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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Prosite-module.html">Package Prosite</a> ::
Module Prodoc
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<h1 class="epydoc">Source Code for <a href="Bio.Prosite.Prodoc-module.html">Module Bio.Prosite.Prodoc</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 2000 by Jeffrey Chang. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with the prosite.doc file from</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Prosite.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">http://www.expasy.ch/prosite/</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">Tested with:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Release 15.0, July 1998</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Release 16.0, July 1999</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">Release 20.22, 13 November 2007</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">Functions:</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring">parse Iterates over entries in a Prodoc file.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">index_file Index a Prodoc file for a Dictionary.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">_extract_record Extract Prodoc data from a web page.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring">Record Holds Prodoc data.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">Reference Holds data from a Prodoc reference.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">Dictionary Accesses a Prodoc file using a dictionary interface.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">RecordParser Parses a Prodoc record into a Record object.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">_Scanner Scans Prodoc-formatted data.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">_RecordConsumer Consumes Prodoc data to a Record object.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">Iterator Iterates over entries in a Prodoc file; DEPRECATED.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</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">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sgmllib</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Module Bio.Index=Bio.Index-module.html,Class Bio.SCOP.Cla.Index=Bio.SCOP.Cla.Index-class.html"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-3', 'Index', 'link-3');">Index</a></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-5', 'ParserSupport', 'link-5');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc-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="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">cStringIO</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-6" 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-6', 'RecordParser', 'link-6');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt id="link-7" 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-7', 'text', 'link-7');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</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-8" 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-8', 'handle', 'link-8');">handle</a></tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-9" 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-9', 'text', 'link-7');">text</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">line</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</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">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'{END}'</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <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-8');">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-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-7');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt id="link-12" 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-12', 'record', 'link-12');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-14', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt id="link-15" 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-15', 'text', 'link-7');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <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-12');">record</a></tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="read"></a><div id="read-def"><a name="L53"></a><tt class="py-lineno"> 53</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.Prosite.Prodoc-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="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-17" 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-17', 'RecordParser', 'link-6');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'record', 'link-12');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-20', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-comment"># We should have reached the end of the record by now</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-21" 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-21', 'remainder', 'link-21');">remainder</a></tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-22', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-23" 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-23', 'read', 'link-23');">read</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 class="py-keyword">if</tt> <tt id="link-24" 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-24', 'remainder', 'link-21');">remainder</a></tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</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 Prodoc record found"</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-25" 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-25', 'record', 'link-12');">record</a></tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"># It may be a good idea to rewrite read(), parse() at some point to avoid</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># using the old-style "parser = RecordParser(); parser.parse(handle)" approach.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Record"></a><div id="Record-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Record-class.html">Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information from a Prodoc record.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> accession Accession number of the record.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> prosite_refs List of tuples (prosite accession, prosite name).</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> text Free format text.</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> references List of reference objects.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L76"></a><tt class="py-lineno"> 76</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Record-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.accession()=Bio.GenBank._FeatureConsumer-class.html#accession,Method Bio.GenBank._RecordConsumer.accession()=Bio.GenBank._RecordConsumer-class.html#accession,Method Bio.Prosite.Prodoc._RecordConsumer.accession()=Bio.Prosite.Prodoc._RecordConsumer-class.html#accession,Method Bio.Prosite._RecordConsumer.accession()=Bio.Prosite._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._RecordConsumer.accession()=Bio.SwissProt.SProt._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._SequenceConsumer.accession()=Bio.SwissProt.SProt._SequenceConsumer-class.html#accession,Variable Bio.expressions.embl.embl65.accession=Bio.expressions.embl.embl65-module.html#accession,Variable Bio.expressions.genbank.accession=Bio.expressions.genbank-module.html#accession"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-26', 'accession', 'link-26');">accession</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">prosite_refs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'text', 'link-7');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">references</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="Reference"></a><div id="Reference-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="Reference-toggle" onclick="return toggle('Reference');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Reference-class.html">Reference</a><tt class="py-op">:</tt> </tt>
</div><div id="Reference-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Reference-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information from a Prodoc citation.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> number Number of the reference. (string)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> authors Names of the authors.</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> citation Describes the citation.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Reference.__init__"></a><div id="Reference.__init__-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Reference.__init__-toggle" onclick="return toggle('Reference.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Reference-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="Reference.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Reference.__init__-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">number</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.authors()=Bio.GenBank._FeatureConsumer-class.html#authors,Method Bio.GenBank._RecordConsumer.authors()=Bio.GenBank._RecordConsumer-class.html#authors"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-28', 'authors', 'link-28');">authors</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
