<?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.LocusLink</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> :: Package LocusLink </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.LocusLink-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.LocusLink-module.html">Package Bio.LocusLink</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-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="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package Martel=Martel-module.html"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-2', 'Martel', 'link-2');">Martel</a></tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</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-2');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Martel.Dispatch=Martel.Dispatch-module.html"><a title="Martel.Dispatch" class="py-name" href="#" onclick="return doclink('link-4', 'Dispatch', 'link-4');">Dispatch</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Martel.Dispatch.Dispatcher=Martel.Dispatch.Dispatcher-class.html"><a title="Martel.Dispatch.Dispatcher" class="py-name" href="#" onclick="return doclink('link-5', 'Dispatcher', 'link-5');">Dispatcher</a></tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-6', 'Martel', 'link-2');">Martel</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" 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-7', 'RecordReader', 'link-7');">RecordReader</a></tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name" targets="Module Bio.LocusLink.locus_format=Bio.LocusLink.locus_format-module.html"><a title="Bio.LocusLink.locus_format" class="py-name" href="#" onclick="return doclink('link-8', 'locus_format', 'link-8');">locus_format</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Variable Bio.LocusLink.locus_format.locus_record=Bio.LocusLink.locus_format-module.html#locus_record"><a title="Bio.LocusLink.locus_format.locus_record" class="py-name" href="#" onclick="return doclink('link-9', 'locus_record', 'link-9');">locus_record</a></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-string">"""Parser for NCBI's LocusLink, curated sequence and descriptive information </tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-string">about genetic loci.</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-string"></tt> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-string">The LocusLink site is:</tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-string">http://www.ncbi.nlm.nih.gov/LocusLink/</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</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.LocusLink was deprecated, as NCBI's LocusLink was superceded by Entrez Gene. If you still need this module, please get in touch with the Biopython developers (biopython-dev@biopython.org) to avoid permanent removal of this module"</tt><tt class="py-op">,</tt> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt> <a name="Record"></a><div id="Record-def"><a name="L17"></a><tt class="py-lineno"> 17</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.LocusLink.Record-class.html">Record</a><tt class="py-op">(</tt> <tt class="py-base-class">dict</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt> <a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L19"></a><tt class="py-lineno"> 19</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.LocusLink.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="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-10" 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 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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-10', '__init__', 'link-10');">__init__</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt> <tt class="py-op">)</tt> </tt> </div><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt> <a name="Record.__str__"></a><div id="Record.__str__-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink.Record-class.html#__str__">__str__</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.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">queue_keys</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</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">queue_keys</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort Bio.PDB.Residue.Residue.sort Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-12', 'sort', 'link-12');">sort</a></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 class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-13" 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-13', 'key', 'link-13');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">queue_keys</tt><tt class="py-op">:</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s:\n'</tt> <tt class="py-op">%</tt> <tt id="link-14" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-14', 'key', 'link-13');">key</a></tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.LocusLink.Record.print_item()=Bio.LocusLink.Record-class.html#print_item,Method Bio.LocusLink.web_parse.Record.print_item()=Bio.LocusLink.web_parse.Record-class.html#print_item"><a title="Bio.LocusLink.Record.print_item Bio.LocusLink.web_parse.Record.print_item" class="py-name" href="#" onclick="return doclink('link-15', 'print_item', 'link-15');">print_item</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt> <tt id="link-16" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-16', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">)</tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">out</tt> </tt> </div><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt> <a name="Record.print_item"></a><div id="Record.print_item-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Record.print_item-toggle" onclick="return toggle('Record.print_item');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink.Record-class.html#print_item">print_item</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">,</tt> <tt class="py-param">level</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="Record.print_item-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.print_item-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">indent</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">indent</tt> <tt class="py-op">=</tt> <tt class="py-name">indent</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-17" 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-17', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt id="link-18" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-18', 'item', 