<?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.NBRF.nbrf_format</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.NBRF-module.html">Package NBRF</a> :: Module nbrf_format </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.NBRF.nbrf_format-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.NBRF.nbrf_format-module.html">Module Bio.NBRF.nbrf_format</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 2001 by Katharine Lindner. 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">"""Martel based parser to read NBRF formatted files.</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">This is a huge regular regular expression for NBRF, built using</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">the 'regular expressiona on steroids' capabilities of Martel.</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">http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-comment"># standard library</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#http://www-nbrf.georgetown.edu/pirwww/pirhome.shtml</tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-comment"># Martel</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-0', 'Martel', 'link-0');">Martel</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-1" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-1', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-2', 'RecordReader', 'link-2');">RecordReader</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-3" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-3', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Class Martel.Expression.Str=Martel.Expression.Str-class.html,Function Martel.Str()=Martel-module.html#Str"><a title="Martel.Expression.Str Martel.Str" class="py-name" href="#" onclick="return doclink('link-4', 'Str', 'link-4');">Str</a></tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-5', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class Martel.Expression.AnyEol=Martel.Expression.AnyEol-class.html"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-6', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">,</tt> <tt id="link-7" class="py-name" targets="Function Martel.UntilEol()=Martel-module.html#UntilEol"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-7', 'UntilEol', 'link-7');">UntilEol</a></tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-8', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Function Martel.ToEol()=Martel-module.html#ToEol"><a title="Martel.ToEol" class="py-name" href="#" onclick="return doclink('link-9', 'ToEol', 'link-9');">ToEol</a></tt> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-10', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Class Martel.Expression.Group=Martel.Expression.Group-class.html,Function Martel.Group()=Martel-module.html#Group"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-11', 'Group', 'link-11');">Group</a></tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-12" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-12', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Function Martel.Alt()=Martel-module.html#Alt,Class Martel.Expression.Alt=Martel.Expression.Alt-class.html"><a title="Martel.Alt Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-13', 'Alt', 'link-13');">Alt</a></tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Function Martel.Opt()=Martel-module.html#Opt"><a title="Martel.Opt" class="py-name" href="#" onclick="return doclink('link-14', 'Opt', 'link-14');">Opt</a></tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-15" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-15', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-16" class="py-name" targets="Package Bio.Pathway.Rep=Bio.Pathway.Rep-module.html,Function Martel.Rep()=Martel-module.html#Rep"><a title="Bio.Pathway.Rep Martel.Rep" class="py-name" href="#" onclick="return doclink('link-16', 'Rep', 'link-16');">Rep</a></tt> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-17" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-17', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-18" class="py-name" targets="Function Martel.Rep1()=Martel-module.html#Rep1"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-18', 'Rep1', 'link-18');">Rep1</a></tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-19" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-19', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-20" class="py-name" targets="Function Martel.Any()=Martel-module.html#Any,Class Martel.Expression.Any=Martel.Expression.Any-class.html"><a title="Martel.Any Martel.Expression.Any" class="py-name" href="#" onclick="return doclink('link-20', 'Any', 