</div></div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="Iterator"></a><div id="Iterator-def"><a name="L96"></a><tt class="py-lineno"> 96</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.Prosite.Prodoc.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="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns one record at a time from a Prodoc file.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> next Return the next record from the stream, or None.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L103"></a><tt class="py-lineno">103</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.Prosite.Prodoc.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="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""__init__(self, handle, parser=None)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> Create a new iterator. handle is a file-like object. parser</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> is an optional Parser object to change the results into another form.</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> If set to None, then the raw contents of the file will be returned.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Prosite.Prodoc.Iterator is deprecated; we recommend using the function Bio.Prosite.Prodoc.parse instead. Please contact the Biopython developers at biopython-dev@biopython.org you cannot use Bio.Prosite.Prodoc.parse instead of Bio.Prosite.Prodoc.Iterator."</tt><tt class="py-op">,</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-29" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-29', 'type', 'link-29');">type</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-30', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">FileType</tt> <tt class="py-keyword">and</tt> <tt id="link-31" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-31', 'type', 'link-29');">type</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-32', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">InstanceType</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I expected a file handle or file-like object"</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uhandle</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-33', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</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="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L119"></a><tt class="py-lineno">119</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.Prosite.Prodoc.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="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-docstring">"""next(self) -> object</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> Return the next Prodoc record from the file. If no more records,</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> return None.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_uhandle</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-37" 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-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</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">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'{END}'</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-38" 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-38', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</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">_parser</tt><tt class="py-op">.</tt><tt id="link-39" 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-39', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-40', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-41', 'data', 'link-38');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">return</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-38');">data</a></tt> </tt>
</div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L143"></a><tt class="py-lineno">143</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.Prosite.Prodoc.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="L144"></a><tt class="py-lineno">144</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-43" 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" class="py-name" href="#" onclick="return doclink('link-43', 'next', 'link-43');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> </tt>
<a name="Dictionary"></a><div id="Dictionary-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="Dictionary-toggle" onclick="return toggle('Dictionary');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Dictionary-class.html">Dictionary</a><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Dictionary-expanded"><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-docstring">"""Accesses a Prodoc file using a dictionary interface.</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt id="link-44" class="py-name" targets="Variable Bio.Gobase.Dictionary.__filename_key=Bio.Gobase.Dictionary-class.html#__filename_key,Variable Bio.Prosite.Dictionary.__filename_key=Bio.Prosite.Dictionary-class.html#__filename_key,Variable Bio.Prosite.Prodoc.Dictionary.__filename_key=Bio.Prosite.Prodoc.Dictionary-class.html#__filename_key,Variable Bio.Rebase.Dictionary.__filename_key=Bio.Rebase.Dictionary-class.html#__filename_key,Variable Bio.SwissProt.SProt.Dictionary.__filename_key=Bio.SwissProt.SProt.Dictionary-class.html#__filename_key"><a title="Bio.Gobase.Dictionary.__filename_key
Bio.Prosite.Dictionary.__filename_key
Bio.Prosite.Prodoc.Dictionary.__filename_key
Bio.Rebase.Dictionary.__filename_key
Bio.SwissProt.SProt.Dictionary.__filename_key" class="py-name" href="#" onclick="return doclink('link-44', '__filename_key', 'link-44');">__filename_key</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'__filename'</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__init__"></a><div id="Dictionary.__init__-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="Dictionary.__init__-toggle" onclick="return toggle('Dictionary.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Dictionary-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">indexname</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="Dictionary.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__init__-expanded"><a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-docstring">"""__init__(self, indexname, parser=None)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> Open a Prodoc Dictionary. indexname is the name of the</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> index for the dictionary. The index should have been created</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> using the index_file function. parser is an optional Parser</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> object to change the results into another form. If set to None,</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> then the raw contents of the file will be returned.</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_index</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-45', 'Index', 'link-3');">Index</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-46', 'Index', 'link-3');">Index</a></tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt> <tt class="py-op">=</tt> <tt id="link-47" 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-47', 'open', 'link-47');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_index</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name" targets="Class Bio.Gobase.Dictionary=Bio.Gobase.Dictionary-class.html,Class Bio.Prosite.Dictionary=Bio.Prosite.Dictionary-class.html,Class Bio.Prosite.Prodoc.Dictionary=Bio.Prosite.Prodoc.Dictionary-class.html,Class Bio.PubMed.Dictionary=Bio.PubMed.Dictionary-class.html,Class Bio.Rebase.Dictionary=Bio.Rebase.Dictionary-class.html,Class Bio.SwissProt.SProt.Dictionary=Bio.SwissProt.SProt.Dictionary-class.html"><a title="Bio.Gobase.Dictionary
Bio.Prosite.Dictionary
Bio.Prosite.Prodoc.Dictionary
Bio.PubMed.Dictionary
Bio.Rebase.Dictionary
Bio.SwissProt.SProt.Dictionary" class="py-name" href="#" onclick="return doclink('link-48', 'Dictionary', 'link-48');">Dictionary</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Gobase.Dictionary.__filename_key
Bio.Prosite.Dictionary.__filename_key
Bio.Prosite.Prodoc.Dictionary.__filename_key
Bio.Rebase.Dictionary.__filename_key
Bio.SwissProt.SProt.Dictionary.__filename_key" class="py-name" href="#" onclick="return doclink('link-49', '__filename_key', 'link-44');">__filename_key</a></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 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="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__len__"></a><div id="Dictionary.__len__-def"><a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="Dictionary.__len__-toggle" onclick="return toggle('Dictionary.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Dictionary-class.html#__len__">__len__</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="Dictionary.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__len__-expanded"><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_index</tt><tt class="py-op">)</tt> </tt>
