<?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.IntelliGenetics</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> :: Package IntelliGenetics </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.IntelliGenetics-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.IntelliGenetics-module.html">Package Bio.IntelliGenetics</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 2001 by Katharine Lindner. 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">"""Parser for the MASE/Intelligenetics alignment file format.</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">http://pbil.univ-lyon1.fr/help/formats.html</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""</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 class="py-comment"># standard library</tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">array</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sgmllib</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">urlparse</tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"># XML from python 2.0</tt> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">xml</tt><tt class="py-op">.</tt><tt class="py-name">sax</tt> <tt class="py-keyword">import</tt> <tt class="py-name">handler</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt> <a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</a></tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</a></tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-3');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-4', 'ParserSupport', 'link-4');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.ParserSupport.EventGenerator=Bio.ParserSupport.EventGenerator-class.html"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-5', 'EventGenerator', 'link-5');">EventGenerator</a></tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-3');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-7', 'ParserSupport', 'link-4');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Class Bio.ParserSupport.AbstractConsumer=Bio.ParserSupport.AbstractConsumer-class.html"><a title="Bio.ParserSupport.AbstractConsumer" class="py-name" href="#" onclick="return doclink('link-8', 'AbstractConsumer', 'link-8');">AbstractConsumer</a></tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-3');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-10', 'File', 'link-10');">File</a></tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Module Bio.IntelliGenetics.intelligenetics_format=Bio.IntelliGenetics.intelligenetics_format-module.html"><a title="Bio.IntelliGenetics.intelligenetics_format" class="py-name" href="#" onclick="return doclink('link-11', 'intelligenetics_format', 'link-11');">intelligenetics_format</a></tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.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.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.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.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.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,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.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.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record Bio.CDD.Record Bio.CDD.Record.Record Bio.Cluster.Record Bio.Compass.Record Bio.ECell.Record Bio.ECell.Record.Record Bio.Fasta.Record Bio.GenBank.Record Bio.GenBank.Record.Record Bio.Geo.Record Bio.Geo.Record.Record Bio.Gobase.Record Bio.IntelliGenetics.Record Bio.IntelliGenetics.Record.Record Bio.InterPro.Record Bio.KEGG.Compound.Record Bio.KEGG.Enzyme.Record Bio.LocusLink.Record Bio.LocusLink.web_parse.Record Bio.Medline.Record Bio.MetaTool.Record Bio.MetaTool.Record.Record Bio.NBRF.Record Bio.NBRF.Record.Record Bio.Ndb.Record Bio.PopGen.FDist.Record Bio.PopGen.GenePop.Record Bio.Prosite.Prodoc.Record Bio.Prosite.Record Bio.Rebase.Record Bio.SCOP.Cla.Record Bio.SCOP.Des.Record Bio.SCOP.Dom.Record Bio.SCOP.Hie.Record Bio.Saf.Record Bio.Saf.Record.Record Bio.Sequencing.Phd.Record Bio.SwissProt.KeyWList.Record Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-12', 'Record', 'link-12');">Record</a></tt> </tt> <a name="Iterator"></a><div id="Iterator-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="Iterator-toggle" onclick="return toggle('Iterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.IntelliGenetics.Iterator-class.html">Iterator</a><tt class="py-op">:</tt> </tt> </div><div id="Iterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Iterator-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterator interface to move over a file of IntelliGenetics entries one at a time.</tt> </tt> <a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="Iterator.