<?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.SwissProt</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 SwissProt </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.SwissProt-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.SwissProt-module.html">Package Bio.SwissProt</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 2007 by Michiel de Hoon. 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">"""Parsers for file formats from the SwissProt database.</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> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># The parse(), read() functions can probably be simplified if we don't</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># use the "parser = RecordParser(); parser.parse(handle)" approach.</tt> </tt> <a name="parse"></a><div id="parse-def"><a name="L10"></a><tt class="py-lineno">10</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SwissProt-module.html#parse">parse</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="parse-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="parse-expanded"><a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Bio.SwissProt.SProt=Bio.SwissProt.SProt-module.html"><a title="Bio.SwissProt.SProt" class="py-name" href="#" onclick="return doclink('link-0', 'SProt', 'link-0');">SProt</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class Bio.CDD.RecordParser=Bio.CDD.RecordParser-class.html,Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.ECell.RecordParser=Bio.ECell.RecordParser-class.html,Class Bio.Enzyme.RecordParser=Bio.Enzyme.RecordParser-class.html,Class Bio.Fasta.RecordParser=Bio.Fasta.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.Gobase.RecordParser=Bio.Gobase.RecordParser-class.html,Class Bio.IntelliGenetics.RecordParser=Bio.IntelliGenetics.RecordParser-class.html,Class Bio.LocusLink.RecordParser=Bio.LocusLink.RecordParser-class.html,Class Bio.Medline.RecordParser=Bio.Medline.RecordParser-class.html,Class Bio.MetaTool.RecordParser=Bio.MetaTool.RecordParser-class.html,Class Bio.NBRF.RecordParser=Bio.NBRF.RecordParser-class.html,Class Bio.PopGen.FDist.RecordParser=Bio.PopGen.FDist.RecordParser-class.html,Class Bio.PopGen.GenePop.RecordParser=Bio.PopGen.GenePop.RecordParser-class.html,Class Bio.Prosite.Prodoc.RecordParser=Bio.Prosite.Prodoc.RecordParser-class.html,Class Bio.Prosite.RecordParser=Bio.Prosite.RecordParser-class.html,Class Bio.Rebase.RecordParser=Bio.Rebase.RecordParser-class.html,Class Bio.Saf.RecordParser=Bio.Saf.RecordParser-class.html,Class Bio.Sequencing.Ace.RecordParser=Bio.Sequencing.Ace.RecordParser-class.html,Class Bio.Sequencing.Phd.RecordParser=Bio.Sequencing.Phd.RecordParser-class.html,Class Bio.SwissProt.SProt.RecordParser=Bio.SwissProt.SProt.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html,Class Martel.Parser.RecordParser=Martel.Parser.RecordParser-class.html"><a title="Bio.CDD.RecordParser Bio.Compass.RecordParser Bio.ECell.RecordParser Bio.Enzyme.RecordParser Bio.Fasta.RecordParser Bio.GenBank.RecordParser Bio.Gobase.RecordParser Bio.IntelliGenetics.RecordParser Bio.LocusLink.RecordParser Bio.Medline.RecordParser Bio.MetaTool.RecordParser Bio.NBRF.RecordParser Bio.PopGen.FDist.RecordParser Bio.PopGen.GenePop.RecordParser Bio.Prosite.Prodoc.RecordParser Bio.Prosite.RecordParser Bio.Rebase.RecordParser Bio.Saf.RecordParser Bio.Sequencing.Ace.RecordParser Bio.Sequencing.Phd.RecordParser Bio.SwissProt.SProt.RecordParser Bio.UniGene.RecordParser Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-1', 'RecordParser', 'link-1');">RecordParser</a></tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">cStringIO</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-2" class="py-name"><a title="Bio.CDD.RecordParser Bio.Compass.RecordParser Bio.ECell.RecordParser Bio.Enzyme.RecordParser Bio.Fasta.RecordParser Bio.GenBank.RecordParser Bio.Gobase.RecordParser Bio.IntelliGenetics.RecordParser Bio.LocusLink.RecordParser Bio.Medline.RecordParser Bio.MetaTool.RecordParser Bio.NBRF.RecordParser Bio.PopGen.FDist.RecordParser Bio.PopGen.GenePop.RecordParser Bio.Prosite.Prodoc.RecordParser Bio.Prosite.RecordParser Bio.Rebase.RecordParser Bio.Saf.RecordParser Bio.Sequencing.Ace.RecordParser Bio.Sequencing.Phd.RecordParser Bio.SwissProt.SProt.RecordParser Bio.UniGene.RecordParser Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-2', 'RecordParser', 'link-1');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt id="link-3" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text Bio.Prosite.Prodoc._RecordConsumer.text Martel.test.test_Iterator.text Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-3', 'text', 