</div><a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__getitem__"></a><div id="Dictionary.__getitem__-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="Dictionary.__getitem__-toggle" onclick="return toggle('Dictionary.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Dictionary-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__getitem__-expanded"><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-50" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-50', 'start', 'link-50');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">len</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_index</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-51', 'key', 'link-51');">key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-52', 'seek', 'link-52');">seek</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-53', 'start', 'link-50');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-54', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_handle</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><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-55', 'read', 'link-23');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">)</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</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">_parser</tt><tt class="py-op">.</tt><tt id="link-56" 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-56', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-57', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</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-38');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-59" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-59', 'data', 'link-38');">data</a></tt> </tt>
</div><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="Dictionary.__getattr__"></a><div id="Dictionary.__getattr__-def"><a name="L177"></a><tt class="py-lineno">177</tt> <a class="py-toggle" href="#" id="Dictionary.__getattr__-toggle" onclick="return toggle('Dictionary.__getattr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.Dictionary-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Dictionary.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Dictionary.__getattr__-expanded"><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_index</tt><tt class="py-op">,</tt> <tt id="link-60" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-60');">name</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="ExPASyDictionary"></a><div id="ExPASyDictionary-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="ExPASyDictionary-toggle" onclick="return toggle('ExPASyDictionary');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html">ExPASyDictionary</a><tt class="py-op">:</tt> </tt>
</div><div id="ExPASyDictionary-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExPASyDictionary-expanded"><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-docstring">"""Access PRODOC at ExPASy using a read-only dictionary interface.</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ExPASyDictionary.__init__"></a><div id="ExPASyDictionary.__init__-def"><a name="L184"></a><tt class="py-lineno">184</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.__init__-toggle" onclick="return toggle('ExPASyDictionary.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-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">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</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="ExPASyDictionary.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.__init__-expanded"><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-docstring">"""__init__(self, delay=5.0, parser=None)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> Create a new Dictionary to access PRODOC. parser is an optional</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> parser (e.g. Prodoc.RecordParser) object to change the results</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> into another form. If set to None, then the raw contents of the</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> file will be returned. delay is the number of seconds to wait</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> between each query.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.Prosite.Prodoc.ExPASyDictionary is deprecated. Please use the function Bio.ExPASy.get_prosite_raw instead."</tt><tt class="py-op">,</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">delay</tt> <tt class="py-op">=</tt> <tt class="py-name">delay</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</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>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_query_time</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="ExPASyDictionary.__len__"></a><div id="ExPASyDictionary.__len__-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.__len__-toggle" onclick="return toggle('ExPASyDictionary.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__len__">__len__</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="ExPASyDictionary.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.__len__-expanded"><a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"Prodoc contains lots of entries"</tt> </tt>
</div><a name="ExPASyDictionary.clear"></a><div id="ExPASyDictionary.clear-def"><a name="L204"></a><tt class="py-lineno">204</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.clear-toggle" onclick="return toggle('ExPASyDictionary.clear');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#clear">clear</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="ExPASyDictionary.clear-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.clear-expanded"><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="ExPASyDictionary.__setitem__"></a><div id="ExPASyDictionary.__setitem__-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.__setitem__-toggle" onclick="return toggle('ExPASyDictionary.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExPASyDictionary.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.__setitem__-expanded"><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="ExPASyDictionary.update"></a><div id="ExPASyDictionary.update-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.update-toggle" onclick="return toggle('ExPASyDictionary.update');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update">update</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="ExPASyDictionary.update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.update-expanded"><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"This is a read-only dictionary"</tt> </tt>
</div><a name="ExPASyDictionary.copy"></a><div id="ExPASyDictionary.copy-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.copy-toggle" onclick="return toggle('ExPASyDictionary.copy');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy">copy</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="ExPASyDictionary.copy-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.copy-expanded"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't need to do this..."</tt> </tt>
</div><a name="ExPASyDictionary.keys"></a><div id="ExPASyDictionary.keys-def"><a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.keys-toggle" onclick="return toggle('ExPASyDictionary.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys">keys</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="ExPASyDictionary.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.keys-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="ExPASyDictionary.items"></a><div id="ExPASyDictionary.items-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.items-toggle" onclick="return toggle('ExPASyDictionary.items');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items">items</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="ExPASyDictionary.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.items-expanded"><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="ExPASyDictionary.values"></a><div id="ExPASyDictionary.values-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.values-toggle" onclick="return toggle('ExPASyDictionary.values');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values">values</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="ExPASyDictionary.values-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.values-expanded"><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"You don't really want to do this..."</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="ExPASyDictionary.has_key"></a><div id="ExPASyDictionary.has_key-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.has_key-toggle" onclick="return toggle('ExPASyDictionary.has_key');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key">has_key</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExPASyDictionary.has_key-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.has_key-expanded"><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-docstring">"""has_key(self, id) -> bool"""</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-61" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-61', 'id', 'link-61');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="ExPASyDictionary.get"></a><div id="ExPASyDictionary.get-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.get-toggle" onclick="return toggle('ExPASyDictionary.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> <tt class="py-param">failobj</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="ExPASyDictionary.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.get-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-62', 'id', 'link-61');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">failobj</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"How did I get here?"</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="ExPASyDictionary.__getitem__"></a><div id="ExPASyDictionary.__getitem__-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="ExPASyDictionary.__getitem__-toggle" onclick="return toggle('ExPASyDictionary.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExPASyDictionary.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ExPASyDictionary.__getitem__-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-docstring">"""__getitem__(self, id) -> object</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> Return a Prodoc entry. id is either the id or accession</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> for the entry. Raises a KeyError if there's an error.</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-63" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-63', 'time', 'link-63');">time</a></tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-64" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-64', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Package Bio.WWW=Bio.WWW-module.html"><a title="Bio.WWW" class="py-name" href="#" onclick="return doclink('link-65', 'WWW', 'link-65');">WWW</a></tt> <tt class="py-keyword">import</tt> <tt id="link-66" class="py-name" targets="Module Bio.ExPASy=Bio.ExPASy-module.html,Module Bio.WWW.ExPASy=Bio.WWW.ExPASy-module.html"><a title="Bio.ExPASy