__init__-toggle" onclick="return toggle('Iterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics.Iterator-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">parser</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Iterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__init__-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the iterator.</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with IntelliGenetics entries to iterate through.</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> o parser - An optional parser to pass the entries through before</tt> </tt> <a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> returning them. If None, then the raw entry will be returned.</tt> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Variable Bio.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-13', 'handle', 'link-13');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-14', 'File', 'link-10');">File</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-15', 'UndoHandle', 'link-15');">UndoHandle</a></tt><tt class="py-op">(</tt> <tt id="link-16" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-16', 'handle', 'link-13');">handle</a></tt> <tt class="py-op">)</tt> </tt> <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">_reader</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Class Bio.IntelliGenetics.IntelliGeneticsReader=Bio.IntelliGenetics.IntelliGeneticsReader-class.html"><a title="Bio.IntelliGenetics.IntelliGeneticsReader" class="py-name" href="#" onclick="return doclink('link-17', 'IntelliGeneticsReader', 'link-17');">IntelliGeneticsReader</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-18', 'handle', 'link-13');">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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt> </tt> </div><a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt> <a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="Iterator.next-toggle" onclick="return toggle('Iterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics.Iterator-class.html#next">next</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="Iterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.next-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the next IntelliGenetics record from the handle.</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> Will return None if we ran out of records.</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt id="link-19" 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-19', 'data', 'link-19');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt><tt class="py-op">.</tt><tt id="link-20" 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.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-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.CDD.Iterator.next()=Bio.CDD.Iterator-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.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-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.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next Bio.AlignIO.EmbossIO.EmbossIterator.next Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next Bio.Compass.Iterator.next Bio.DocSQL.IterationCursor.next Bio.ECell.Iterator.next Bio.Enzyme.Iterator.next Bio.Fasta.Iterator.next Bio.GenBank.Iterator.next Bio.Gobase.Iterator.next Bio.IntelliGenetics.IntelliGeneticsReader.next Bio.IntelliGenetics.Iterator.next Bio.LocusLink.Iterator.next Bio.Medline.Iterator.next Bio.MetaTool.Iterator.next Bio.NBRF.Iterator.next Bio.Nexus.Nexus.CharBuffer.next Bio.Prosite.Iterator.next Bio.Prosite.Prodoc.Iterator.next Bio.Rebase.Iterator.next Bio.SCOP.Cla.Iterator.next Bio.SCOP.Des.Iterator.next Bio.SCOP.Dom.Iterator.next Bio.SCOP.Hie.Iterator.next Bio.SCOP.Raf.Iterator.next Bio.Saf.Iterator.next Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next Bio.SeqIO.Interfaces.SequenceIterator.next Bio.Sequencing.Ace.Iterator.next Bio.Sequencing.Phd.Iterator.next Bio.SwissProt.SProt.Iterator.next Bio.UniGene.Iterator.next Martel.Iterator.EventStream.next Martel.Iterator.HeaderFooterEventStream.next Martel.Iterator.Iterate.next Martel.Iterator.RecordEventStream.next Martel.RecordReader.CountLines.next Martel.RecordReader.EndsWith.next Martel.RecordReader.Everything.next Martel.RecordReader.Nothing.next Martel.RecordReader.RecordReader.next Martel.RecordReader.StartsWith.next Martel.RecordReader.Until.next" 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Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse Bio.AlignAce.Parser.AlignAceParser.parse Bio.AlignAce.Parser.CompareAceParser.parse Bio.AlignIO.parse Bio.Blast.NCBIStandalone.BlastErrorParser.parse Bio.Blast.NCBIStandalone.BlastParser.parse Bio.Blast.NCBIStandalone.PSIBlastParser.parse Bio.Blast.NCBIWWW.BlastParser.parse Bio.Blast.NCBIXML.BlastParser.parse Bio.Blast.NCBIXML.parse Bio.CDD.RecordParser.parse Bio.Compass.RecordParser.parse Bio.Decode.parse