<?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.dbdefs.swissprot</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.dbdefs-module.html">Package dbdefs</a> :: Module swissprot </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.dbdefs.swissprot-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.dbdefs.swissprot-module.html">Module Bio.dbdefs.swissprot</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 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-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.DBRegistry=Bio.config.DBRegistry-module.html,Class Bio.config.DBRegistry.DBRegistry=Bio.config.DBRegistry.DBRegistry-class.html"><a title="Bio.config.DBRegistry Bio.config.DBRegistry.DBRegistry" class="py-name" href="#" onclick="return doclink('link-2', 'DBRegistry', 'link-2');">DBRegistry</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.config.DBRegistry.CGIDB=Bio.config.DBRegistry.CGIDB-class.html"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-3', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Class Bio.config.DBRegistry.DBGroup=Bio.config.DBRegistry.DBGroup-class.html"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-4', 'DBGroup', 'link-4');">DBGroup</a></tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name" targets="Module Bio.config._support=Bio.config._support-module.html,Module Bio.dbdefs._support=Bio.dbdefs._support-module.html"><a title="Bio.config._support Bio.dbdefs._support" class="py-name" href="#" onclick="return doclink('link-5', '_support', 'link-5');">_support</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable Bio.dbdefs.swissprot.swissprot_expasy_cgi=Bio.dbdefs.swissprot-module.html#swissprot_expasy_cgi"><a title="Bio.dbdefs.swissprot.swissprot_expasy_cgi" class="py-name" href="#" onclick="return doclink('link-6', 'swissprot_expasy_cgi', 'link-6');">swissprot_expasy_cgi</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-7', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">(</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt id="link-8" 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-8', 'name', 'link-8');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"swissprot-expasy-cgi"</tt><tt class="py-op">,</tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-name">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Retrieve a swiss-prot entry by ID from ExPASy."</tt><tt class="py-op">,</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">cgi</tt><tt class="py-op">=</tt><tt class="py-string">"http://www.expasy.ch/cgi-bin/get-sprot-raw.pl"</tt><tt class="py-op">,</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt id="link-9" 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-9', 'key', 'link-9');">key</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">failure_cases</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-10" class="py-name" targets="Variable Bio.dbdefs._support.blank_expr=Bio.dbdefs._support-module.html#blank_expr"><a title="Bio.dbdefs._support.blank_expr" class="py-name" href="#" onclick="return doclink('link-10', 'blank_expr', 'link-10');">blank_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"no results"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Variable Bio.dbdefs.swissprot.swissprot_usmirror_cgi=Bio.dbdefs.swissprot-module.html#swissprot_usmirror_cgi"><a title="Bio.dbdefs.swissprot.swissprot_usmirror_cgi" class="py-name" href="#" onclick="return doclink('link-11', 'swissprot_usmirror_cgi', 'link-11');">swissprot_usmirror_cgi</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.config.DBRegistry.CGIDB" class="py-name" href="#" onclick="return doclink('link-12', 'CGIDB', 'link-3');">CGIDB</a></tt><tt class="py-op">(</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-8');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"swissprot-usmirror-cgi"</tt><tt class="py-op">,</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-name">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Retrieve a swiss-prot entry by ID from the US mirror."</tt><tt class="py-op">,</tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-name">cgi</tt><tt class="py-op">=</tt><tt class="py-string">"http://us.expasy.org/cgi-bin/get-sprot-raw.pl"</tt><tt class="py-op">,</tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">delay</tt><tt class="py-op">=</tt><tt class="py-number">5.0</tt><tt class="py-op">,</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">params</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-14', 'key', 'link-9');">key</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">failure_cases</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Bio.dbdefs._support.blank_expr" class="py-name" href="#" onclick="return doclink('link-15', 'blank_expr', 'link-10');">blank_expr</a></tt><tt class="py-op">,</tt> <tt class="py-string">"no results"</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt id="link-16" class="py-name" targets="Module Bio.dbdefs.swissprot=Bio.dbdefs.swissprot-module.html,Variable Bio.dbdefs.swissprot.swissprot=Bio.dbdefs.swissprot-module.html#swissprot,Package Bio.expressions.swissprot=Bio.expressions.swissprot-module.html,Module Bio.formatdefs.swissprot=Bio.formatdefs.swissprot-module.html,Variable Bio.formatdefs.swissprot.swissprot=Bio.formatdefs.swissprot-module.html#swissprot"><a title="Bio.dbdefs.swissprot Bio.dbdefs.swissprot.swissprot Bio.expressions.swissprot Bio.formatdefs.swissprot Bio.formatdefs.swissprot.swissprot" class="py-name" href="#" onclick="return doclink('link-16', 'swissprot', 'link-16');">swissprot</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.config.DBRegistry.DBGroup" class="py-name" href="#" onclick="return doclink('link-17', 'DBGroup', 'link-4');">DBGroup</a></tt><tt class="py-op">(</tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt id="link-18" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-18', 'name', 'link-8');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"swissprot"</tt><tt class="py-op">,</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">behavior</tt><tt class="py-op">=</tt><tt class="py-string">"serial"</tt><tt class="py-op">,</tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Retrieve a swiss-prot entry by ID. Will try different servers until one works."</tt><tt class="py-op">,</tt> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt id="link-19" class="py-name"><a title="Bio.dbdefs.swissprot Bio.dbdefs.swissprot.swissprot Bio.expressions.swissprot Bio.formatdefs.swissprot Bio.formatdefs.swissprot.swissprot" class="py-name" href="#" onclick="return doclink('link-19', 'swissprot', 'link-16');">swissprot</a></tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'add', 'link-20');">add</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.dbdefs.swissprot.swissprot_expasy_cgi" class="py-name" href="#" onclick="return doclink('link-21', 'swissprot_expasy_cgi', 'link-6');">swissprot_expasy_cgi</a></tt><tt class="py-op">)</tt> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt id="link-22" class="py-name"><a title="Bio.dbdefs.swissprot Bio.dbdefs.swissprot.swissprot Bio.expressions.swissprot Bio.formatdefs.swissprot Bio.formatdefs.swissprot.swissprot" class="py-name" href="#" onclick="return doclink('link-22', 'swissprot', 'link-16');">swissprot</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><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-23', 'add', 'link-20');">add</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.dbdefs.swissprot.swissprot_usmirror_cgi" class="py-name" href="#" onclick="return doclink('link-24', 'swissprot_usmirror_cgi', 'link-11');">swissprot_usmirror_cgi</a></tt><tt class="py-op">)</tt> </tt> <a name="L36"></a><tt class="py-lineno">36</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 target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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