'link-3');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</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-4" 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-4', 'handle', 'link-4');">handle</a></tt><tt class="py-op">:</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt id="link-5" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text Bio.Prosite.Prodoc._RecordConsumer.text Martel.test.test_Iterator.text Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-5', 'text', 'link-3');">text</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">line</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'//'</tt><tt class="py-op">:</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt id="link-6" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-6', 'handle', 'link-4');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cStringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text Bio.Prosite.Prodoc._RecordConsumer.text Martel.test.test_Iterator.text Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-7', 'text', 'link-3');">text</a></tt><tt class="py-op">)</tt> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt id="link-8" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><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-8', 'record', 'link-8');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method 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-9', 'parse', 'link-9');">parse</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-10', 'handle', 'link-4');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text Bio.Prosite.Prodoc._RecordConsumer.text Martel.test.test_Iterator.text Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-11', 'text', 'link-3');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-12" 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-12', 'record', 'link-8');">record</a></tt> </tt> </div><a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt> <a name="read"></a><div id="read-def"><a name="L23"></a><tt class="py-lineno">23</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.SwissProt-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="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio.SwissProt.SProt" class="py-name" href="#" onclick="return doclink('link-13', 'SProt', 'link-0');">SProt</a></tt> <tt class="py-keyword">import</tt> <tt id="link-14" class="py-name"><a title="Bio.CDD.RecordParser Bio.Compass.RecordParser Bio.ECell.RecordParser Bio.Enzyme.RecordParser Bio.Fasta.RecordParser Bio.GenBank.RecordParser Bio.Gobase.RecordParser Bio.IntelliGenetics.RecordParser Bio.LocusLink.RecordParser Bio.Medline.RecordParser Bio.MetaTool.RecordParser Bio.NBRF.RecordParser Bio.PopGen.FDist.RecordParser Bio.PopGen.GenePop.RecordParser Bio.Prosite.Prodoc.RecordParser Bio.Prosite.RecordParser Bio.Rebase.RecordParser Bio.Saf.RecordParser Bio.Sequencing.Ace.RecordParser Bio.Sequencing.Phd.RecordParser Bio.SwissProt.SProt.RecordParser Bio.UniGene.RecordParser Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-14', 'RecordParser', 'link-1');">RecordParser</a></tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="Bio.CDD.RecordParser Bio.Compass.RecordParser Bio.ECell.RecordParser Bio.Enzyme.RecordParser Bio.Fasta.RecordParser Bio.GenBank.RecordParser Bio.Gobase.RecordParser Bio.IntelliGenetics.RecordParser Bio.LocusLink.RecordParser Bio.Medline.RecordParser Bio.MetaTool.RecordParser Bio.NBRF.RecordParser Bio.PopGen.FDist.RecordParser Bio.PopGen.GenePop.RecordParser Bio.Prosite.Prodoc.RecordParser Bio.Prosite.RecordParser Bio.Rebase.RecordParser Bio.Saf.RecordParser Bio.Sequencing.Ace.RecordParser Bio.Sequencing.Phd.RecordParser Bio.SwissProt.SProt.RecordParser Bio.UniGene.RecordParser Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-15', 'RecordParser', 'link-1');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt id="link-16" 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-16', 'record', 'link-8');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><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-17', 'parse', 'link-9');">parse</a></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-4');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.error()=Bio.Parsers.spark.GenericParser-class.html#error,Method Bio.Parsers.spark.GenericScanner.error()=Bio.Parsers.spark.GenericScanner-class.html#error,Method Martel.Iterator.StoreEvents.error()=Martel.Iterator.StoreEvents-class.html#error,Class Martel.msre_constants.error=Martel.msre_constants.error-class.html,Method Martel.test.support.Dump.error()=Martel.test.support.Dump-class.html#error,Method Martel.test.test_Parser.CountErrors.error()=Martel.test.test_Parser.CountErrors-class.html#error,Method