Bio.ECell.RecordParser.parse Bio.EUtils.POM.POMDocument.parse Bio.EUtils.parse Bio.Emboss.Primer.Primer3Parser.parse Bio.Emboss.Primer.PrimerSearchParser.parse Bio.Enzyme.RecordParser.parse Bio.Fasta.RecordParser.parse Bio.Fasta.SequenceParser.parse Bio.GenBank.FeatureParser.parse Bio.GenBank.LocationParser.parse Bio.GenBank.RecordParser.parse Bio.GenBank.Scanner.InsdcScanner.parse Bio.Geo.parse Bio.Gobase.RecordParser.parse Bio.IntelliGenetics.RecordParser.parse Bio.InterPro.InterProParser.parse Bio.KEGG.Compound.parse Bio.KEGG.Enzyme.parse Bio.KEGG.Map.parse Bio.LocusLink.RecordParser.parse Bio.LocusLink.web_parse.LocusLinkParser.parse Bio.MEME.Parser.MASTParser.parse Bio.MEME.Parser.MEMEParser.parse Bio.Medline.RecordParser.parse Bio.MetaTool.RecordParser.parse Bio.NBRF.RecordParser.parse Bio.Ndb.NdbParser.parse Bio.ParserSupport.AbstractParser.parse Bio.Parsers.spark.GenericParser.parse Bio.PopGen.FDist.RecordParser.parse Bio.PopGen.GenePop.RecordParser.parse Bio.PopGen.GenePop.parse Bio.Prosite.Prodoc.RecordParser.parse Bio.Prosite.Prodoc.parse Bio.Prosite.RecordParser.parse Bio.Prosite.parse Bio.Rebase.RecordParser.parse Bio.SCOP.Cla.Parser.parse Bio.SCOP.Cla.parse Bio.SCOP.Des.Parser.parse Bio.SCOP.Des.parse Bio.SCOP.Dom.Parser.parse Bio.SCOP.Dom.parse Bio.SCOP.Hie.Parser.parse Bio.SCOP.Hie.parse Bio.SCOP.Raf.Parser.parse Bio.SCOP.Raf.parse Bio.Saf.RecordParser.parse Bio.SeqIO.parse Bio.Sequencing.Ace.ACEParser.parse Bio.Sequencing.Ace.RecordParser.parse Bio.Sequencing.Phd.RecordParser.parse Bio.SwissProt.KeyWList.ListParser.parse Bio.SwissProt.KeyWList.parse Bio.SwissProt.SProt.RecordParser.parse Bio.SwissProt.SProt.SequenceParser.parse Bio.SwissProt.parse Bio.UniGene.RecordParser.parse Bio.Wise.psw.parse Martel.Parser.HeaderFooterParser.parse Martel.Parser.Parser.parse Martel.Parser.RecordParser.parse Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-26', 'parse', 'link-26');">parse</a></tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-27', 'File', 'link-10');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-28', 'data', 'link-19');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-29" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-29', 'data', 'link-19');">data</a></tt> </tt> </div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt> <a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="Iterator.__iter__-toggle" onclick="return toggle('Iterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics.Iterator-class.html#__iter__">__iter__</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="Iterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Iterator.__iter__-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next Bio.AlignIO.EmbossIO.EmbossIterator.next Bio.AlignIO.FastaIO.FastaM10Iterator.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.CDD.Iterator.next Bio.Compass.Iterator.next Bio.DocSQL.IterationCursor.next Bio.ECell.Iterator.next Bio.Enzyme.Iterator.next Bio.Fasta.Iterator.next Bio.GenBank.Iterator.next Bio.Gobase.Iterator.next Bio.IntelliGenetics.IntelliGeneticsReader.next Bio.IntelliGenetics.Iterator.next Bio.LocusLink.Iterator.next Bio.Medline.Iterator.next Bio.MetaTool.Iterator.next Bio.NBRF.Iterator.next Bio.Nexus.Nexus.CharBuffer.next Bio.Prosite.Iterator.next Bio.Prosite.Prodoc.Iterator.next Bio.Rebase.Iterator.next Bio.SCOP.Cla.Iterator.next Bio.SCOP.Des.Iterator.next Bio.SCOP.Dom.Iterator.next Bio.SCOP.Hie.Iterator.next Bio.SCOP.Raf.Iterator.next Bio.Saf.Iterator.next Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next Bio.SeqIO.Interfaces.SequenceIterator.next Bio.Sequencing.Ace.Iterator.next Bio.Sequencing.Phd.Iterator.next Bio.SwissProt.SProt.Iterator.next Bio.UniGene.Iterator.next Martel.Iterator.EventStream.next Martel.Iterator.HeaderFooterEventStream.next Martel.Iterator.Iterate.next Martel.Iterator.RecordEventStream.next Martel.RecordReader.CountLines.next Martel.RecordReader.EndsWith.next Martel.RecordReader.Everything.next Martel.RecordReader.Nothing.next Martel.RecordReader.RecordReader.next Martel.RecordReader.StartsWith.next Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-30', 'next', 'link-20');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt> <a name="_Scanner"></a><div id="_Scanner-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="_Scanner-toggle" onclick="return toggle('_Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.IntelliGenetics._Scanner-class.html">_Scanner</a><tt class="py-op">:</tt> </tt> </div><div id="_Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Scanner-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-docstring">"""Start up Martel to do the scanning of the file.</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> This initialzes the Martel based parser and connects it to a handler</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> that will generate events for a Feature Consumer.