.Motif
Bio.Motif._Motif.Motif
Bio.NeuralNetwork.Gene.Motif" class="py-name" href="#" onclick="return doclink('link-4', 'Motif', 'link-4');">Motif</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.Motif.Parsers=Bio.Motif.Parsers-module.html,Package Bio.Parsers=Bio.Parsers-module.html"><a title="Bio.Motif.Parsers
Bio.Parsers" class="py-name" href="#" onclick="return doclink('link-5', 'Parsers', 'link-5');">Parsers</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Module Bio.Motif.Parsers.MEME=Bio.Motif.Parsers.MEME-module.html"><a title="Bio.Motif.Parsers.MEME" class="py-name" href="#" onclick="return doclink('link-6', 'MEME', 'link-6');">MEME</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Class Bio.Motif.Parsers.MEME.MEMEMotif=Bio.Motif.Parsers.MEME.MEMEMotif-class.html"><a title="Bio.Motif.Parsers.MEME.MEMEMotif" class="py-name" href="#" onclick="return doclink('link-7', 'MEMEMotif', 'link-7');">MEMEMotif</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L11"></a><tt class="py-lineno"> 11</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST.Record-class.html">Record</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-docstring">"""The class for holding the results from a MAST run.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> A MAST.Record holds data about matches between motifs and sequences.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> The motifs held by the Record are objects of the class MEMEMotif.</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"> Methods:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</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="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> name.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST.Record-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="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><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">sequences</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-8" class="py-name" targets="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"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-8', 'version', 'link-8');">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 id="link-9" 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-9', 'database', 'link-9');">database</a></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">diagrams</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</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 class="py-name">alphabet</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">motifs</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="Record.get_motif_by_name"></a><div id="Record.get_motif_by_name-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="Record.get_motif_by_name-toggle" onclick="return toggle('Record.get_motif_by_name');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST.Record-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="Record.get_motif_by_name-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.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-10" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-10');">name</a></tt> <tt class="py-op">==</tt> <tt id="link-11" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-10');">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="read"></a><div id="read-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="read-toggle" onclick="return toggle('read');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#read">read</a><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="read-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="read-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""read(handle)"""</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">record</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Class Bio.Affy.CelFile.Record=Bio.Affy.CelFile.Record-class.html,Module Bio.Blast.Record=Bio.Blast.Record-module.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Class Bio.Emboss.Primer3.Record=Bio.Emboss.Primer3.Record-class.html,Class Bio.ExPASy.Enzyme.Record=Bio.ExPASy.Enzyme.Record-class.html,Class Bio.ExPASy.Prodoc.Record=Bio.ExPASy.Prodoc.Record-class.html,Class Bio.ExPASy.Prosite.Record=Bio.ExPASy.Prosite.Record-class.html,Class Bio.ExPASy.ScanProsite.Record=Bio.ExPASy.ScanProsite.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Class Bio.Motif.Parsers.AlignAce.Record=Bio.Motif.Parsers.AlignAce.Record-class.html,Class Bio.Motif.Parsers.MAST.Record=Bio.Motif.Parsers.MAST.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.LargeFileParser.Record=Bio.PopGen.GenePop.LargeFileParser.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.Record=Bio.SwissProt.Record-class.html,Class Bio.UniGene.Record=Bio.UniGene.Record-class.html"><a title="Bio.Affy.CelFile.Record
Bio.Blast.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.Emboss.Primer3.Record
Bio.ExPASy.Enzyme.Record
Bio.ExPASy.Prodoc.Record
Bio.ExPASy.Prosite.Record
Bio.ExPASy.ScanProsite.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.Medline.Record
Bio.Motif.Parsers.AlignAce.Record
Bio.Motif.Parsers.MAST.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.LargeFileParser.Record
Bio.PopGen.GenePop.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.Record
Bio.UniGene.Record" class="py-name" href="#" onclick="return doclink('link-12', 'Record', 'link-12');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt id="link-13" class="py-name" targets="Function Bio.Motif.Parsers.MAST.__read_version()=Bio.Motif.Parsers.MAST-module.html#__read_version,Function Bio.Motif.Parsers.MEME.__read_version()=Bio.Motif.Parsers.MEME-module.html#__read_version"><a title="Bio.Motif.Parsers.MAST.__read_version
Bio.Motif.Parsers.MEME.__read_version" class="py-name" href="#" onclick="return doclink('link-13', '__read_version', 'link-13');">__read_version</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt id="link-15" class="py-name" targets="Function Bio.Motif.Parsers.MAST.__read_database_and_motifs()=Bio.Motif.Parsers.MAST-module.html#__read_database_and_motifs"><a title="Bio.Motif.Parsers.MAST.__read_database_and_motifs" class="py-name" href="#" onclick="return doclink('link-15', '__read_database_and_motifs', 'link-15');">__read_database_and_motifs</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-16', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-17" class="py-name" targets="Function Bio.Motif.Parsers.MAST.__read_section_i()=Bio.Motif.Parsers.MAST-module.html#__read_section_i"><a title="Bio.Motif.Parsers.MAST.__read_section_i" class="py-name" href="#" onclick="return doclink('link-17', '__read_section_i', 'link-17');">__read_section_i</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-18', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-19" class="py-name" targets="Function Bio.Motif.Parsers.MAST.__read_section_ii()=Bio.Motif.Parsers.MAST-module.html#__read_section_ii"><a title="Bio.Motif.Parsers.MAST.__read_section_ii" class="py-name" href="#" onclick="return doclink('link-19', '__read_section_ii', 'link-19');">__read_section_ii</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-20', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt id="link-21" class="py-name" targets="Function Bio.Motif.Parsers.MAST.__read_section_iii()=Bio.Motif.Parsers.MAST-module.html#__read_section_iii"><a title="Bio.Motif.Parsers.MAST.