'link-20');">Any</a></tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-21" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-21', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-22" class="py-name" targets="Function Martel.AnyBut()=Martel-module.html#AnyBut"><a title="Martel.AnyBut" class="py-name" href="#" onclick="return doclink('link-22', 'AnyBut', 'link-22');">AnyBut</a></tt> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-23" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-23', 'Martel', 'link-0');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-24" class="py-name" targets="Function Martel.UntilSep()=Martel-module.html#UntilSep"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-24', 'UntilSep', 'link-24');">UntilSep</a></tt> </tt> <a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> </tt> <a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-25" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-25', 'Bio', 'link-25');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Package Bio.NBRF=Bio.NBRF-module.html"><a title="Bio.NBRF" class="py-name" href="#" onclick="return doclink('link-26', 'NBRF', 'link-26');">NBRF</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Module Bio.NBRF.ValSeq=Bio.NBRF.ValSeq-module.html"><a title="Bio.NBRF.ValSeq" class="py-name" href="#" onclick="return doclink('link-27', 'ValSeq', 'link-27');">ValSeq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-28" class="py-name" targets="Variable Bio.NBRF.ValSeq.valid_sequence_dict=Bio.NBRF.ValSeq-module.html#valid_sequence_dict"><a title="Bio.NBRF.ValSeq.valid_sequence_dict" class="py-name" href="#" onclick="return doclink('link-28', 'valid_sequence_dict', 'link-28');">valid_sequence_dict</a></tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt id="link-29" class="py-name" targets="Variable Bio.NBRF.nbrf_format.sequence_types=Bio.NBRF.nbrf_format-module.html#sequence_types"><a title="Bio.NBRF.nbrf_format.sequence_types" class="py-name" href="#" onclick="return doclink('link-29', 'sequence_types', 'link-29');">sequence_types</a></tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-30', 'map', 'link-30');">map</a></tt><tt class="py-op">(</tt> <tt id="link-31" class="py-name"><a title="Martel.Expression.Str Martel.Str" class="py-name" href="#" onclick="return doclink('link-31', 'Str', 'link-4');">Str</a></tt><tt class="py-op">,</tt> <tt id="link-32" class="py-name"><a title="Bio.NBRF.ValSeq.valid_sequence_dict" class="py-name" href="#" onclick="return doclink('link-32', 'valid_sequence_dict', 'link-28');">valid_sequence_dict</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-33', 'keys', 'link-33');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt id="link-34" class="py-name" targets="Method Bio.NBRF._RecordConsumer.sequence_type()=Bio.NBRF._RecordConsumer-class.html#sequence_type,Variable Bio.NBRF.nbrf_format.sequence_type=Bio.NBRF.nbrf_format-module.html#sequence_type"><a title="Bio.NBRF._RecordConsumer.sequence_type Bio.NBRF.nbrf_format.sequence_type" class="py-name" href="#" onclick="return doclink('link-34', 'sequence_type', 'link-34');">sequence_type</a></tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-35', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"sequence_type"</tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name"><a title="Martel.Alt Martel.Expression.Alt" class="py-name" href="#" onclick="return doclink('link-36', 'Alt', 'link-13');">Alt</a></tt><tt class="py-op">(</tt> <tt class="py-op">*</tt><tt id="link-37" class="py-name"><a title="Bio.NBRF.nbrf_format.sequence_types" class="py-name" href="#" onclick="return doclink('link-37', 'sequence_types', 'link-29');">sequence_types</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"><tt id="link-38" class="py-name" targets="Variable Bio.NBRF.nbrf_format.name_line=Bio.NBRF.nbrf_format-module.html#name_line"><a title="Bio.NBRF.nbrf_format.name_line" class="py-name" href="#" onclick="return doclink('link-38', 'name_line', 'link-38');">name_line</a></tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-39', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-40', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"name_line"</tt><tt class="py-op">,</tt> \ </tt> <a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Martel.Expression.Str Martel.Str" class="py-name" href="#" onclick="return doclink('link-41', 'Str', 'link-4');">Str</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="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.NBRF._RecordConsumer.sequence_type Bio.NBRF.nbrf_format.sequence_type" class="py-name" href="#" onclick="return doclink('link-42', 'sequence_type', 'link-34');">sequence_type</a></tt> <tt class="py-op">+</tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt id="link-43" class="py-name"><a title="Martel.Expression.Str