Bio.WWW.ExPASy" class="py-name" href="#" onclick="return doclink('link-66', 'ExPASy', 'link-66');">ExPASy</a></tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-comment"># First, check to see if enough time has passed since my</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># last query.</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_query_time</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">delay</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_query_time</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">delay</tt> <tt class="py-op">-</tt> <tt id="link-67" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-67', 'time', 'link-63');">time</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-68', 'time', 'link-63');">time</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">delay</tt> <tt class="py-op">></tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt id="link-69" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-69', 'time', 'link-63');">time</a></tt><tt class="py-op">.</tt><tt class="py-name">sleep</tt><tt class="py-op">(</tt><tt class="py-name">delay</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">last_query_time</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-70', 'time', 'link-63');">time</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-71', 'time', 'link-63');">time</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt id="link-72" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-72', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.ExPASy
Bio.WWW.ExPASy" class="py-name" href="#" onclick="return doclink('link-73', 'ExPASy', 'link-66');">ExPASy</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name" targets="Function Bio.ExPASy.get_prodoc_entry()=Bio.ExPASy-module.html#get_prodoc_entry,Function Bio.WWW.ExPASy.get_prodoc_entry()=Bio.WWW.ExPASy-module.html#get_prodoc_entry"><a title="Bio.ExPASy.get_prodoc_entry
Bio.WWW.ExPASy.get_prodoc_entry" class="py-name" href="#" onclick="return doclink('link-74', 'get_prodoc_entry', 'link-74');">get_prodoc_entry</a></tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-75', 'id', 'link-61');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-76" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-76', 'id', 'link-61');">id</a></tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-77', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-78', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt class="py-name">StringHandle</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name" targets="Function Bio.Prosite.Prodoc._extract_record()=Bio.Prosite.Prodoc-module.html#_extract_record,Function Bio.Prosite._extract_record()=Bio.Prosite-module.html#_extract_record"><a title="Bio.Prosite.Prodoc._extract_record
Bio.Prosite._extract_record" class="py-name" href="#" onclick="return doclink('link-79', '_extract_record', 'link-79');">_extract_record</a></tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-80', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-81', 'id', 'link-61');">id</a></tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">parser</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</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">parser</tt><tt class="py-op">.</tt><tt id="link-82" 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-82', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-83', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-84" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-84', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><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-85', 'read', 'link-23');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> </tt>
<a name="RecordParser"></a><div id="RecordParser-def"><a name="L264"></a><tt class="py-lineno">264</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.Prosite.Prodoc.RecordParser-class.html">RecordParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses Prodoc data into a Record object.</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L268"></a><tt class="py-lineno">268</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.Prosite.Prodoc.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-op">:</tt> </tt>
</div><div id="RecordParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.__init__-expanded"><a name="L269"></a><tt class="py-lineno">269</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-86" 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-86', '_Scanner', 'link-86');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</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-87" 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-87', '_RecordConsumer', 'link-87');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
<a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L272"></a><tt class="py-lineno">272</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.Prosite.Prodoc.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="L273"></a><tt class="py-lineno">273</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-88" 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-88', 'feed', 'link-88');">feed</a></tt><tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-89', 'handle', 'link-8');">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="L274"></a><tt class="py-lineno">274</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-90" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-90', 'data', 'link-38');">data</a></tt> </tt>
</div></div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L276"></a><tt class="py-lineno">276</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.Prosite.Prodoc._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="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-docstring">"""Scans Prodoc-formatted data.</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-docstring"> Tested with:</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-docstring"> Release 15.0, July 1998</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L283"></a><tt class="py-lineno">283</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.Prosite.Prodoc._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="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-docstring">"""feed(self, handle, consumer)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-docstring"> Feed in Prodoc data for scanning. handle is a file-like</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"> object that contains prosite data. consumer is a</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"> Consumer object that will receive events as the report is scanned.</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-91" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-91', 'handle', 'link-8');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-92', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-93', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-94" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-94', 'handle', 'link-8');">handle</a></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt> <tt class="py-op">=</tt> <tt id="link-95" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-95', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-96', 'UndoHandle', 'link-34');">UndoHandle</a></tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-97', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name" targets="Method Bio.File.UndoHandle.peekline()=Bio.File.UndoHandle-class.html#peekline"><a title="Bio.File.UndoHandle.peekline" class="py-name" href="#" onclick="return doclink('link-98', 'peekline', 'link-98');">peekline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-99" class="py-name" targets="Function Bio.ParserSupport.is_blank_line()=Bio.ParserSupport-module.html#is_blank_line"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-99', 'is_blank_line', 'link-99');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-comment"># Skip blank lines between records</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><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-100', 'readline', 'link-36');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name" targets="Method Bio.Compass._Scanner._scan_record()=Bio.Compass._Scanner-class.html#_scan_record,Method Bio.Enzyme._Scanner._scan_record()=Bio.Enzyme._Scanner-class.html#_scan_record,Method Bio.Gobase._Scanner._scan_record()=Bio.Gobase._Scanner-class.html#_scan_record,Method Bio.Medline._Scanner._scan_record()=Bio.Medline._Scanner-class.html#_scan_record,Method Bio.Prosite.Prodoc._Scanner._scan_record()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_record,Method Bio.Prosite._Scanner._scan_record()=Bio.Prosite._Scanner-class.html#_scan_record,Method Bio.Rebase._Scanner._scan_record()=Bio.Rebase._Scanner-class.html#_scan_record,Method Bio.Sequencing.Ace._Scanner._scan_record()=Bio.Sequencing.Ace._Scanner-class.html#_scan_record,Method Bio.Sequencing.Phd._Scanner._scan_record()=Bio.Sequencing.Phd._Scanner-class.html#_scan_record,Method Bio.SwissProt.SProt._Scanner._scan_record()=Bio.SwissProt.SProt._Scanner-class.html#_scan_record"><a title="Bio.Compass._Scanner._scan_record