Martel.test.test_optimize.GetErrorPos.error()=Martel.test.test_optimize.GetErrorPos-class.html#error"><a title="Bio.Parsers.spark.GenericParser.error Bio.Parsers.spark.GenericScanner.error Martel.Iterator.StoreEvents.error Martel.msre_constants.error Martel.test.support.Dump.error Martel.test.test_Parser.CountErrors.error Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-19', 'error', 'link-19');">error</a></tt><tt class="py-op">:</tt> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-20" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error Bio.Parsers.spark.GenericScanner.error Martel.Iterator.StoreEvents.error Martel.msre_constants.error Martel.test.support.Dump.error Martel.test.test_Parser.CountErrors.error Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-20', 'error', 'link-19');">error</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Bio.DocSQL.Query.message=Bio.DocSQL.Query-class.html#message"><a title="Bio.DocSQL.Query.message" class="py-name" href="#" onclick="return doclink('link-21', 'message', 'link-21');">message</a></tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"Line does not start with 'ID':"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L30"></a><tt class="py-lineno">30</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">"No SwissProt record found"</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-22" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error Bio.Parsers.spark.GenericScanner.error Martel.Iterator.StoreEvents.error Martel.msre_constants.error Martel.test.support.Dump.error Martel.test.test_Parser.CountErrors.error Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-22', 'error', 'link-19');">error</a></tt> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-comment"># We should have reached the end of the record by now</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-23" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder,Variable Bio.LogisticRegression.remainder=Bio.LogisticRegression-module.html#remainder,Variable Bio.MarkovModel.remainder=Bio.MarkovModel-module.html#remainder,Variable Bio.MaxEntropy.remainder=Bio.MaxEntropy-module.html#remainder,Variable Bio.NaiveBayes.remainder=Bio.NaiveBayes-module.html#remainder,Variable Bio.Statistics.lowess.remainder=Bio.Statistics.lowess-module.html#remainder,Variable Bio.distance.remainder=Bio.distance-module.html#remainder,Variable Bio.kNN.remainder=Bio.kNN-module.html#remainder,Method Martel.RecordReader.CountLines.remainder()=Martel.RecordReader.CountLines-class.html#remainder,Method Martel.RecordReader.EndsWith.remainder()=Martel.RecordReader.EndsWith-class.html#remainder,Method Martel.RecordReader.Everything.remainder()=Martel.RecordReader.Everything-class.html#remainder,Method Martel.RecordReader.Nothing.remainder()=Martel.RecordReader.Nothing-class.html#remainder,Method Martel.RecordReader.RecordReader.remainder()=Martel.RecordReader.RecordReader-class.html#remainder,Method Martel.RecordReader.StartsWith.remainder()=Martel.RecordReader.StartsWith-class.html#remainder,Method Martel.RecordReader.Until.remainder()=Martel.RecordReader.Until-class.html#remainder"><a title="Bio.Affy.CelFile.remainder Bio.LogisticRegression.remainder Bio.MarkovModel.remainder Bio.MaxEntropy.remainder Bio.NaiveBayes.remainder Bio.Statistics.lowess.remainder Bio.distance.remainder Bio.kNN.remainder Martel.RecordReader.CountLines.remainder Martel.RecordReader.EndsWith.remainder Martel.RecordReader.Everything.remainder Martel.RecordReader.Nothing.remainder Martel.RecordReader.RecordReader.remainder Martel.RecordReader.StartsWith.remainder Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-23', 'remainder', 'link-23');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-24', 'handle', 'link-4');">handle</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read Bio.AlignIO.read Bio.Cluster.read Bio.EUtils.ReseekFile.ReseekFile.read Bio.Entrez.read Bio.File.SGMLHandle.read Bio.File.UndoHandle.read Bio.FilteredReader.FilteredReader.read Bio.NeuralNetwork.Gene.Pattern.PatternIO.read Bio.Nexus.Nexus.Nexus.read Bio.Prosite.Prodoc.read Bio.Prosite.read Bio.SGMLExtractor.SGMLExtractorHandle.read Bio.SeqIO.read Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-25', 'read', 'link-25');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-26" class="py-name"><a title="Bio.Affy.CelFile.remainder Bio.LogisticRegression.remainder Bio.MarkovModel.remainder Bio.MaxEntropy.remainder Bio.NaiveBayes.remainder Bio.Statistics.lowess.remainder Bio.distance.remainder Bio.kNN.remainder Martel.RecordReader.CountLines.remainder Martel.RecordReader.EndsWith.remainder Martel.RecordReader.Everything.remainder