</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="_Scanner.__init__"></a><div id="_Scanner.__init__-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="_Scanner.__init__-toggle" onclick="return toggle('_Scanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._Scanner-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">debug</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_Scanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.__init__-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the scanner by setting up our caches.</tt> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> Creating the parser takes a long time, so we want to cache it</tt> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> to reduce parsing time.</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> o debug - The level of debugging that the parser should</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> display. Level 0 is no debugging, Level 2 displays the most</tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> debugging info (but is much slower). See Martel documentation</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> for more info on this.</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-comment"># a listing of all tags we are interested in scanning for</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the MartelParser</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"comment"</tt><tt class="py-op">,</tt> <tt class="py-string">"title_line"</tt><tt class="py-op">,</tt> <tt class="py-string">"sequence"</tt> <tt class="py-op">]</tt> </tt> <a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment"># make a parser that returns only the tags we are interested in</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-31', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-32', 'select_names', 'link-32');">select_names</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.IntelliGenetics.intelligenetics_format" class="py-name" href="#" onclick="return doclink('link-33', 'intelligenetics_format', 'link-11');">intelligenetics_format</a></tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Variable Bio.IntelliGenetics.intelligenetics_format.intelligenetics_record=Bio.IntelliGenetics.intelligenetics_format-module.html#intelligenetics_record"><a title="Bio.IntelliGenetics.intelligenetics_format.intelligenetics_record" class="py-name" href="#" onclick="return doclink('link-34', 'intelligenetics_record', 'link-34');">intelligenetics_record</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">)</tt> </tt> <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 class="py-name">_parser</tt> <tt class="py-op">=</tt> <tt class="py-name">expression</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser Bio.config._support.make_cached_expression.make_parser Martel.Expression.Expression.make_parser Martel.Expression.HeaderFooter.make_parser Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-35', 'make_parser', 'link-35');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt> </div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt> <a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="_Scanner.feed-toggle" onclick="return toggle('_Scanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.feed-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-docstring">"""Feeed a set of data into the scanner.</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"> Arguments:</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with the information to parse.</tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> o consumer - The consumer that should be informed of events.</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> """</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">_parser</tt><tt class="py-op">.</tt><tt class="py-name">setContentHandler</tt><tt class="py-op">(</tt> <tt id="link-36" class="py-name"><a title="Bio.ParserSupport.EventGenerator" class="py-name" href="#" onclick="return doclink('link-36', 'EventGenerator', 'link-5');">EventGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">consumer</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">interest_tags</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-comment"># self._parser.setErrorHandler(handle.ErrorHandler())</tt> </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile Martel.Parser.HeaderFooterParser.parseFile Martel.Parser.Parser.parseFile Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-37', 'parseFile', 'link-37');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-38', 'handle', 'link-13');">handle</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="_RecordConsumer-toggle" onclick="return toggle('_RecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.IntelliGenetics._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_RecordConsumer-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""Create an IntelliGenetics Record object from scanner generated information.