Bio.Enzyme._Scanner._scan_record
Bio.Gobase._Scanner._scan_record
Bio.Medline._Scanner._scan_record
Bio.Prosite.Prodoc._Scanner._scan_record
Bio.Prosite._Scanner._scan_record
Bio.Rebase._Scanner._scan_record
Bio.Sequencing.Ace._Scanner._scan_record
Bio.Sequencing.Phd._Scanner._scan_record
Bio.SwissProt.SProt._Scanner._scan_record" class="py-name" href="#" onclick="return doclink('link-101', '_scan_record', 'link-101');">_scan_record</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
</div><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_record"></a><div id="_Scanner._scan_record-def"><a name="L307"></a><tt class="py-lineno">307</tt> <a class="py-toggle" href="#" id="_Scanner._scan_record-toggle" onclick="return toggle('_Scanner._scan_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_record">_scan_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_record-expanded"><a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Medline._RecordConsumer.start_record()=Bio.Medline._RecordConsumer-class.html#start_record,Method Bio.PopGen.FDist._RecordConsumer.start_record()=Bio.PopGen.FDist._RecordConsumer-class.html#start_record,Method Bio.PopGen.GenePop._RecordConsumer.start_record()=Bio.PopGen.GenePop._RecordConsumer-class.html#start_record,Method Bio.Prosite.Prodoc._RecordConsumer.start_record()=Bio.Prosite.Prodoc._RecordConsumer-class.html#start_record,Method Bio.Prosite._RecordConsumer.start_record()=Bio.Prosite._RecordConsumer-class.html#start_record,Method Bio.SwissProt.SProt._RecordConsumer.start_record()=Bio.SwissProt.SProt._RecordConsumer-class.html#start_record,Method Bio.SwissProt.SProt._SequenceConsumer.start_record()=Bio.SwissProt.SProt._SequenceConsumer-class.html#start_record,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.start_record()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#start_record"><a title="Bio.Medline._RecordConsumer.start_record
Bio.PopGen.FDist._RecordConsumer.start_record
Bio.PopGen.GenePop._RecordConsumer.start_record
Bio.Prosite.Prodoc._RecordConsumer.start_record
Bio.Prosite._RecordConsumer.start_record
Bio.SwissProt.SProt._RecordConsumer.start_record
Bio.SwissProt.SProt._SequenceConsumer.start_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.start_record" class="py-name" href="#" onclick="return doclink('link-102', 'start_record', 'link-102');">start_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method Bio.Prosite.Prodoc._Scanner._scan_accession()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_accession"><a title="Bio.Prosite.Prodoc._Scanner._scan_accession" class="py-name" href="#" onclick="return doclink('link-103', '_scan_accession', 'link-103');">_scan_accession</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Method Bio.Prosite.Prodoc._Scanner._scan_prosite_refs()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_prosite_refs"><a title="Bio.Prosite.Prodoc._Scanner._scan_prosite_refs" class="py-name" href="#" onclick="return doclink('link-104', '_scan_prosite_refs', 'link-104');">_scan_prosite_refs</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt id="link-105" class="py-name" targets="Function Bio.ParserSupport.read_and_call()=Bio.ParserSupport-module.html#read_and_call"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-105', 'read_and_call', 'link-105');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.noevent()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#noevent,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#noevent,Method Bio.MEME.Parser._MASTConsumer.noevent()=Bio.MEME.Parser._MASTConsumer-class.html#noevent,Method Bio.MEME.Parser._MEMEConsumer.noevent()=Bio.MEME.Parser._MEMEConsumer-class.html#noevent"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-106', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-107" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-107', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'{BEGIN}'</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Method Bio.Prosite.Prodoc._Scanner._scan_text()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_text"><a title="Bio.Prosite.Prodoc._Scanner._scan_text" class="py-name" href="#" onclick="return doclink('link-108', '_scan_text', 'link-108');">_scan_text</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method Bio.Prosite.Prodoc._Scanner._scan_refs()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_refs"><a title="Bio.Prosite.Prodoc._Scanner._scan_refs" class="py-name" href="#" onclick="return doclink('link-109', '_scan_refs', 'link-109');">_scan_refs</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Method Bio.Prosite.Prodoc._Scanner._scan_copyright()=Bio.Prosite.Prodoc._Scanner-class.html#_scan_copyright"><a title="Bio.Prosite.Prodoc._Scanner._scan_copyright" class="py-name" href="#" onclick="return doclink('link-110', '_scan_copyright', 'link-110');">_scan_copyright</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-111', 'read_and_call', 'link-105');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-112', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-113" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-113', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'{END}'</tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.end_record()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#end_record,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#end_record,Method Bio.Medline._RecordConsumer.end_record()=Bio.Medline._RecordConsumer-class.html#end_record,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#end_record,Method Bio.PopGen.FDist._RecordConsumer.end_record()=Bio.PopGen.FDist._RecordConsumer-class.html#end_record,Method Bio.PopGen.GenePop._RecordConsumer.end_record()=Bio.PopGen.GenePop._RecordConsumer-class.html#end_record,Method Bio.Prosite.Prodoc._RecordConsumer.end_record()=Bio.Prosite.Prodoc._RecordConsumer-class.html#end_record,Method Bio.Prosite._RecordConsumer.end_record()=Bio.Prosite._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._RecordConsumer.end_record()=Bio.SwissProt.SProt._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._SequenceConsumer.end_record()=Bio.SwissProt.SProt._SequenceConsumer-class.html#end_record,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#end_record"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.end_record
Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record
Bio.Medline._RecordConsumer.end_record
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record
Bio.PopGen.FDist._RecordConsumer.end_record
Bio.PopGen.GenePop._RecordConsumer.end_record
Bio.Prosite.Prodoc._RecordConsumer.end_record
Bio.Prosite._RecordConsumer.end_record
Bio.SwissProt.SProt._RecordConsumer.end_record
Bio.SwissProt.SProt._SequenceConsumer.end_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record" class="py-name" href="#" onclick="return doclink('link-114', 'end_record', 'link-114');">end_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_accession"></a><div id="_Scanner._scan_accession-def"><a name="L320"></a><tt class="py-lineno">320</tt> <a class="py-toggle" href="#" id="_Scanner._scan_accession-toggle" onclick="return toggle('_Scanner._scan_accession');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_accession">_scan_accession</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_accession-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_accession-expanded"><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-115', 'read_and_call', 'link-105');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-116', 'accession', 'link-26');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-117', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'{PDOC'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_prosite_refs"></a><div id="_Scanner._scan_prosite_refs-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="_Scanner._scan_prosite_refs-toggle" onclick="return toggle('_Scanner._scan_prosite_refs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_prosite_refs">_scan_prosite_refs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_prosite_refs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_prosite_refs-expanded"><a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-118" class="py-name" targets="Function Bio.ParserSupport.attempt_read_and_call()=Bio.ParserSupport-module.html#attempt_read_and_call"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-118', 'attempt_read_and_call', 'link-118');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name" targets="Method Bio.Enzyme._RecordConsumer.prosite_reference()=Bio.Enzyme._RecordConsumer-class.html#prosite_reference,Method Bio.Prosite.Prodoc._RecordConsumer.prosite_reference()=Bio.Prosite.Prodoc._RecordConsumer-class.html#prosite_reference"><a title="Bio.Enzyme._RecordConsumer.prosite_reference