'link-18');">item</a></tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-19" 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-19', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-20" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-20', 'item', 'link-18');">item</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 class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s%s\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt id="link-21" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-21', 'item', 'link-18');">item</a></tt> <tt class="py-op">)</tt> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-22" 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-22', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt id="link-23" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-23', 'item', 'link-18');">item</a></tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-24" 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-24', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</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 class="py-keyword">for</tt> <tt class="py-name">subitem</tt> <tt class="py-keyword">in</tt> <tt id="link-25" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-25', 'item', 'link-18');">item</a></tt><tt class="py-op">:</tt> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.LocusLink.Record.print_item Bio.LocusLink.web_parse.Record.print_item" class="py-name" href="#" onclick="return doclink('link-26', 'print_item', 'link-15');">print_item</a></tt><tt class="py-op">(</tt> <tt class="py-name">subitem</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt> <tt id="link-27" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-27', 'item', 'link-18');">item</a></tt><tt class="py-op">,</tt> <tt class="py-name">dict</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-28" class="py-name"><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-28', 'keys', 'link-11');">keys</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-29', 'item', 'link-18');">item</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><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-30', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><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-31', 'keys', 'link-11');">keys</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort Bio.PDB.Residue.Residue.sort Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-32', 'sort', 'link-12');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subitem</tt> <tt class="py-keyword">in</tt> <tt id="link-33" class="py-name"><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-11');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s %s:\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">subitem</tt> <tt class="py-op">)</tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.LocusLink.Record.print_item Bio.LocusLink.web_parse.Record.print_item" class="py-name" href="#" onclick="return doclink('link-34', 'print_item', 'link-15');">print_item</a></tt><tt class="py-op">(</tt> <tt id="link-35" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-35', 'item', 'link-18');">item</a></tt><tt class="py-op">[</tt> <tt class="py-name">subitem</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-36" 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-36', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt id="link-37" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-37', 'item', 'link-18');">item</a></tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-38" 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-38', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">{</tt><tt class="py-op">}</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 id="link-39" class="py-name"><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-39', 'keys', 'link-11');">keys</a></tt> <tt class="py-op">=</tt> <tt id="link-40" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-40', 'item', 'link-18');">item</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><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-41', 'keys', 'link-11');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><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-42', 'keys', 'link-11');">keys</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort Bio.PDB.Residue.Residue.sort Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-43', 'sort', 'link-12');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">subitem</tt> <tt class="py-keyword">in</tt> <tt id="link-44" class="py-name"><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-44', 'keys', 'link-11');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s %s:\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> <tt class="py-name">indent</tt><tt class="py-op">,</tt> <tt class="py-name">subitem</tt> <tt class="py-op">)</tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.LocusLink.Record.print_item Bio.LocusLink.web_parse.Record.print_item" class="py-name" href="#" onclick="return doclink('link-45', 'print_item', 'link-15');">print_item</a></tt><tt class="py-op">(</tt> <tt id="link-46" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-46', 'item', 'link-18');">item</a></tt><tt class="py-op">[</tt> <tt class="py-name">subitem</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">level</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">out</tt> <tt class="py-op">=</tt> <tt class="py-name">out</tt> <tt class="py-op">+</tt> <tt class="py-string">'%s\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt> <tt id="link-47" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-47', 'item', 'link-18');">item</a></tt> <tt class="py-op">)</tt> </tt> <a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">out</tt> </tt> </div></div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt> <a name="Iterator"></a><div id="Iterator-def"><a name="L62"></a><tt class="py-lineno"> 62</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.LocusLink.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="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterator interface to move over a file of LocusLink entries one at a time.</tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="Iterator.__init__"></a><div id="Iterator.__init__-def"><a name="L66"></a><tt class="py-lineno"> 66</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.LocusLink.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="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the iterator.