</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L106"></a><tt class="py-lineno">106</tt> <a class="py-toggle" href="#" id="_RecordConsumer.__init__-toggle" onclick="return toggle('_RecordConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._RecordConsumer-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="_RecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.__init__-expanded"><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-39', 'data', 'link-19');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Bio.Blast.Record Bio.CDD.Record Bio.CDD.Record.Record Bio.Cluster.Record Bio.Compass.Record Bio.ECell.Record Bio.ECell.Record.Record Bio.Fasta.Record Bio.GenBank.Record Bio.GenBank.Record.Record Bio.Geo.Record Bio.Geo.Record.Record Bio.Gobase.Record Bio.IntelliGenetics.Record Bio.IntelliGenetics.Record.Record Bio.InterPro.Record Bio.KEGG.Compound.Record Bio.KEGG.Enzyme.Record Bio.LocusLink.Record Bio.LocusLink.web_parse.Record Bio.Medline.Record Bio.MetaTool.Record Bio.MetaTool.Record.Record Bio.NBRF.Record Bio.NBRF.Record.Record Bio.Ndb.Record Bio.PopGen.FDist.Record Bio.PopGen.GenePop.Record Bio.Prosite.Prodoc.Record Bio.Prosite.Record Bio.Rebase.Record Bio.SCOP.Cla.Record Bio.SCOP.Des.Record Bio.SCOP.Dom.Record Bio.SCOP.Hie.Record Bio.Saf.Record Bio.Saf.Record.Record Bio.Sequencing.Phd.Record Bio.SwissProt.KeyWList.Record Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-40', 'Record', 'link-12');">Record</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Blast.Record Bio.CDD.Record Bio.CDD.Record.Record Bio.Cluster.Record Bio.Compass.Record Bio.ECell.Record Bio.ECell.Record.Record Bio.Fasta.Record Bio.GenBank.Record Bio.GenBank.Record.Record Bio.Geo.Record Bio.Geo.Record.Record Bio.Gobase.Record Bio.IntelliGenetics.Record Bio.IntelliGenetics.Record.Record Bio.InterPro.Record Bio.KEGG.Compound.Record Bio.KEGG.Enzyme.Record Bio.LocusLink.Record Bio.LocusLink.web_parse.Record Bio.Medline.Record Bio.MetaTool.Record Bio.MetaTool.Record.Record Bio.NBRF.Record Bio.NBRF.Record.Record Bio.Ndb.Record Bio.PopGen.FDist.Record Bio.PopGen.GenePop.Record Bio.Prosite.Prodoc.Record Bio.Prosite.Record Bio.Rebase.Record Bio.SCOP.Cla.Record Bio.SCOP.Des.Record Bio.SCOP.Dom.Record Bio.SCOP.Hie.Record Bio.Saf.Record Bio.Saf.Record.Record Bio.Sequencing.Phd.Record Bio.SwissProt.KeyWList.Record Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-41', 'Record', 'link-12');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.title_line"></a><div id="_RecordConsumer.title_line-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="_RecordConsumer.title_line-toggle" onclick="return toggle('_RecordConsumer.title_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._RecordConsumer-class.html#title_line">title_line</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">title</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.title_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.title_line-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-42', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title Bio.GenBank._FeatureConsumer.title Bio.GenBank._RecordConsumer.title Bio.Medline._RecordConsumer.title Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-43', 'title', 'link-43');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title Bio.GenBank._FeatureConsumer.title Bio.GenBank._RecordConsumer.title Bio.Medline._RecordConsumer.title Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-44', 'title', 'link-43');">title</a></tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt> </div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.comment"></a><div id="_RecordConsumer.comment-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="_RecordConsumer.comment-toggle" onclick="return toggle('_RecordConsumer.comment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._RecordConsumer-class.html#comment">comment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">comments</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.comment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.comment-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-45" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.comment()=Bio.EUtils.POM.ElementNode-class.html#comment,Method Bio.Enzyme._RecordConsumer.comment()=Bio.Enzyme._RecordConsumer-class.html#comment,Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment,Method Bio.IntelliGenetics._RecordConsumer.comment()=Bio.IntelliGenetics._RecordConsumer-class.html#comment,Method Bio.NBRF._RecordConsumer.comment()=Bio.NBRF._RecordConsumer-class.html#comment,Method