Bio.Prosite.Prodoc._RecordConsumer.prosite_reference" class="py-name" href="#" onclick="return doclink('link-119', 'prosite_reference', 'link-119');">prosite_reference</a></tt><tt class="py-op">,</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-120', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'{PS'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_text"></a><div id="_Scanner._scan_text-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="_Scanner._scan_text-toggle" onclick="return toggle('_Scanner._scan_text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_text">_scan_text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_text-expanded"><a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name" targets="Function Bio.ParserSupport.safe_readline()=Bio.ParserSupport-module.html#safe_readline"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-121', 'safe_readline', 'link-121');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</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-keyword">and</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">']'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'{END}'</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-122" 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-122', 'saveline', 'link-122');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-123" 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-123', 'text', 'link-7');">text</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_refs"></a><div id="_Scanner._scan_refs-def"><a name="L337"></a><tt class="py-lineno">337</tt> <a class="py-toggle" href="#" id="_Scanner._scan_refs-toggle" onclick="return toggle('_Scanner._scan_refs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_refs">_scan_refs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_refs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_refs-expanded"><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-124" class="py-name"><a title="Bio.ParserSupport.safe_readline" class="py-name" href="#" onclick="return doclink('link-124', 'safe_readline', 'link-121');">safe_readline</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</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">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'{END}'</tt> <tt class="py-keyword">or</tt> <tt id="link-125" class="py-name"><a title="Bio.ParserSupport.is_blank_line" class="py-name" href="#" onclick="return doclink('link-125', 'is_blank_line', 'link-99');">is_blank_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">uhandle</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.File.UndoHandle.saveline" class="py-name" href="#" onclick="return doclink('link-126', 'saveline', 'link-122');">saveline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.reference()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#reference,Method Bio.Prosite.Prodoc._RecordConsumer.reference()=Bio.Prosite.Prodoc._RecordConsumer-class.html#reference,Variable Bio.expressions.embl.embl65.reference=Bio.expressions.embl.embl65-module.html#reference,Variable Bio.expressions.genbank.reference=Bio.expressions.genbank-module.html#reference,Variable Bio.expressions.swissprot.sprot38.reference=Bio.expressions.swissprot.sprot38-module.html#reference,Variable Martel.test.test_swissprot38.reference=Martel.test.test_swissprot38-module.html#reference,Variable Martel.test.testformats.swissprot38.reference=Martel.test.testformats.swissprot38-module.html#reference"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-127', 'reference', 'link-127');">reference</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
</div><a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="_Scanner._scan_copyright"></a><div id="_Scanner._scan_copyright-def"><a name="L345"></a><tt class="py-lineno">345</tt> <a class="py-toggle" href="#" id="_Scanner._scan_copyright-toggle" onclick="return toggle('_Scanner._scan_copyright');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._Scanner-class.html#_scan_copyright">_scan_copyright</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">uhandle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner._scan_copyright-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner._scan_copyright-expanded"><a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-comment"># Cayte Lindner found some PRODOC records with the copyrights</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># appended at the end. We'll try and recognize these.</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-128" class="py-name" targets="Function Bio.ParserSupport.read_and_call_while()=Bio.ParserSupport-module.html#read_and_call_while"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-128', 'read_and_call_while', 'link-128');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-129', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-130" class="py-name" targets="Variable Bio.MetaTool.metatool_format.blank=Bio.MetaTool.metatool_format-module.html#blank"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-130', 'blank', 'link-130');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-131" class="py-name"><a title="Bio.ParserSupport.attempt_read_and_call" class="py-name" href="#" onclick="return doclink('link-131', 'attempt_read_and_call', 'link-118');">attempt_read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-132', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-133" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-133', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'+----'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt id="link-134" class="py-name" targets="Function Bio.ParserSupport.read_and_call_until()=Bio.ParserSupport-module.html#read_and_call_until"><a title="Bio.ParserSupport.read_and_call_until" class="py-name" href="#" onclick="return doclink('link-134', 'read_and_call_until', 'link-134');">read_and_call_until</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-135', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-136" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-136', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'+----'</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt id="link-137" class="py-name"><a title="Bio.ParserSupport.read_and_call" class="py-name" href="#" onclick="return doclink('link-137', 'read_and_call', 'link-105');">read_and_call</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-138', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-139" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-139', 'start', 'link-50');">start</a></tt><tt class="py-op">=</tt><tt class="py-string">'+----'</tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt id="link-140" class="py-name"><a title="Bio.ParserSupport.read_and_call_while" class="py-name" href="#" onclick="return doclink('link-140', 'read_and_call_while', 'link-128');">read_and_call_while</a></tt><tt class="py-op">(</tt><tt class="py-name">uhandle</tt><tt class="py-op">,</tt> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.noevent
Bio.Blast.NCBIStandalone._BlastErrorConsumer.noevent
Bio.MEME.Parser._MASTConsumer.noevent
Bio.MEME.Parser._MEMEConsumer.noevent" class="py-name" href="#" onclick="return doclink('link-141', 'noevent', 'link-106');">noevent</a></tt><tt class="py-op">,</tt> <tt id="link-142" class="py-name"><a title="Bio.MetaTool.metatool_format.blank" class="py-name" href="#" onclick="return doclink('link-142', 'blank', 'link-130');">blank</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L354"></a><tt class="py-lineno">354</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.Prosite.Prodoc._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_RecordConsumer-expanded"><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-docstring">"""Consumer that converts a Prodoc record to a Record object.</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> data Record with Prodoc data.</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L361"></a><tt class="py-lineno">361</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.Prosite.Prodoc._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="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-143', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.start_record"></a><div id="_RecordConsumer.start_record-def"><a name="L364"></a><tt class="py-lineno">364</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_record-toggle" onclick="return toggle('_RecordConsumer.start_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#start_record">start_record</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.start_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_record-expanded"><a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-144', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-145" 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-145', 'Record', 'link-145');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_record"></a><div id="_RecordConsumer.end_record-def"><a name="L367"></a><tt class="py-lineno">367</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_record-toggle" onclick="return toggle('_RecordConsumer.end_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#end_record">end_record</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.end_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_record-expanded"><a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-146" class="py-name" targets="Method Bio.Prosite.Prodoc._RecordConsumer._clean_data()=Bio.Prosite.Prodoc._RecordConsumer-class.html#_clean_data"><a title="Bio.Prosite.Prodoc._RecordConsumer._clean_data" class="py-name" href="#" onclick="return doclink('link-146', '_clean_data', 'link-146');">_clean_data</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.accession"></a><div id="_RecordConsumer.accession-def"><a name="L370"></a><tt class="py-lineno">370</tt> <a class="py-toggle" href="#" id="_RecordConsumer.accession-toggle" onclick="return toggle('_RecordConsumer.accession');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#accession">accession</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.accession-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.accession-expanded"><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">if</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-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">'}'</tt><tt class="py-op">:</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand accession line\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt id="link-147" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.acc=Bio.FSSP.fssp_rec.align-class.html#acc"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-147', 'acc', 'link-147');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-148" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-148', 'acc', 'link-147');">acc</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">'PDOC'</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</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">"Invalid accession in line\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-149', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-150', 'accession', 'link-26');">accession</a></tt> <tt class="py-op">=</tt> <tt id="link-151" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-151', 'acc', 'link-147');">acc</a></tt> </tt>