</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"> Arguments:</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with LocusLink entries to iterate through.</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> o parser - An optional parser to pass the entries through before</tt> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> returning them. If None, then the raw entry will be returned.</tt> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" 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-48', 'handle', 'link-48');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-49', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-50" 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-50', 'UndoHandle', 'link-50');">UndoHandle</a></tt><tt class="py-op">(</tt> <tt id="link-51" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-51', 'handle', 'link-48');">handle</a></tt> <tt class="py-op">)</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name"><a title="Martel.RecordReader Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-52', 'RecordReader', 'link-7');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-53', 'StartsWith', 'link-53');">StartsWith</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-54', 'handle', 'link-48');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">'>>'</tt> <tt class="py-op">)</tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</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="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt> <a name="Iterator.next"></a><div id="Iterator.next-def"><a name="L78"></a><tt class="py-lineno"> 78</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.LocusLink.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="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the next LocusLink record from the handle.</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> Will return None if we ran out of records.</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt id="link-55" 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-55', 'data', 'link-55');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_reader</tt><tt class="py-op">.</tt><tt id="link-56" 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-56', 'next', 'link-56');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</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="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-57', 'data', 'link-55');">data</a></tt><tt class="py-op">:</tt> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt> <tt class="py-op">=</tt> <tt id="link-58" 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-58', 'open', 'link-58');">open</a></tt><tt class="py-op">(</tt> <tt class="py-string">'dump'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt> <tt class="py-op">)</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write Bio.AlignIO.write Bio.EUtils.sourcegen.SourceFile.write Bio.EUtils.sourcegen.SourceGen.write Bio.NeuralNetwork.Gene.Pattern.PatternIO.write Bio.SeqIO.write Bio.Writer.Writer.write Bio.writers.SeqRecord.embl.WriteEmbl.write Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-59', 'write', 'link-59');">write</a></tt><tt class="py-op">(</tt> <tt id="link-60" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-60', 'data', 'link-55');">data</a></tt> <tt class="py-op">)</tt> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">dumpfile</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-61', 'close', 'link-61');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L89"></a><tt class="py-lineno"> 89</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-62" 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-62', 'parse', 'link-62');">parse</a></tt><tt class="py-op">(</tt><tt id="link-63" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-63', '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-64" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-64', 'data', 'link-55');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-65" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-55');">data</a></tt> </tt> </div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt> <a name="Iterator.__iter__"></a><div id="Iterator.__iter__-def"><a name="L93"></a><tt class="py-lineno"> 93</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.LocusLink.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="L94"></a><tt class="py-lineno"> 94</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-66" class="py-name"><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-66', 'next', 'link-56');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt> <a name="_Scanner"></a><div id="_Scanner-def"><a name="L96"></a><tt class="py-lineno"> 96</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.LocusLink._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="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-docstring">"""Start up Martel to do the scanning of the 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"> This initialzes the Martel based parser and connects it to a handler</tt> </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> that will generate events for a Feature Consumer.</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="_Scanner.__init__"></a><div id="_Scanner.__init__-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="_Scanner.__init__-toggle" onclick="return toggle('_Scanner.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._Scanner-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">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_Scanner.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.__init__-expanded"><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the scanner by setting up our caches.</tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> Creating the parser takes a long time, so we want to cache it</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> to reduce parsing time.</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> o debug - The level of debugging that the parser should</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> display. Level 0 is no debugging, Level 2 displays the most</tt> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> debugging info (but is much slower). See Martel documentation</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> for more info on this.