__read_section_iii" class="py-name" href="#" onclick="return doclink('link-21', '__read_section_iii', 'link-21');">__read_section_iii</a></tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-22', 'handle', 'link-14');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">record</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-comment"># Everything below is private</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="__read_version"></a><div id="__read_version-def"><a name="L49"></a><tt class="py-lineno"> 49</tt> <a class="py-toggle" href="#" id="__read_version-toggle" onclick="return toggle('__read_version');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#__read_version">__read_version</a><tt class="py-op">(</tt><tt class="py-param">record</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="__read_version-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__read_version-expanded"><a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-23" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-23', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"MAST version"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">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 class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version" class="py-name" href="#" onclick="return doclink('link-24', 'version', 'link-8');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.Seq.Seq.strip()=Bio.Seq.Seq-class.html#strip"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-25', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Phylo.BaseTree.TreeMixin.split()=Bio.Phylo.BaseTree.TreeMixin-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split,Method Bio.Seq.Seq.split()=Bio.Seq.Seq-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-26', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="__read_database_and_motifs"></a><div id="__read_database_and_motifs-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="__read_database_and_motifs-toggle" onclick="return toggle('__read_database_and_motifs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#__read_database_and_motifs">__read_database_and_motifs</a><tt class="py-op">(</tt><tt class="py-param">record</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="__read_database_and_motifs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__read_database_and_motifs-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-27" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-27', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Seq.Seq.startswith()=Bio.Seq.Seq-class.html#startswith"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-28', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'DATABASE AND MOTIFS'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-29', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-30', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-31', 'startswith', 'link-28');">startswith</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="L64"></a><tt class="py-lineno"> 64</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">"Line does not start with '****':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-32', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-33', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-string">'DATABASE'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</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">"Line does not contain 'DATABASE':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-name">words</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.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-34', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-35', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Blast.NCBIStandalone._DatabaseReportConsumer.database" class="py-name" href="#" onclick="return doclink('link-36', 'database', 'link-9');">database</a></tt> <tt class="py-op">=</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">words</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="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-37', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'unambiguous_dna', 'link-38');">unambiguous_dna</a></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">words</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">'(peptide)'</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-39', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'protein', 'link-40');">protein</a></tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-41" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-41', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'MOTIF WIDTH'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</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">break</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-42', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-43', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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-keyword">not</tt> <tt class="py-string">'----'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Line does not contain '----':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-44" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-44', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</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 id="link-45" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-45', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">words</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-46', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-47', 'split', 'link-26');">split</a></tt><tt class="py-op">(</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">motif</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Motif.Parsers.MEME.MEMEMotif" class="py-name" href="#" onclick="return doclink('link-48', 'MEMEMotif', 'link-7');">MEMEMotif</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">motif</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-49', 'name', 'link-10');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">words</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">motif</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length" class="py-name" href="#" onclick="return doclink('link-50', 'length', 'link-50');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">words</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="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-comment"># motif.add_instance(words[2])</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">motifs</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-51', 'append', 'link-51');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">motif</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="__read_section_i"></a><div id="__read_section_i-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="__read_section_i-toggle" onclick="return toggle('__read_section_i');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#__read_section_i">__read_section_i</a><tt class="py-op">(</tt><tt class="py-param">record</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="__read_section_i-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__read_section_i-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-52" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-52', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-53', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'SECTION I:'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-54" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-54', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-55', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'SEQUENCE NAME'</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-keyword">break</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-56', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-57', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</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 