</div><a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.prosite_reference"></a><div id="_RecordConsumer.prosite_reference-def"><a name="L379"></a><tt class="py-lineno">379</tt> <a class="py-toggle" href="#" id="_RecordConsumer.prosite_reference-toggle" onclick="return toggle('_RecordConsumer.prosite_reference');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#prosite_reference">prosite_reference</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.prosite_reference-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.prosite_reference-expanded"><a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">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-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt class="py-string">'}'</tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"I don't understand accession line\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-152', 'acc', 'link-147');">acc</a></tt><tt class="py-op">,</tt> <tt id="link-153" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-153', 'name', 'link-60');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-154', 'split', 'link-154');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'; '</tt><tt class="py-op">)</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-155', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">prosite_refs</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-156', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-157', 'acc', 'link-147');">acc</a></tt><tt class="py-op">,</tt> <tt id="link-158" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-158', 'name', 'link-60');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.text"></a><div id="_RecordConsumer.text-def"><a name="L386"></a><tt class="py-lineno">386</tt> <a class="py-toggle" href="#" id="_RecordConsumer.text-toggle" onclick="return toggle('_RecordConsumer.text');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#text">text</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.text-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.text-expanded"><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-159', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt id="link-160" 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-160', 'text', 'link-7');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-161', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt id="link-162" 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-162', 'text', 'link-7');">text</a></tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.reference"></a><div id="_RecordConsumer.reference-def"><a name="L389"></a><tt class="py-lineno">389</tt> <a class="py-toggle" href="#" id="_RecordConsumer.reference-toggle" onclick="return toggle('_RecordConsumer.reference');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#reference">reference</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.reference-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.reference-expanded"><a name="L390"></a><tt class="py-lineno">390</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-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'['</tt> <tt class="py-keyword">and</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">']'</tt><tt class="py-op">:</tt> <tt class="py-comment"># new reference</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name" targets="Class Bio.GenBank.Record.Reference=Bio.GenBank.Record.Reference-class.html,Class Bio.Prosite.Prodoc.Reference=Bio.Prosite.Prodoc.Reference-class.html,Class Bio.SeqFeature.Reference=Bio.SeqFeature.Reference-class.html,Class Bio.SwissProt.SProt.Reference=Bio.SwissProt.SProt.Reference-class.html"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-163', 'Reference', 'link-163');">Reference</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">.</tt><tt class="py-name">number</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-164" 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-164', 'strip', 'link-164');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'E'</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-comment"># If it's an electronic reference, then the URL is on the</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># line, instead of the author.</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</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">_ref</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-165', 'strip', 'link-164');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-166', 'authors', 'link-28');">authors</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-167', 'strip', 'link-164');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-168', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">references</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-169', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">' '</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</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">"Unnumbered reference lines\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ref</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-string">"I don't understand the reference line\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt> </tt>
</div><a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer._clean_data"></a><div id="_RecordConsumer._clean_data-def"><a name="L407"></a><tt class="py-lineno">407</tt> <a class="py-toggle" href="#" id="_RecordConsumer._clean_data-toggle" onclick="return toggle('_RecordConsumer._clean_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc._RecordConsumer-class.html#_clean_data">_clean_data</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._clean_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer._clean_data-expanded"><a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-comment"># get rid of trailing newlines</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">ref</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-170', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">references</tt><tt class="py-op">:</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">ref</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt> <tt class="py-op">=</tt> <tt class="py-name">ref</tt><tt class="py-op">.</tt><tt class="py-name">citation</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">ref</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-171', 'authors', 'link-28');">authors</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ref</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-172', 'authors', 'link-28');">authors</a></tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> </tt>
<a name="index_file"></a><div id="index_file-def"><a name="L413"></a><tt class="py-lineno">413</tt> <a class="py-toggle" href="#" id="index_file-toggle" onclick="return toggle('index_file');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc-module.html#index_file">index_file</a><tt class="py-op">(</tt><tt class="py-param">filename</tt><tt class="py-op">,</tt> <tt class="py-param">indexname</tt><tt class="py-op">,</tt> <tt class="py-param">rec2key</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="index_file-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="index_file-expanded"><a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-docstring">"""index_file(filename, indexname, rec2key=None)</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> Index a Prodoc file. filename is the name of the file.</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-docstring"> indexname is the name of the dictionary. rec2key is an</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-docstring"> optional callback that takes a Record and generates a unique key</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"> (e.g. the accession number) for the record. If not specified,</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> the id name will be used.</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</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 id="link-173" class="py-name" targets="Method Bio.biblio.Biblio.exists()=Bio.biblio.Biblio-class.html#exists,Method Bio.biblio.BiblioCollection.exists()=Bio.biblio.BiblioCollection-class.html#exists"><a title="Bio.biblio.Biblio.exists
Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-173', 'exists', 'link-173');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"%s does not exist"</tt> <tt class="py-op">%</tt> <tt class="py-name">filename</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt id="link-174" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-174', 'index', 'link-174');">index</a></tt> <tt class="py-op">=</tt> <tt id="link-175" class="py-name"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-175', 'Index', 'link-3');">Index</a></tt><tt class="py-op">.</tt><tt id="link-176" class="py-name"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-176', 'Index', 'link-3');">Index</a></tt><tt class="py-op">(</tt><tt class="py-name">indexname</tt><tt class="py-op">,</tt> <tt class="py-name">truncate</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt id="link-177" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-177', 'index', 'link-174');">index</a></tt><tt class="py-op">[</tt><tt id="link-178" class="py-name"><a title="Bio.Gobase.Dictionary
Bio.Prosite.Dictionary
Bio.Prosite.Prodoc.Dictionary
Bio.PubMed.Dictionary
Bio.Rebase.Dictionary
Bio.SwissProt.SProt.Dictionary" class="py-name" href="#" onclick="return doclink('link-178', 'Dictionary', 'link-48');">Dictionary</a></tt><tt class="py-op">.</tt><tt class="py-name">_Dictionary__filename_key</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">filename</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt id="link-179" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-179', 'handle', 'link-8');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-180" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-180', 'open', 'link-47');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-181" 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-181', 'parse', 'link-13');">parse</a></tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-182', 'handle', 'link-8');">handle</a></tt><tt class="py-op">)</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt id="link-183" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-183', 'end', 'link-183');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0L</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-184" 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-184', 'record', 'link-12');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt id="link-185" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-185', 'start', 'link-50');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-186" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-186', 'end', 'link-183');">end</a></tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt id="link-187" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-187', 'end', 'link-183');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-188', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-189" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-189', 'tell', 'link-189');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt id="link-190" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-190', 'length', 'link-190');">length</a></tt> <tt class="py-op">=</tt> <tt id="link-191" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-191', 'end', 'link-183');">end</a></tt> <tt class="py-op">-</tt> <tt id="link-192" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-192', 'start', 'link-50');">start</a></tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rec2key</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt id="link-193" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-193', 'key', 'link-51');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rec2key</tt><tt class="py-op">(</tt><tt id="link-194" 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-194', 'record', 'link-12');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt id="link-195" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-195', 'key', 'link-51');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-196" 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-196', 'record', 'link-12');">record</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-197', 'accession', 'link-26');">accession</a></tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-198" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-198', 'key', 'link-51');">key</a></tt><tt class="py-op">:</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-string">"empty key was produced"</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-199" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-199', 'index', 'link-174');">index</a></tt><tt class="py-op">.</tt><tt id="link-200" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-200', 'has_key', 'link-200');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-201" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-201', 'key', 'link-51');">key</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-string">"duplicate key %s found"</tt> <tt class="py-op">%</tt> <tt id="link-202" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-202', 'key', 'link-51');">key</a></tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt id="link-203" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-203', 'index', 'link-174');">index</a></tt><tt class="py-op">[</tt><tt id="link-204" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-204', 'key', 'link-51');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-205" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-205', 'start', 'link-50');">start</a></tt><tt class="py-op">,</tt> <tt id="link-206" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-206', 'length', 'link-190');">length</a></tt> </tt>
</div><a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-comment"># This function can be deprecated once Bio.Prosite.Prodoc.ExPASyDictionary</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># is removed.</tt> </tt>
<a name="_extract_record"></a><div id="_extract_record-def"><a name="L452"></a><tt class="py-lineno">452</tt> <a class="py-toggle" href="#" id="_extract_record-toggle" onclick="return toggle('_extract_record');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Prosite.Prodoc-module.html#_extract_record">_extract_record</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="_extract_record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_extract_record-expanded"><a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-docstring">"""_extract_record(handle) -> str</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"> Extract PRODOC data from a web page. Raises a ValueError if no</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-docstring"> data was found in the web page.</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-comment"># All the data appears between tags:</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># <pre width = 80>ID NIR_SIR; PATTERN.</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </PRE></tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">class</tt> <tt class="py-def-name">parser</tt><tt class="py-op">(</tt><tt class="py-base-class">sgmllib</tt><tt class="py-op">.</tt><tt class="py-base-class">SGMLParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">sgmllib</tt><tt class="py-op">.</tt><tt class="py-name">SGMLParser</tt><tt class="py-op">.</tt><tt id="link-207" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method 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Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-207', '__init__', 'link-207');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_pre</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-208', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">handle_data</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_pre</tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-209', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-210', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt id="link-211" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-211', 'data', 'link-38');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">do_br</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_pre</tt><tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-212', 'data', 'link-38');">data</a></tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-213', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">start_pre</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attrs</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_pre</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">end_pre</tt><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_in_pre</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div></div><a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-214', 'feed', 'link-88');">feed</a></tt><tt class="py-op">(</tt><tt id="link-215" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-215', 'handle', 'link-8');">handle</a></tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><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-216', 'read', 'link-23');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt id="link-217" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-217', 'data', 'link-38');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-218', 'data', 'link-38');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-219" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-219', 'data', 'link-38');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</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 data found in web page."</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-220" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-220', 'data', 'link-38');">data</a></tt> </tt>
</div><a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> </tt><script type="text/javascript">
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