</tt> </tt> <a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-comment"># a listing of all tags we are interested in scanning for</tt> </tt> <a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the MartelParser</tt> </tt> <a name="L116"></a><tt class="py-lineno">116</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">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">"locus_line"</tt><tt class="py-op">,</tt> <tt class="py-string">"accnum_block"</tt><tt class="py-op">,</tt> <tt class="py-string">"phenotype_block"</tt><tt class="py-op">,</tt> <tt class="py-string">"db_block"</tt> <tt class="py-op">]</tt> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-comment"># make a parser that returns only the tags we are interested in</tt> </tt> <a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">expression</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Martel" class="py-name" href="#" onclick="return doclink('link-67', 'Martel', 'link-2');">Martel</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Function Martel.select_names()=Martel-module.html#select_names"><a title="Martel.select_names" class="py-name" href="#" onclick="return doclink('link-68', 'select_names', 'link-68');">select_names</a></tt><tt class="py-op">(</tt> <tt id="link-69" class="py-name"><a title="Bio.LocusLink.locus_format" class="py-name" href="#" onclick="return doclink('link-69', 'locus_format', 'link-8');">locus_format</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.LocusLink.locus_format.locus_record" class="py-name" href="#" onclick="return doclink('link-70', 'locus_record', 'link-9');">locus_record</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt><tt class="py-op">)</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</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">expression</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method Bio.config.FormatRegistry.FormatObject.make_parser()=Bio.config.FormatRegistry.FormatObject-class.html#make_parser,Method Bio.config._support.make_cached_expression.make_parser()=Bio.config._support.make_cached_expression-class.html#make_parser,Method Martel.Expression.Expression.make_parser()=Martel.Expression.Expression-class.html#make_parser,Method Martel.Expression.HeaderFooter.make_parser()=Martel.Expression.HeaderFooter-class.html#make_parser,Method Martel.Expression.ParseRecords.make_parser()=Martel.Expression.ParseRecords-class.html#make_parser"><a title="Bio.config.FormatRegistry.FormatObject.make_parser Bio.config._support.make_cached_expression.make_parser Martel.Expression.Expression.make_parser Martel.Expression.HeaderFooter.make_parser Martel.Expression.ParseRecords.make_parser" class="py-name" href="#" onclick="return doclink('link-71', 'make_parser', 'link-71');">make_parser</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt> <tt class="py-op">)</tt> </tt> </div><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt> <a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L122"></a><tt class="py-lineno">122</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.LocusLink._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="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-docstring">"""Feeed a set of data into the scanner.</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"> Arguments:</tt> </tt> <a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> o handle - A handle with the information to parse.</tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> o consumer - The consumer that should be informed of events.</tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name" targets="Method Bio.CDD._RecordConsumer.set_interest_tags()=Bio.CDD._RecordConsumer-class.html#set_interest_tags,Method Bio.LocusLink._RecordConsumer.set_interest_tags()=Bio.LocusLink._RecordConsumer-class.html#set_interest_tags,Method Bio.Saf._RecordConsumer.set_interest_tags()=Bio.Saf._RecordConsumer-class.html#set_interest_tags"><a title="Bio.CDD._RecordConsumer.set_interest_tags Bio.LocusLink._RecordConsumer.set_interest_tags Bio.Saf._RecordConsumer.set_interest_tags" class="py-name" href="#" onclick="return doclink('link-72', 'set_interest_tags', 'link-72');">set_interest_tags</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">)</tt> </tt> <a name="L130"></a><tt class="py-lineno">130</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">setContentHandler</tt><tt class="py-op">(</tt> <tt class="py-name">consumer</tt> <tt class="py-op">)</tt> </tt> <a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"># self._parser.setErrorHandler(handle.ErrorHandler())</tt> </tt> <a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L133"></a><tt class="py-lineno">133</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 id="link-73" class="py-name" targets="Method Bio.EUtils.POM.POMDocument.parseFile()=Bio.EUtils.POM.POMDocument-class.html#parseFile,Method Martel.Parser.HeaderFooterParser.parseFile()=Martel.Parser.HeaderFooterParser-class.html#parseFile,Method Martel.Parser.Parser.parseFile()=Martel.Parser.Parser-class.html#parseFile,Method Martel.Parser.RecordParser.parseFile()=Martel.Parser.RecordParser-class.html#parseFile"><a title="Bio.EUtils.POM.POMDocument.parseFile Martel.Parser.HeaderFooterParser.parseFile Martel.Parser.Parser.parseFile Martel.Parser.RecordParser.parseFile" class="py-name" href="#" onclick="return doclink('link-73', 'parseFile', 'link-73');">parseFile</a></tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.LocusLink.web_parse.handle Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-74', 'handle', 'link-48');">handle</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L135"></a><tt class="py-lineno">135</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.LocusLink._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">(</tt> <tt class="py-base-class">Dispatcher</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="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a LocusLink Record object from scanner generated information.</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L138"></a><tt class="py-lineno">138</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.LocusLink._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="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Martel.Dispatch.Dispatcher" class="py-name" href="#" onclick="return doclink('link-75', 'Dispatcher', 'link-5');">Dispatcher</a></tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__ Bio.Affy.CelFile.CelParser.__init__ Bio.Affy.CelFile.CelRecord.__init__ Bio.Ais.Immune.__init__ Bio.Ais.Lymphocyte.__init__ Bio.Align.AlignInfo.PSSM.__init__ Bio.Align.AlignInfo.SummaryInfo.__init__ Bio.Align.FormatConvert.FormatConverter.__init__ Bio.Align.Generic.Alignment.__init__ Bio.AlignAce.Applications.AlignAceCommandline.