<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.formatdefs.sequence</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.formatdefs-module.html">Package formatdefs</a> :: Module sequence </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.formatdefs.sequence-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.formatdefs.sequence-module.html">Module Bio.formatdefs.sequence</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-1', 'config', 'link-1');">config</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.config.FormatRegistry=Bio.config.FormatRegistry-module.html,Class Bio.config.FormatRegistry.FormatRegistry=Bio.config.FormatRegistry.FormatRegistry-class.html"><a title="Bio.config.FormatRegistry Bio.config.FormatRegistry.FormatRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'FormatRegistry', 'link-2');">FormatRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.FormatRegistry.FormatObject=Bio.config.FormatRegistry.FormatObject-class.html"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-3', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.FormatRegistry.FormatGroup=Bio.config.FormatRegistry.FormatGroup-class.html"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-4', 'FormatGroup', 'link-4');">FormatGroup</a></tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Module Bio.dbdefs.fasta=Bio.dbdefs.fasta-module.html,Variable Bio.dbdefs.fasta.fasta=Bio.dbdefs.fasta-module.html#fasta,Module Bio.expressions.fasta=Bio.expressions.fasta-module.html,Variable Bio.formatdefs.sequence.fasta=Bio.formatdefs.sequence-module.html#fasta,Module Bio.writers.SeqRecord.fasta=Bio.writers.SeqRecord.fasta-module.html"><a title="Bio.dbdefs.fasta Bio.dbdefs.fasta.fasta Bio.expressions.fasta Bio.formatdefs.sequence.fasta Bio.writers.SeqRecord.fasta" class="py-name" href="#" onclick="return doclink('link-5', 'fasta', 'link-5');">fasta</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.config.FormatRegistry.FormatObject" class="py-name" href="#" onclick="return doclink('link-6', 'FormatObject', 'link-3');">FormatObject</a></tt><tt class="py-op">(</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> <tt id="link-7" 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-7', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"fasta"</tt><tt class="py-op">,</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> <tt class="py-name">expression</tt><tt class="py-op">=</tt><tt class="py-string">"Bio.expressions.fasta.format"</tt><tt class="py-op">,</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt id="link-8" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.empty()=Bio.Pathway.Rep.HashSet.HashSet-class.html#empty,Variable Bio.formatdefs.sequence.empty=Bio.formatdefs.sequence-module.html#empty,Module Bio.writers.SeqRecord.empty=Bio.writers.SeqRecord.empty-module.html"><a title="Bio.Pathway.Rep.HashSet.HashSet.empty Bio.formatdefs.sequence.empty Bio.writers.SeqRecord.empty" class="py-name" href="#" onclick="return doclink('link-8', 'empty', 'link-8');">empty</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-9', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"empty"</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-11', 'sequence', 'link-11');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.config.FormatRegistry.FormatGroup" class="py-name" href="#" onclick="return doclink('link-12', 'FormatGroup', 'link-4');">FormatGroup</a></tt><tt class="py-op">(</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-7');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"sequence"</tt><tt class="py-op">,</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt id="link-14" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence Bio.Emboss.primer3_format.sequence Bio.FSSP.FSSPAlignDict.sequence Bio.GenBank._FeatureConsumer.sequence Bio.GenBank._RecordConsumer.sequence Bio.IntelliGenetics._RecordConsumer.sequence Bio.Rebase._RecordConsumer.sequence Bio.Std.sequence Bio.builders.SeqRecord.sequence Bio.expressions.fasta.sequence Bio.expressions.genbank.sequence Bio.expressions.swissprot.sprot38.sequence Bio.formatdefs.sequence Bio.formatdefs.sequence.sequence Martel.test.test_swissprot38.sequence Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-14', 'sequence', 'link-11');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add Bio.EUtils.POM.ElementNode.add Bio.GFF.easy.Location.add Bio.Graphics.BasicChromosome._ChromosomeComponent.add Bio.LogisticRegression.add Bio.MarkovModel.add Bio.MaxEntropy.add Bio.NaiveBayes.add Bio.Nexus.Nexus.StepMatrix.add Bio.Nexus.Nodes.Chain.add Bio.PDB.Entity.Entity.add Bio.PDB.Residue.DisorderedResidue.add Bio.PDB.Residue.Residue.add Bio.Pathway.Rep.HashSet.HashSet.add Bio.Restriction.Restriction.RestrictionBatch.add Bio.Statistics.lowess.add Bio.config.FormatRegistry.FormatGroup.add Bio.config.Registry.RegisterableGroup.add Bio.distance.add Bio.kNN.add Martel.Dispatch.MulticallEnd.add Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-15', 'add', 'link-15');">add</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.dbdefs.fasta Bio.dbdefs.fasta.fasta Bio.expressions.fasta Bio.formatdefs.sequence.fasta Bio.writers.SeqRecord.fasta" class="py-name" href="#" onclick="return doclink('link-16', 'fasta', 'link-5');">fasta</a></tt><tt class="py-op">)</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:52 2008 </td> <td align="right" class="footer"> <a 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