Martel.RecordReader.Nothing.remainder Martel.RecordReader.RecordReader.remainder Martel.RecordReader.StartsWith.remainder Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-26', 'remainder', 'link-23');">remainder</a></tt><tt class="py-op">:</tt> </tt> <a name="L36"></a><tt class="py-lineno">36</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">"More than one SwissProt record found"</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-27" 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-27', 'record', 'link-8');">record</a></tt> </tt> </div><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt> <tt class="py-op">:</tt> </tt> <a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Quick self test..."</tt> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">example_filename</tt> <tt class="py-op">=</tt> <tt class="py-string">"../../Tests/SwissProt/sp008"</tt> </tt> <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 class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt> <a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-name">example_filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Missing test file %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">example_filename</tt> </tt> <a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-comment">#Try parsing it!</tt> </tt> <a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-28', 'handle', 'link-4');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-29', 'open', 'link-29');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">example_filename</tt><tt class="py-op">)</tt> </tt> <a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><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-30', 'parse', 'link-9');">parse</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-31', 'handle', 'link-4');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-32" 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-32', 'record', 'link-8');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</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">print</tt> <tt id="link-33" 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-33', 'record', 'link-8');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">entry_name</tt> </tt> <a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">","</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-34" 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-34', 'record', 'link-8');">record</a></tt><tt class="py-op">.</tt><tt class="py-name">accessions</tt><tt class="py-op">)</tt> </tt> <a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-35" 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-35', 'record', 'link-8');">record</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.keywords()=Bio.GenBank._FeatureConsumer-class.html#keywords,Method Bio.GenBank._RecordConsumer.keywords()=Bio.GenBank._RecordConsumer-class.html#keywords"><a title="Bio.GenBank._FeatureConsumer.keywords Bio.GenBank._RecordConsumer.keywords" class="py-name" href="#" onclick="return doclink('link-36', 'keywords', 'link-36');">keywords</a></tt> </tt> <a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-37" 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-37', 'record', 'link-8');">record</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.organism()=Bio.GenBank._FeatureConsumer-class.html#organism,Method Bio.GenBank._RecordConsumer.organism()=Bio.GenBank._RecordConsumer-class.html#organism,Variable Bio.expressions.embl.embl65.organism=Bio.expressions.embl.embl65-module.html#organism,Variable Bio.expressions.genbank.organism=Bio.expressions.genbank-module.html#organism"><a title="Bio.GenBank._FeatureConsumer.organism Bio.GenBank._RecordConsumer.organism Bio.expressions.embl.embl65.organism Bio.expressions.genbank.organism" class="py-name" href="#" onclick="return doclink('link-38', 'organism', 'link-38');">organism</a></tt><tt class="py-op">)</tt> </tt> <a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-39" 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-39', 'record', 'link-8');">record</a></tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'sequence', 'link-40');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">20</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-string">"..."</tt> </tt> <a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-41', 'handle', 'link-4');">handle</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-42', 'close', 'link-42');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L60"></a><tt class="py-lineno">60</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> 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