__init__ Bio.AlignAce.Applications.CompareAceCommandline.__init__ Bio.AlignAce.Motif.Motif.__init__ Bio.AlignAce.Parser.AlignAceConsumer.__init__ Bio.AlignAce.Parser.AlignAceParser.__init__ Bio.AlignAce.Parser.CompareAceConsumer.__init__ Bio.AlignAce.Parser.CompareAceParser.__init__ Bio.AlignIO.Interfaces.AlignmentIterator.__init__ Bio.AlignIO.Interfaces.AlignmentWriter.__init__ Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__ Bio.Alphabet.AlphabetEncoder.__init__ Bio.Alphabet.Gapped.__init__ Bio.Alphabet.HasStopCodon.__init__ Bio.Application.AbstractCommandline.__init__ Bio.Application.ApplicationResult.__init__ Bio.Application._AbstractParameter.__init__ Bio.Blast.Applications.BlastallCommandline.__init__ Bio.Blast.Applications.FastacmdCommandline.__init__ Bio.Blast.NCBIStandalone.BlastErrorParser.__init__ Bio.Blast.NCBIStandalone.BlastParser.__init__ Bio.Blast.NCBIStandalone.Iterator.__init__ Bio.Blast.NCBIStandalone.PSIBlastParser.__init__ Bio.Blast.NCBIStandalone._BlastConsumer.__init__ Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__ Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__ Bio.Blast.NCBIWWW.BlastParser.__init__ Bio.Blast.NCBIXML.BlastParser.__init__ Bio.Blast.NCBIXML._XMLparser.__init__ Bio.Blast.ParseBlastTable.BlastTableEntry.__init__ Bio.Blast.ParseBlastTable.BlastTableReader.__init__ Bio.Blast.ParseBlastTable.BlastTableRec.__init__ Bio.Blast.Record.Alignment.__init__ Bio.Blast.Record.Blast.__init__ Bio.Blast.Record.DatabaseReport.__init__ Bio.Blast.Record.Description.__init__ Bio.Blast.Record.HSP.__init__ Bio.Blast.Record.Header.__init__ Bio.Blast.Record.MultipleAlignment.__init__ Bio.Blast.Record.PSIBlast.__init__ Bio.Blast.Record.Parameters.__init__ Bio.Blast.Record.Round.__init__ Bio.CAPS.CAPSMap.__init__ Bio.CAPS.DifferentialCutsite.__init__ Bio.CDD.Iterator.__init__ Bio.CDD.Record.Record.__init__ Bio.CDD.RecordParser.__init__ Bio.CDD._RecordConsumer.__init__ Bio.CDD._Scanner.__init__ Bio.Clustalw.ClustalAlignment.__init__ Bio.Clustalw.MultipleAlignCL.__init__ Bio.Cluster.DataFile.__init__ Bio.Cluster.Record.__init__ Bio.Compass.Iterator.__init__ Bio.Compass.Record.__init__ Bio.Compass.RecordParser.__init__ Bio.Compass._Consumer.__init__ Bio.Crystal.Chain.__init__ Bio.Crystal.Crystal.__init__ Bio.Crystal.CrystalError.__init__ Bio.Crystal.Error.__init__ Bio.Crystal.Hetero.__init__ Bio.DBXRef.DBXRef.__init__ Bio.Data.CodonTable.AmbiguousCodonTable.__init__ Bio.Data.CodonTable.AmbiguousForwardTable.__init__ Bio.Data.CodonTable.CodonTable.__init__ Bio.Data.CodonTable.NCBICodonTable.__init__ Bio.Decode.DecodeParser.__init__ Bio.Decode.DecodeScanner.__init__ Bio.Decode.Float.__init__ Bio.Decode.Function.__init__ Bio.Decode.FunctionCall.__init__ Bio.Decode.FunctionCallChain.__init__ Bio.Decode.FunctionName.__init__ Bio.Decode.Integer.__init__ Bio.Decode.String.__init__ Bio.Decode.Token.__init__ Bio.Decode.ValueToken.__init__ Bio.DocSQL.Create.__init__ Bio.DocSQL.Insert.__init__ Bio.DocSQL.IterationCursor.__init__ Bio.DocSQL.Query.__init__ Bio.DocSQL.QueryAll.__init__ Bio.DocSQL.QueryGeneric.__init__ Bio.DocSQL.QueryRow.__init__ Bio.DocSQL.QuerySingle.__init__ Bio.ECell.ECellError.__init__ Bio.ECell.Error.__init__ Bio.ECell.Iterator.__init__ Bio.ECell.Record.Record.__init__ Bio.ECell.RecordParser.__init__ Bio.ECell._RecordConsumer.__init__ Bio.ECell._Scanner.__init__ Bio.EUtils.Config.DatabaseInfo.__init__ Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__ Bio.EUtils.DBIdsClient.DBIdsClient.__init__ Bio.EUtils.DBIdsClient.DBIdsLookup.__init__ Bio.EUtils.Datatypes.BinaryOp.__init__ Bio.EUtils.Datatypes.CheckLinkSet.__init__ Bio.EUtils.Datatypes.DBIds.__init__ Bio.EUtils.Datatypes.Date.__init__ Bio.EUtils.Datatypes.DateRange.__init__ Bio.EUtils.Datatypes.EUtilsSearchError.__init__ Bio.EUtils.Datatypes.IdCheck.__init__ Bio.EUtils.Datatypes.IdUrlSet.__init__ Bio.EUtils.Datatypes.Link.__init__ Bio.EUtils.Datatypes.LinkSetDb.__init__ Bio.EUtils.Datatypes.LinksLinkSet.__init__ Bio.EUtils.Datatypes.NeighborLinkSet.__init__ Bio.EUtils.Datatypes.ObjUrl.__init__ Bio.EUtils.Datatypes.PostResult.__init__ Bio.EUtils.Datatypes.Problem.__init__ Bio.EUtils.Datatypes.Provider.__init__ Bio.EUtils.Datatypes.Range.__init__ Bio.EUtils.Datatypes.SearchResult.__init__ Bio.EUtils.Datatypes.Summary.__init__ Bio.EUtils.Datatypes.Term.__init__ Bio.EUtils.Datatypes.WithinNDays.__init__ Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__ Bio.EUtils.HistoryClient.HistoryClient.__init__ Bio.EUtils.HistoryClient.HistoryCookie.__init__ Bio.EUtils.HistoryClient.HistoryLookup.__init__ Bio.EUtils.HistoryClient.HistoryRecord.__init__ Bio.EUtils.MultiDict.OrderedMultiDict.__init__ Bio.EUtils.MultiDict.UnorderedMultiDict.__init__ Bio.EUtils.POM.Comment.__init__ Bio.EUtils.POM.ContentModel.__init__ Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__ Bio.EUtils.POM.ElementNode.__init__ Bio.EUtils.POM.IndentedText.__init__ Bio.EUtils.POM.ObjectParserHandler.__init__ Bio.EUtils.POM.POMDocument.__init__ Bio.EUtils.POM.XMLAttribute.__init__ Bio.EUtils.POM._ContentModelGenerator.__init__ Bio.EUtils.ReseekFile.ReseekFile.__init__ Bio.EUtils.ThinClient.ThinClient.__init__ Bio.EUtils.parse.UsePOMParser.__init__ Bio.EUtils.sourcegen.ClassHolder.__init__ Bio.EUtils.sourcegen.FunctionHolder.__init__ Bio.EUtils.sourcegen.MethodHolder.__init__ Bio.EUtils.sourcegen.SourceFile.__init__ Bio.EUtils.sourcegen.SourceGen.__init__ Bio.Emboss.Applications.EConsenseCommandline.__init__ Bio.Emboss.Applications.EInvertedCommandline.__init__ Bio.Emboss.Applications.ENeighborCommandline.__init__ Bio.Emboss.Applications.EProtDistCommandline.__init__ Bio.Emboss.Applications.EProtParsCommandline.__init__ Bio.Emboss.Applications.ESeqBootCommandline.__init__ Bio.Emboss.Applications.ETandemCommandline.__init__ Bio.Emboss.Applications.Est2GenomeCommandline.__init__ Bio.Emboss.Applications.FuzznucCommandline.__init__ Bio.Emboss.Applications.PalindromeCommandline.__init__ Bio.Emboss.Applications.Primer3Commandline.__init__ Bio.Emboss.Applications.PrimerSearchCommandline.__init__ Bio.Emboss.Applications.TranalignCommandline.__init__ Bio.Emboss.Applications.WaterCommandline.__init__ Bio.Emboss.Primer.Primer3Parser.__init__ Bio.Emboss.Primer.Primer3Primers.__init__ Bio.Emboss.Primer.Primer3Record.__init__ Bio.Emboss.Primer.PrimerSearchAmplifier.__init__ Bio.Emboss.Primer.PrimerSearchInputRecord.__init__ Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__ Bio.Emboss.Primer.PrimerSearchParser.__init__ Bio.Emboss.Primer._Primer3RecordConsumer.__init__ Bio.Emboss.Primer._Primer3Scanner.