Bio.PopGen.GenePop._RecordConsumer.comment()=Bio.PopGen.GenePop._RecordConsumer-class.html#comment,Method Bio.Prosite._RecordConsumer.comment()=Bio.Prosite._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._RecordConsumer.comment()=Bio.SwissProt.SProt._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._SequenceConsumer.comment()=Bio.SwissProt.SProt._SequenceConsumer-class.html#comment,Variable Bio.expressions.swissprot.sprot38.comment=Bio.expressions.swissprot.sprot38-module.html#comment,Variable Martel.test.test_swissprot38.comment=Martel.test.test_swissprot38-module.html#comment,Variable Martel.test.testformats.swissprot38.comment=Martel.test.testformats.swissprot38-module.html#comment"><a title="Bio.EUtils.POM.ElementNode.comment Bio.Enzyme._RecordConsumer.comment Bio.GenBank._FeatureConsumer.comment Bio.GenBank._RecordConsumer.comment Bio.IntelliGenetics._RecordConsumer.comment Bio.NBRF._RecordConsumer.comment Bio.PopGen.GenePop._RecordConsumer.comment Bio.Prosite._RecordConsumer.comment Bio.SwissProt.SProt._RecordConsumer.comment Bio.SwissProt.SProt._SequenceConsumer.comment Bio.expressions.swissprot.sprot38.comment Martel.test.test_swissprot38.comment Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-45', 'comment', 'link-45');">comment</a></tt> <tt class="py-keyword">in</tt> <tt id="link-46" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.comments()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#comments,Variable Bio.Emboss.primer3_format.comments=Bio.Emboss.primer3_format-module.html#comments,Method Bio.Medline._RecordConsumer.comments()=Bio.Medline._RecordConsumer-class.html#comments"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.comments Bio.Emboss.primer3_format.comments Bio.Medline._RecordConsumer.comments" class="py-name" href="#" onclick="return doclink('link-46', 'comments', 'link-46');">comments</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-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-47', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.comments Bio.Emboss.primer3_format.comments Bio.Medline._RecordConsumer.comments" class="py-name" href="#" onclick="return doclink('link-48', 'comments', 'link-46');">comments</a></tt><tt class="py-op">.</tt><tt id="link-49" 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-49', 'append', 'link-49');">append</a></tt><tt class="py-op">(</tt> <tt id="link-50" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment Bio.Enzyme._RecordConsumer.comment Bio.GenBank._FeatureConsumer.comment Bio.GenBank._RecordConsumer.comment Bio.IntelliGenetics._RecordConsumer.comment Bio.NBRF._RecordConsumer.comment Bio.PopGen.GenePop._RecordConsumer.comment Bio.Prosite._RecordConsumer.comment Bio.SwissProt.SProt._RecordConsumer.comment Bio.SwissProt.SProt._SequenceConsumer.comment Bio.expressions.swissprot.sprot38.comment Martel.test.test_swissprot38.comment Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-50', 'comment', 'link-45');">comment</a></tt> <tt class="py-op">)</tt> </tt> </div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.sequence"></a><div id="_RecordConsumer.sequence-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="_RecordConsumer.sequence-toggle" onclick="return toggle('_RecordConsumer.sequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics._RecordConsumer-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">sequences</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.sequence-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-51" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-51', 'sequence', 'link-51');">sequence</a></tt> <tt class="py-keyword">in</tt> <tt id="link-52" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequences()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequences"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-52', 'sequences', 'link-52');">sequences</a></tt><tt class="py-op">:</tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-53', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-54', 'sequence', 'link-51');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-55', 'data', 'link-19');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-56', 'data', 'link-19');">data</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-57', 'sequence', 'link-51');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-58', 'data', 'link-19');">data</a></tt> <tt class="py-op">+</tt> <tt id="link-59" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-59', 'sequence', 'link-51');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-60" 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-60', 'strip', 'link-60');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> </tt> <a name="RecordParser"></a><div id="RecordParser-def"><a name="L121"></a><tt class="py-lineno">121</tt> <a class="py-toggle" href="#" id="RecordParser-toggle" onclick="return toggle('RecordParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.IntelliGenetics.RecordParser-class.html">RecordParser</a><tt class="py-op">:</tt> </tt> </div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse IntelliGenetics files into Record objects</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L124"></a><tt class="py-lineno">124</tt> <a class="py-toggle" href="#" id="RecordParser.