<?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.SeqIO.NexusIO</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.SeqIO-module.html">Package SeqIO</a> :: Module NexusIO </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.SeqIO.NexusIO-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.SeqIO.NexusIO-module.html">Module Bio.SeqIO.NexusIO</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 2006 by Peter Cock. 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">#</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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""Bio.SeqIO support for the "nexus" file format.</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">You were expected to use this module via the Bio.SeqIO functions.</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">This module has now been replaced by Bio.AlignIO.NexusIO, and is</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">deprecated."""</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 class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</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.SeqIO.NexusIO is deprecated. You can continue to read"</tt> \ </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">" 'nexus' files with Bio.SeqIO, but this is now"</tt> \ </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">" handled via Bio.AlignIO internally."</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">DeprecationWarning</tt><tt class="py-op">)</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-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="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html,Package Bio.builders.SeqRecord=Bio.builders.SeqRecord-module.html,Package Bio.writers.SeqRecord=Bio.writers.SeqRecord-module.html"><a title="Bio.SeqRecord Bio.SeqRecord.SeqRecord Bio.builders.SeqRecord Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord Bio.SeqRecord.SeqRecord Bio.builders.SeqRecord Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.Nexus=Bio.Nexus-module.html,Module Bio.Nexus.Nexus=Bio.Nexus.Nexus-module.html,Class Bio.Nexus.Nexus.Nexus=Bio.Nexus.Nexus.Nexus-class.html"><a title="Bio.Nexus Bio.Nexus.Nexus Bio.Nexus.Nexus.Nexus" class="py-name" href="#" onclick="return doclink('link-7', 'Nexus', 'link-7');">Nexus</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.Nexus Bio.Nexus.Nexus Bio.Nexus.Nexus.Nexus" class="py-name" href="#" onclick="return doclink('link-8', 'Nexus', 'link-7');">Nexus</a></tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-comment">#You can get a couple of example files here:</tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#http://www.molecularevolution.org/resources/fileformats/</tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function!</tt> </tt> <a name="NexusIterator"></a><div id="NexusIterator-def"><a name="L26"></a><tt class="py-lineno">26</tt> <a class="py-toggle" href="#" id="NexusIterator-toggle" onclick="return toggle('NexusIterator');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.NexusIO-module.html#NexusIterator">NexusIterator</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="NexusIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="NexusIterator-expanded"><a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns SeqRecord objects from a Nexus file.</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"> Thus uses the Bio.Nexus module to do the hard work."""</tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.Nexus Bio.Nexus.Nexus Bio.Nexus.Nexus.Nexus" class="py-name" href="#" onclick="return doclink('link-9', 'Nexus', 'link-7');">Nexus</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.Nexus Bio.Nexus.Nexus Bio.Nexus.Nexus.Nexus" class="py-name" href="#" onclick="return doclink('link-10', 'Nexus', 'link-7');">Nexus</a></tt><tt class="py-op">(</tt><tt id="link-11" 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-11', 'handle', 'link-11');">handle</a></tt><tt class="py-op">)</tt> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-12" 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-12', 'id', 'link-12');">id</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Variable Bio.Nexus.Nexus.Nexus.original_taxon_order=Bio.Nexus.Nexus.Nexus-class.html#original_taxon_order"><a title="Bio.Nexus.Nexus.Nexus.original_taxon_order" class="py-name" href="#" onclick="return doclink('link-13', 'original_taxon_order', 'link-13');">original_taxon_order</a></tt> <tt class="py-op">:</tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-14" 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-14', 'id', 'link-12');">id</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Blast.NCBIStandalone._ParametersConsumer.matrix()=Bio.Blast.NCBIStandalone._ParametersConsumer-class.html#matrix,Variable Bio.MetaTool.metatool_format.matrix=Bio.MetaTool.metatool_format-module.html#matrix,Method Bio.Prosite._RecordConsumer.matrix()=Bio.Prosite._RecordConsumer-class.html#matrix"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix Bio.MetaTool.metatool_format.matrix Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-15', 'matrix', 'link-15');">matrix</a></tt> <tt class="py-op">:</tt> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq Bio.GFF.FeatureAggregate.seq BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-16', 'seq', 'link-16');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.Blast.NCBIStandalone._ParametersConsumer.matrix Bio.MetaTool.metatool_format.matrix Bio.Prosite._RecordConsumer.matrix" class="py-name" href="#" onclick="return doclink('link-17', 'matrix', 'link-15');">matrix</a></tt><tt class="py-op">[</tt><tt id="link-18" 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-18', 'id', 'link-12');">id</a></tt><tt class="py-op">]</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-comment">#Missing the sequence?</tt> </tt> <a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-19" class="py-name"><a title="Bio.GFF.Feature.seq Bio.GFF.FeatureAggregate.seq BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-19', 'seq', 'link-16');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-20', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-21', 'alphabet', 'link-21');">alphabet</a></tt><tt class="py-op">)</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-comment">#ToDo - Can we extract any annotation too?</tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">yield</tt> <tt id="link-22" class="py-name"><a title="Bio.SeqRecord Bio.SeqRecord.SeqRecord Bio.builders.SeqRecord Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-22', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.GFF.Feature.seq Bio.GFF.FeatureAggregate.seq BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-23', 'seq', 'link-16');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-24" 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-24', 'id', 'link-12');">id</a></tt><tt class="py-op">=</tt><tt id="link-25" 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-25', 'id', 'link-12');">id</a></tt><tt class="py-op">,</tt> <tt id="link-26" 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-26', 'name', 'link-26');">name</a></tt><tt class="py-op">=</tt><tt id="link-27" 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-27', 'id', 'link-12');">id</a></tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description Bio.Enzyme._RecordConsumer.description Bio.Prosite._RecordConsumer.description Bio.Std.description Bio.SwissProt.SProt._RecordConsumer.description Bio.SwissProt.SProt._SequenceConsumer.description Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-28', 'description', 'link-28');">description</a></tt><tt class="py-op">=</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-comment">#All done</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> </tt> </div><a name="L41"></a><tt class="py-lineno">41</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 09:26:44 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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