__init__ Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__ Bio.Emboss.Primer._PrimerSearchScanner.__init__ Bio.Entrez.Parser.DataHandler.__init__ Bio.Entrez.Parser.StructureElement.__init__ Bio.Enzyme.DataRecord.__init__ Bio.Enzyme.EnzymeRecord.__init__ Bio.Enzyme.Iterator.__init__ Bio.Enzyme.RecordParser.__init__ Bio.Enzyme._RecordConsumer.__init__ Bio.FSSP.FSSPAlignDict.__init__ Bio.FSSP.FSSPAlignRec.__init__ Bio.FSSP.FSSPHeader.__init__ Bio.FSSP.FSSPSumRec.__init__ Bio.FSSP.FSSPTools.FSSPMultAlign.__init__ Bio.FSSP.PosAlign.__init__ Bio.FSSP.fssp_rec.fff_rec.__init__ Bio.Fasta.FastaAlign.FastaAlignment.__init__ Bio.Fasta.Iterator.__init__ Bio.Fasta.Record.__init__ Bio.Fasta.RecordParser.__init__ Bio.Fasta.SequenceParser.__init__ Bio.File.SGMLHandle.__init__ Bio.File.SGMLStripper.MyParser.__init__ Bio.File.SGMLStripper.__init__ Bio.File.UndoHandle.__init__ Bio.FilteredReader.FilteredReader.__init__ Bio.GA.Crossover.General.SafeFitnessCrossover.__init__ Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__ Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__ Bio.GA.Crossover.Point.SinglePointCrossover.__init__ Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__ Bio.GA.Crossover.Uniform.UniformCrossover.__init__ Bio.GA.Evolver.GenerationEvolver.__init__ Bio.GA.Evolver.SteadyStateEvolver.__init__ Bio.GA.Mutation.General.SafeFitnessMutation.__init__ Bio.GA.Mutation.Simple.ConversionMutation.__init__ Bio.GA.Mutation.Simple.SinglePositionMutation.__init__ Bio.GA.Organism.Organism.__init__ Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__ Bio.GA.Selection.Abstract.AbstractSelection.__init__ Bio.GA.Selection.Diversity.DiversitySelection.__init__ Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__ Bio.GA.Selection.Tournament.TournamentSelection.__init__ Bio.GFF.Connection.__init__ Bio.GFF.Feature.__init__ Bio.GFF.FeatureAggregate.__init__ Bio.GFF.FeatureQuery.__init__ Bio.GFF.FeatureQueryRow.__init__ Bio.GFF.GenericTools.ArgsParser.__init__ Bio.GFF.GenericTools.Surrogate.__init__ Bio.GFF.GenericTools.TempFile.__init__ Bio.GFF.RetrieveSeqname.__init__ Bio.GFF.Segment.__init__ Bio.GFF.easy.FeatureDict.__init__ Bio.GFF.easy.Location.__init__ Bio.GFF.easy.LocationFromCoords.__init__ Bio.GFF.easy.LocationFromString.__init__ Bio.GFF.easy.LocationJoin.__init__ Bio.GenBank.FeatureParser.__init__ Bio.GenBank.Iterator.__init__ Bio.GenBank.LocationParser.AbsoluteLocation.__init__ Bio.GenBank.LocationParser.Between.__init__ Bio.GenBank.LocationParser.FeatureName.__init__ Bio.GenBank.LocationParser.Function.__init__ Bio.GenBank.LocationParser.HighBound.__init__ Bio.GenBank.LocationParser.Integer.__init__ Bio.GenBank.LocationParser.LocationParser.__init__ Bio.GenBank.LocationParser.LocationScanner.__init__ Bio.GenBank.LocationParser.LowBound.__init__ Bio.GenBank.LocationParser.Path.__init__ Bio.GenBank.LocationParser.Range.__init__ Bio.GenBank.LocationParser.Symbol.__init__ Bio.GenBank.LocationParser.Token.__init__ Bio.GenBank.LocationParser.TwoBound.__init__ Bio.GenBank.NCBIDictionary.__init__ Bio.GenBank.Record.Feature.__init__ Bio.GenBank.Record.Qualifier.__init__ Bio.GenBank.Record.Record.__init__ Bio.GenBank.Record.Reference.__init__ Bio.GenBank.RecordParser.__init__ Bio.GenBank.Scanner.InsdcScanner.__init__ Bio.GenBank._BaseGenBankConsumer.__init__ Bio.GenBank._FeatureConsumer.__init__ Bio.GenBank._RecordConsumer.__init__ Bio.GenBank.utils.FeatureValueCleaner.__init__ Bio.Geo.Record.Record.__init__ Bio.Gobase.Dictionary.__init__ Bio.Gobase.GeneRecord.__init__ Bio.Gobase.Iterator.__init__ Bio.Gobase.ProteinRecord.__init__ Bio.Gobase.Record.__init__ Bio.Gobase.RecordParser.__init__ Bio.Gobase.SequenceRecord.__init__ Bio.Gobase._RecordConsumer.__init__ Bio.Graphics.BasicChromosome.Chromosome.__init__ Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__ Bio.Graphics.BasicChromosome.Organism.__init__ Bio.Graphics.BasicChromosome.TelomereSegment.__init__ Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__ Bio.Graphics.Comparative.ComparativeScatterPlot.__init__ Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__ Bio.Graphics.Distribution.BarChartDistribution.__init__ Bio.Graphics.Distribution.DistributionPage.__init__ Bio.Graphics.Distribution.LineDistribution.__init__ Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__ Bio.HMM.MarkovModel.HiddenMarkovModel.__init__ Bio.HMM.MarkovModel.MarkovModelBuilder.__init__ Bio.HMM.Trainer.AbstractTrainer.__init__ Bio.HMM.Trainer.BaumWelchTrainer.__init__ Bio.HMM.Trainer.KnownStateTrainer.__init__ Bio.HMM.Trainer.TrainingSequence.__init__ Bio.HotRand.HotCache.__init__ Bio.HotRand.HotRandom.__init__ Bio.Index._InMemoryIndex.__init__ Bio.Index._ShelveIndex.__init__ Bio.IntelliGenetics.IntelliGeneticsReader.__init__ Bio.IntelliGenetics.Iterator.__init__ Bio.IntelliGenetics.Record.Record.__init__ Bio.IntelliGenetics.RecordParser.__init__ Bio.IntelliGenetics._RecordConsumer.__init__ Bio.IntelliGenetics._Scanner.__init__ Bio.KDTree.CKDTree.KDTree.__init__ Bio.KDTree.CKDTree.KDTreePtr.__init__ Bio.KDTree.KDTree.KDTree.__init__ Bio.KEGG.Compound.Record.__init__ Bio.KEGG.Enzyme.Record.__init__ Bio.LocusLink.Iterator.__init__ Bio.LocusLink.Record.__init__ Bio.LocusLink.RecordParser.__init__ Bio.LocusLink._RecordConsumer.__init__ Bio.LocusLink._Scanner.__init__ Bio.LocusLink.web_parse.Record.__init__ Bio.LocusLink.web_parse.Token.__init__ Bio.LocusLink.web_parse.Url.__init__ Bio.LogisticRegression.LogisticRegression.__init__ Bio.MEME.Motif.Instance.__init__ Bio.MEME.Motif.MEMEMotif.__init__ Bio.MEME.Motif.Motif.__init__ Bio.MEME.Parser.MASTParser.__init__ Bio.MEME.Parser.MASTRecord.__init__ Bio.MEME.Parser.MEMEParser.__init__ Bio.MEME.Parser.MEMERecord.__init__ Bio.MEME.Parser._MASTConsumer.__init__ Bio.MEME.Parser._MEMEConsumer.__init__ Bio.MarkovModel.MarkovModel.__init__ Bio.MaxEntropy.MaxEntropy.__init__ Bio.Medline.Iterator.__init__ Bio.Medline.Record.__init__ Bio.Medline.RecordParser.__init__ Bio.Medline._RecordConsumer.__init__ Bio.MetaTool.Iterator.__init__ Bio.MetaTool.Record.Metabolite.__init__ Bio.MetaTool.Record.MetaboliteRole.__init__ Bio.MetaTool.Record.PathwayTransform.__init__ Bio.MetaTool.Record.Record.__init__ Bio.MetaTool.RecordParser.__init__ Bio.MetaTool._RecordConsumer.__init__ Bio.MetaTool._Scanner.__init__ Bio.Mindy.BaseDB.OpenDB.__init__ Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__ Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__ Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__ Bio.Mindy.FlatDB.BaseFlatDB.__init__ Bio.Mindy.FlatDB.BisectFile.__init__ Bio.Mindy.FlatDB.DiskFlatDB.