Martel.Str" class="py-name" href="#" onclick="return doclink('link-43', 'Str', 'link-4');">Str</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="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-44', 'UntilEol', 'link-7');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequence_name"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt id="link-45" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-45', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt> <a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"><tt id="link-46" class="py-name" targets="Variable Bio.Emboss.primer3_format.comment_line=Bio.Emboss.primer3_format-module.html#comment_line,Variable Bio.IntelliGenetics.intelligenetics_format.comment_line=Bio.IntelliGenetics.intelligenetics_format-module.html#comment_line,Variable Bio.NBRF.nbrf_format.comment_line=Bio.NBRF.nbrf_format-module.html#comment_line,Variable Bio.Saf.saf_format.comment_line=Bio.Saf.saf_format-module.html#comment_line"><a title="Bio.Emboss.primer3_format.comment_line Bio.IntelliGenetics.intelligenetics_format.comment_line Bio.NBRF.nbrf_format.comment_line Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-46', 'comment_line', 'link-46');">comment_line</a></tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Martel.UntilEol" class="py-name" href="#" onclick="return doclink('link-47', 'UntilEol', 'link-7');">UntilEol</a></tt><tt class="py-op">(</tt><tt class="py-string">"comment"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-48" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-48', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> </tt> <a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"># 0x2a -- '*'</tt> </tt> <a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 10 -- '\n', 13 -- '\r' newline endings</tt> </tt> <a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-49" class="py-name" targets="Variable Bio.ECell.ecell_format.excluded_chars=Bio.ECell.ecell_format-module.html#excluded_chars,Variable Bio.NBRF.nbrf_format.excluded_chars=Bio.NBRF.nbrf_format-module.html#excluded_chars"><a title="Bio.ECell.ecell_format.excluded_chars Bio.NBRF.nbrf_format.excluded_chars" class="py-name" href="#" onclick="return doclink('link-49', 'excluded_chars', 'link-49');">excluded_chars</a></tt> <tt class="py-op">=</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt><tt class="py-number">0x2a</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt><tt class="py-number">10</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt><tt class="py-number">13</tt><tt class="py-op">)</tt> </tt> <a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"># sequence lines with only sequence</tt> </tt> <a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-50" class="py-name" targets="Variable Bio.NBRF.nbrf_format.sequence_text=Bio.NBRF.nbrf_format-module.html#sequence_text"><a title="Bio.NBRF.nbrf_format.sequence_text" class="py-name" href="#" onclick="return doclink('link-50', 'sequence_text', 'link-50');">sequence_text</a></tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-51', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"sequence_text"</tt><tt class="py-op">,</tt> \ </tt> <a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-52', 'Martel', 'link-0');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-53', 'Rep1', 'link-18');">Rep1</a></tt><tt class="py-op">(</tt> <tt id="link-54" class="py-name"><a title="Martel.AnyBut" class="py-name" href="#" onclick="return doclink('link-54', 'AnyBut', 'link-22');">AnyBut</a></tt><tt class="py-op">(</tt> <tt id="link-55" class="py-name"><a title="Bio.ECell.ecell_format.excluded_chars Bio.NBRF.nbrf_format.excluded_chars" class="py-name" href="#" onclick="return doclink('link-55', 'excluded_chars', 'link-49');">excluded_chars</a></tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt> <a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt id="link-56" class="py-name" targets="Method Bio.NBRF._RecordConsumer.sequence_line()=Bio.NBRF._RecordConsumer-class.html#sequence_line,Variable Bio.NBRF.nbrf_format.sequence_line=Bio.NBRF.nbrf_format-module.html#sequence_line,Variable Bio.expressions.genbank.sequence_line=Bio.expressions.genbank-module.html#sequence_line"><a title="Bio.NBRF._RecordConsumer.sequence_line Bio.NBRF.nbrf_format.sequence_line Bio.expressions.genbank.sequence_line" class="py-name" href="#" onclick="return doclink('link-56', 'sequence_line', 'link-56');">sequence_line</a></tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-57', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"sequence_line"</tt><tt class="py-op">,</tt> <tt id="link-58" class="py-name"><a title="Bio.NBRF.nbrf_format.sequence_text" class="py-name" href="#" onclick="return doclink('link-58', 