__init__-toggle" onclick="return toggle('RecordParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics.RecordParser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="RecordParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.__init__-expanded"><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the parser.</tt> </tt> <a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> o debug_level - An optional argument that specifies the amount of</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> debugging information Martel should spit out. By default we have</tt> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> no debugging info (the fastest way to do things), but if you want</tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> you can set this as high as two and see exactly where a parse fails.</tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Blast.NCBIWWW._Scanner=Bio.Blast.NCBIWWW._Scanner-class.html,Class Bio.CDD._Scanner=Bio.CDD._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.ECell._Scanner=Bio.ECell._Scanner-class.html,Class Bio.Enzyme._Scanner=Bio.Enzyme._Scanner-class.html,Class Bio.Gobase._Scanner=Bio.Gobase._Scanner-class.html,Class Bio.IntelliGenetics._Scanner=Bio.IntelliGenetics._Scanner-class.html,Class Bio.LocusLink._Scanner=Bio.LocusLink._Scanner-class.html,Class Bio.Medline._Scanner=Bio.Medline._Scanner-class.html,Class Bio.MetaTool._Scanner=Bio.MetaTool._Scanner-class.html,Class Bio.NBRF._Scanner=Bio.NBRF._Scanner-class.html,Class Bio.PopGen.FDist._Scanner=Bio.PopGen.FDist._Scanner-class.html,Class Bio.PopGen.GenePop._Scanner=Bio.PopGen.GenePop._Scanner-class.html,Class Bio.Prosite.Prodoc._Scanner=Bio.Prosite.Prodoc._Scanner-class.html,Class Bio.Prosite._Scanner=Bio.Prosite._Scanner-class.html,Class Bio.Rebase._Scanner=Bio.Rebase._Scanner-class.html,Class Bio.Saf._Scanner=Bio.Saf._Scanner-class.html,Class Bio.Sequencing.Ace._Scanner=Bio.Sequencing.Ace._Scanner-class.html,Class Bio.Sequencing.Phd._Scanner=Bio.Sequencing.Phd._Scanner-class.html,Class Bio.SwissProt.KeyWList._Scanner=Bio.SwissProt.KeyWList._Scanner-class.html,Class Bio.SwissProt.SProt._Scanner=Bio.SwissProt.SProt._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner Bio.Blast.NCBIWWW._Scanner Bio.CDD._Scanner Bio.Compass._Scanner Bio.ECell._Scanner Bio.Enzyme._Scanner Bio.Gobase._Scanner Bio.IntelliGenetics._Scanner Bio.LocusLink._Scanner Bio.Medline._Scanner Bio.MetaTool._Scanner Bio.NBRF._Scanner Bio.PopGen.FDist._Scanner Bio.PopGen.GenePop._Scanner Bio.Prosite.Prodoc._Scanner Bio.Prosite._Scanner Bio.Rebase._Scanner Bio.Saf._Scanner Bio.Sequencing.Ace._Scanner Bio.Sequencing.Phd._Scanner Bio.SwissProt.KeyWList._Scanner Bio.SwissProt.SProt._Scanner Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-61', '_Scanner', 'link-61');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt> </div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt> <a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="RecordParser.parse-toggle" onclick="return toggle('RecordParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.IntelliGenetics.RecordParser-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="RecordParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.parse-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse the specified handle into a GenBank record.</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name" targets="Class Bio.CDD._RecordConsumer=Bio.CDD._RecordConsumer-class.html,Class Bio.ECell._RecordConsumer=Bio.ECell._RecordConsumer-class.html,Class Bio.Enzyme._RecordConsumer=Bio.Enzyme._RecordConsumer-class.html,Class Bio.GenBank._RecordConsumer=Bio.GenBank._RecordConsumer-class.html,Class Bio.Gobase._RecordConsumer=Bio.Gobase._RecordConsumer-class.html,Class Bio.IntelliGenetics._RecordConsumer=Bio.IntelliGenetics._RecordConsumer-class.html,Class Bio.LocusLink._RecordConsumer=Bio.LocusLink._RecordConsumer-class.html,Class Bio.Medline._RecordConsumer=Bio.Medline._RecordConsumer-class.html,Class Bio.MetaTool._RecordConsumer=Bio.MetaTool._RecordConsumer-class.html,Class Bio.NBRF._RecordConsumer=Bio.NBRF._RecordConsumer-class.html,Class Bio.PopGen.FDist._RecordConsumer=Bio.PopGen.FDist._RecordConsumer-class.html,Class Bio.PopGen.GenePop._RecordConsumer=Bio.PopGen.GenePop._RecordConsumer-class.html,Class