id="link-58" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-58', 'startswith', 'link-28');">startswith</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="L101"></a><tt class="py-lineno">101</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">"Line does not start with '---':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-59" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-59', 'handle', 'link-14');">handle</a></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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-60', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt id="link-61" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.Phylo.PhyloXMLIO.Writer.sequence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#sequence"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-61', 'sequence', 'link-61');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">description_evalue_length</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-62', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">sequences</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-63', 'append', 'link-51');">append</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-64', 'sequence', 'link-61');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-65', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-66', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-67', 'startswith', 'link-28');">startswith</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="L110"></a><tt class="py-lineno">110</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">"Line does not start with '****':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
<a name="__read_section_ii"></a><div id="__read_section_ii-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="__read_section_ii-toggle" onclick="return toggle('__read_section_ii');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#__read_section_ii">__read_section_ii</a><tt class="py-op">(</tt><tt class="py-param">record</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="__read_section_ii-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__read_section_ii-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-68" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-68', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</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-69" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-69', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'SECTION II:'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-70" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-70', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-71', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'SEQUENCE NAME'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-72', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-73', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</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 id="link-74" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-74', 'startswith', 'link-28');">startswith</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="L122"></a><tt class="py-lineno">122</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">"Line does not start with '---':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-75" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-75', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</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 id="link-76" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-76', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</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-77" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-77', 'startswith', 'link-28');">startswith</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="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">diagram</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-78', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">diagrams</tt><tt class="py-op">[</tt><tt id="link-79" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-79', 'sequence', 'link-61');">sequence</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">diagram</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt id="link-80" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-80', 'sequence', 'link-61');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">pvalue</tt><tt class="py-op">,</tt> <tt class="py-name">diagram</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Phylo.BaseTree.TreeMixin.split
Bio.Restriction.Restriction.RestrictionBatch.split
Bio.Seq.Seq.split" class="py-name" href="#" onclick="return doclink('link-81', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt class="py-name">diagrams</tt><tt class="py-op">[</tt><tt id="link-82" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-82', 'sequence', 'link-61');">sequence</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">diagram</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-83', 'handle', 'link-14');">handle</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-84', 'next', 'link-30');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-85', 'startswith', 'link-28');">startswith</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="L134"></a><tt class="py-lineno">134</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">"Line does not start with '****':\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="__read_section_iii"></a><div id="__read_section_iii-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="__read_section_iii-toggle" onclick="return toggle('__read_section_iii');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Motif.Parsers.MAST-module.html#__read_section_iii">__read_section_iii</a><tt class="py-op">(</tt><tt class="py-param">record</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="__read_section_iii-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__read_section_iii-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-86" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-86', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-87', 'startswith', 'link-28');">startswith</a></tt><tt class="py-op">(</tt><tt class="py-string">'SECTION III:'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-88" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-88', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</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-89" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-89', 'startswith', 'link-28');">startswith</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="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-90" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-90', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Seq.Seq.startswith" class="py-name" href="#" onclick="return doclink('link-91', 'startswith', 'link-28');">startswith</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="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt id="link-92" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-92', 'handle', 'link-14');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-93', 'strip', 'link-25');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
</div><a name="L150"></a><tt class="py-lineno">150</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> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </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 Thu Aug 18 18:22:40 2011
</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>