'sequence_text', 'link-50');">sequence_text</a></tt> <tt class="py-op">+</tt> </tt> <a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-59', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-comment"># the final line, has a '*' and potentially some sequence</tt> </tt> <a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-60" class="py-name" targets="Variable Bio.NBRF.nbrf_format.sequence_final_line=Bio.NBRF.nbrf_format-module.html#sequence_final_line"><a title="Bio.NBRF.nbrf_format.sequence_final_line" class="py-name" href="#" onclick="return doclink('link-60', 'sequence_final_line', 'link-60');">sequence_final_line</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-61', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt> <tt class="py-string">"sequence_final_line"</tt><tt class="py-op">,</tt> </tt> <a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt id="link-62" class="py-name"><a title="Martel.UntilSep" class="py-name" href="#" onclick="return doclink('link-62', 'UntilSep', 'link-24');">UntilSep</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequence_final_text"</tt><tt class="py-op">,</tt> <tt class="py-name">chr</tt><tt class="py-op">(</tt><tt class="py-number">0x2a</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-63" class="py-name"><a title="Martel.Expression.Str Martel.Str" class="py-name" href="#" onclick="return doclink('link-63', 'Str', 'link-4');">Str</a></tt><tt class="py-op">(</tt><tt class="py-name">chr</tt><tt class="py-op">(</tt><tt class="py-number">0x2a</tt><tt class="py-op">)</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-64" class="py-name"><a title="Martel.Rep1" class="py-name" href="#" onclick="return doclink('link-64', 'Rep1', 'link-18');">Rep1</a></tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.Expression.AnyEol" class="py-name" href="#" onclick="return doclink('link-65', 'AnyEol', 'link-6');">AnyEol</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> </tt> <a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt id="link-66" class="py-name" targets="Variable Bio.CDD.cdd_format.sequence_block=Bio.CDD.cdd_format-module.html#sequence_block,Variable Bio.NBRF.nbrf_format.sequence_block=Bio.NBRF.nbrf_format-module.html#sequence_block,Function Bio.Std.sequence_block()=Bio.Std-module.html#sequence_block"><a title="Bio.CDD.cdd_format.sequence_block Bio.NBRF.nbrf_format.sequence_block Bio.Std.sequence_block" class="py-name" href="#" onclick="return doclink('link-66', 'sequence_block', 'link-66');">sequence_block</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Martel.Expression.Group Martel.Group" class="py-name" href="#" onclick="return doclink('link-67', 'Group', 'link-11');">Group</a></tt><tt class="py-op">(</tt><tt class="py-string">"sequence_block"</tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="Bio.Pathway.Rep Martel.Rep" class="py-name" href="#" onclick="return doclink('link-68', 'Rep', 'link-16');">Rep</a></tt><tt class="py-op">(</tt> <tt id="link-69" class="py-name"><a title="Bio.NBRF._RecordConsumer.sequence_line Bio.NBRF.nbrf_format.sequence_line Bio.expressions.genbank.sequence_line" class="py-name" href="#" onclick="return doclink('link-69', 'sequence_line', 'link-56');">sequence_line</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 id="link-70" class="py-name" targets="Variable Bio.NBRF.nbrf_format.nbrf_record=Bio.NBRF.nbrf_format-module.html#nbrf_record"><a title="Bio.NBRF.nbrf_format.nbrf_record" class="py-name" href="#" onclick="return doclink('link-70', 'nbrf_record', 'link-70');">nbrf_record</a></tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.NBRF.nbrf_format.name_line" class="py-name" href="#" onclick="return doclink('link-71', 'name_line', 'link-38');">name_line</a></tt> <tt class="py-op">+</tt> <tt id="link-72" class="py-name"><a title="Bio.Emboss.primer3_format.comment_line Bio.IntelliGenetics.intelligenetics_format.comment_line Bio.NBRF.nbrf_format.comment_line Bio.Saf.saf_format.comment_line" class="py-name" href="#" onclick="return doclink('link-72', 'comment_line', 'link-46');">comment_line</a></tt> <tt class="py-op">+</tt> <tt id="link-73" class="py-name"><a title="Bio.CDD.cdd_format.sequence_block Bio.NBRF.nbrf_format.sequence_block Bio.Std.sequence_block" class="py-name" href="#" onclick="return doclink('link-73', 'sequence_block', 'link-66');">sequence_block</a></tt> <tt class="py-op">+</tt> <tt id="link-74" class="py-name"><a title="Bio.NBRF.nbrf_format.sequence_final_line" class="py-name" href="#" onclick="return doclink('link-74', 'sequence_final_line', 'link-60');">sequence_final_line</a></tt> </tt> <a name="L59"></a><tt class="py-lineno">59</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" 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