Bio.Prosite.Prodoc._RecordConsumer=Bio.Prosite.Prodoc._RecordConsumer-class.html,Class Bio.Prosite._RecordConsumer=Bio.Prosite._RecordConsumer-class.html,Class Bio.Rebase._RecordConsumer=Bio.Rebase._RecordConsumer-class.html,Class Bio.Saf._RecordConsumer=Bio.Saf._RecordConsumer-class.html,Class Bio.Sequencing.Ace._RecordConsumer=Bio.Sequencing.Ace._RecordConsumer-class.html,Class Bio.Sequencing.Phd._RecordConsumer=Bio.Sequencing.Phd._RecordConsumer-class.html,Class Bio.SwissProt.SProt._RecordConsumer=Bio.SwissProt.SProt._RecordConsumer-class.html,Class Bio.UniGene._RecordConsumer=Bio.UniGene._RecordConsumer-class.html"><a title="Bio.CDD._RecordConsumer Bio.ECell._RecordConsumer Bio.Enzyme._RecordConsumer Bio.GenBank._RecordConsumer Bio.Gobase._RecordConsumer Bio.IntelliGenetics._RecordConsumer Bio.LocusLink._RecordConsumer Bio.Medline._RecordConsumer Bio.MetaTool._RecordConsumer Bio.NBRF._RecordConsumer Bio.PopGen.FDist._RecordConsumer Bio.PopGen.GenePop._RecordConsumer Bio.Prosite.Prodoc._RecordConsumer Bio.Prosite._RecordConsumer Bio.Rebase._RecordConsumer Bio.Saf._RecordConsumer Bio.Sequencing.Ace._RecordConsumer Bio.Sequencing.Phd._RecordConsumer Bio.SwissProt.SProt._RecordConsumer Bio.UniGene._RecordConsumer" class="py-name" href="#" onclick="return doclink('link-62', '_RecordConsumer', 'link-62');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</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-63" 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-63', 'feed', 'link-63');">feed</a></tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-64', 'handle', 'link-13');">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="L140"></a><tt class="py-lineno">140</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-65" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-19');">data</a></tt> </tt> </div></div><a 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class="py-keyword">while</tt><tt class="py-op">(</tt> <tt class="py-name">state</tt> <tt class="py-op">!=</tt> <tt class="py-string">'DONE'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline Bio.File.SGMLHandle.readline Bio.File.UndoHandle.readline Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-71', 'readline', 'link-71');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">'DONE'</tt> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">';'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">state</tt> <tt class="py-op">==</tt> <tt class="py-string">'SEQUENCE_STATE'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">'DONE'</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Method Bio.File.UndoHandle.saveline()=Bio.File.UndoHandle-class.html#saveline"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-72', 'saveline', 'link-72');">saveline</a></tt><tt class="py-op">(</tt> <tt class="py-name">line</tt> <tt class="py-op">)</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">state</tt> <tt class="py-op">==</tt> <tt class="py-string">'COMMENT_STATE'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-73" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-73', 'record', 'link-70');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-74', 'record', 'link-70');">record</a></tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt class="py-name">state</tt> <tt class="py-op">==</tt> <tt class="py-string">'COMMENT_STATE'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-75', 'record', 'link-70');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-76', 'record', 'link-70');">record</a></tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">state</tt> <tt class="py-op">=</tt> <tt class="py-string">'SEQUENCE_STATE'</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">state</tt> <tt class="py-op">==</tt> <tt class="py-string">'SEQUENCE_STATE'</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-77', 'record', 'link-70');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-78', 'record', 'link-70');">record</a></tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-79" class="py-name"><a title="Bio.Emboss.primer3_format.record Bio.Emboss.primersearch_format.record Bio.GFF.Feature.record Bio.LocusLink.web_parse.record Bio.Ndb.record Bio.Std.record Bio.expressions.blocks.record Bio.expressions.embl.embl65.record Bio.expressions.fasta.record Bio.expressions.genbank.record Bio.expressions.hmmpfam.record Bio.expressions.swissprot.ipi.record Bio.expressions.swissprot.speclist.record Bio.expressions.swissprot.sprot38.record Bio.expressions.swissprot.sprot40.record Martel.test.test_swissprot38.record Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-79', 'record', 'link-70');">record</a></tt> </tt> </div></div><a name="L169"></a><tt class="py-lineno">169</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 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