__init__ 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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-76', '__init__', 'link-10');">__init__</a></tt><tt class="py-op">(</tt> <tt class="py-name">self</tt> <tt class="py-op">)</tt> </tt> </div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt> <a 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toggle('_RecordConsumer.set_interest_tags');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#set_interest_tags">set_interest_tags</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">interest_tags</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.set_interest_tags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.set_interest_tags-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">interest_tags</tt> <tt class="py-op">=</tt> <tt class="py-name">interest_tags</tt> </tt> </div><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.start_locus_line"></a><div id="_RecordConsumer.start_locus_line-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_locus_line-toggle" onclick="return toggle('_RecordConsumer.start_locus_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#start_locus_line">start_locus_line</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-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.start_locus_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_locus_line-expanded"><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name" targets="Method Martel.Dispatch.DispatchHandler.save_characters()=Martel.Dispatch.DispatchHandler-class.html#save_characters,Method Martel.Dispatch.Dispatcher.save_characters()=Martel.Dispatch.Dispatcher-class.html#save_characters"><a title="Martel.Dispatch.DispatchHandler.save_characters Martel.Dispatch.Dispatcher.save_characters" class="py-name" href="#" onclick="return doclink('link-79', 'save_characters', 'link-79');">save_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.end_locus_line"></a><div id="_RecordConsumer.end_locus_line-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_locus_line-toggle" onclick="return toggle('_RecordConsumer.end_locus_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#end_locus_line">end_locus_line</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">locus_record</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.end_locus_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_locus_line-expanded"><a name="L152"></a><tt class="py-lineno">152</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 id="link-80" class="py-name" targets="Method Martel.Dispatch.DispatchHandler.get_characters()=Martel.Dispatch.DispatchHandler-class.html#get_characters,Method Martel.Dispatch.Dispatcher.get_characters()=Martel.Dispatch.Dispatcher-class.html#get_characters"><a title="Martel.Dispatch.DispatchHandler.get_characters Martel.Dispatch.Dispatcher.get_characters" class="py-name" href="#" onclick="return doclink('link-80', 'get_characters', 'link-80');">get_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">cols</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-81" 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-81', 'split', 'link-81');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">':'</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-82" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-82', 'key', 'link-13');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt id="link-83" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-83', 'key', 'link-13');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-84', 'key', 'link-13');">key</a></tt><tt class="py-op">.</tt><tt id="link-85" 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-85', 'strip', 'link-85');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">newval</tt> <tt class="py-op">=</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">newval</tt> <tt class="py-op">=</tt> <tt class="py-name">newval</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'strip', 'link-85');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-87" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-87', 'key', 'link-13');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'BUTTON'</tt><tt class="py-op">:</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-88', 'data', 'link-55');">data</a></tt><tt class="py-op">.</tt><tt id="link-89" 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-89', 'has_key', 'link-89');">has_key</a></tt><tt class="py-op">(</tt> <tt id="link-90" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-90', 'key', 'link-13');">key</a></tt> <tt class="py-op">)</tt><tt class="py-op">:</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 id="link-91" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-91', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt id="link-92" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-92', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">newval</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-93', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt id="link-94" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-94', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">if</tt><tt class="py-op">(</tt> <tt id="link-95" 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-95', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-96" 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-96', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-string">''</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-97', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt id="link-98" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-98', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-name">val</tt><tt class="py-op">,</tt> <tt class="py-name">newval</tt> <tt class="py-op">]</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt><tt class="py-op">(</tt> <tt id="link-99" 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-99', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-name">val</tt> <tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-100" 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-100', 'type', 'link-17');">type</a></tt><tt class="py-op">(</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-op">)</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-101" 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-101', 'append', 'link-101');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">newval</tt> <tt class="py-op">)</tt> </tt> <a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-102', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt id="link-103" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-103', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt> </div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.start_accnum_block"></a><div id="_RecordConsumer.start_accnum_block-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_accnum_block-toggle" onclick="return toggle('_RecordConsumer.start_accnum_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#start_accnum_block">start_accnum_block</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-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.start_accnum_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_accnum_block-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name"><a title="Martel.Dispatch.DispatchHandler.save_characters Martel.Dispatch.Dispatcher.save_characters" class="py-name" href="#" onclick="return doclink('link-104', 'save_characters', 'link-79');">save_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.end_accnum_block"></a><div id="_RecordConsumer.end_accnum_block-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_accnum_block-toggle" onclick="return toggle('_RecordConsumer.end_accnum_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#end_accnum_block">end_accnum_block</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">locus_record</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.end_accnum_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_accnum_block-expanded"><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">block</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-105" class="py-name"><a title="Martel.Dispatch.DispatchHandler.get_characters Martel.Dispatch.Dispatcher.get_characters" class="py-name" href="#" onclick="return doclink('link-105', 'get_characters', 'link-80');">get_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-106" class="py-name" targets="Method Bio.LocusLink._RecordConsumer.parse_block()=Bio.LocusLink._RecordConsumer-class.html#parse_block"><a title="Bio.LocusLink._RecordConsumer.parse_block" class="py-name" href="#" onclick="return doclink('link-106', 'parse_block', 'link-106');">parse_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">block</tt><tt class="py-op">,</tt> <tt class="py-string">'ACCNUM'</tt> <tt class="py-op">)</tt> </tt> </div><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.start_phenotype_block"></a><div id="_RecordConsumer.start_phenotype_block-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_phenotype_block-toggle" onclick="return toggle('_RecordConsumer.start_phenotype_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#start_phenotype_block">start_phenotype_block</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-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.start_phenotype_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_phenotype_block-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Martel.Dispatch.DispatchHandler.save_characters Martel.Dispatch.Dispatcher.save_characters" class="py-name" href="#" onclick="return doclink('link-107', 'save_characters', 'link-79');">save_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.end_phenotype_block"></a><div id="_RecordConsumer.end_phenotype_block-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_phenotype_block-toggle" onclick="return toggle('_RecordConsumer.end_phenotype_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#end_phenotype_block">end_phenotype_block</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">locus_record</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.end_phenotype_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_phenotype_block-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">block</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Martel.Dispatch.DispatchHandler.get_characters Martel.Dispatch.Dispatcher.get_characters" class="py-name" href="#" onclick="return doclink('link-108', 'get_characters', 'link-80');">get_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.LocusLink._RecordConsumer.parse_block" class="py-name" href="#" onclick="return doclink('link-109', 'parse_block', 'link-106');">parse_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">block</tt><tt class="py-op">,</tt> <tt class="py-string">'PHENOTYPE'</tt> <tt class="py-op">)</tt> </tt> </div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.start_db_block"></a><div id="_RecordConsumer.start_db_block-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_db_block-toggle" onclick="return toggle('_RecordConsumer.start_db_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#start_db_block">start_db_block</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-param">attrs</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.start_db_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_db_block-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Martel.Dispatch.DispatchHandler.save_characters Martel.Dispatch.Dispatcher.save_characters" class="py-name" href="#" onclick="return doclink('link-110', 'save_characters', 'link-79');">save_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.end_db_block"></a><div id="_RecordConsumer.end_db_block-def"><a name="L189"></a><tt class="py-lineno">189</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_db_block-toggle" onclick="return toggle('_RecordConsumer.end_db_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#end_db_block">end_db_block</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">locus_record</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.end_db_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_db_block-expanded"><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">block</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-111" class="py-name"><a title="Martel.Dispatch.DispatchHandler.get_characters Martel.Dispatch.Dispatcher.get_characters" class="py-name" href="#" onclick="return doclink('link-111', 'get_characters', 'link-80');">get_characters</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.LocusLink._RecordConsumer.parse_block" class="py-name" href="#" onclick="return doclink('link-112', 'parse_block', 'link-106');">parse_block</a></tt><tt class="py-op">(</tt> <tt class="py-name">block</tt><tt class="py-op">,</tt> <tt class="py-string">'DB'</tt> <tt class="py-op">)</tt> </tt> </div><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt> <a name="_RecordConsumer.parse_block"></a><div id="_RecordConsumer.parse_block-def"><a name="L193"></a><tt class="py-lineno">193</tt> <a class="py-toggle" href="#" id="_RecordConsumer.parse_block-toggle" onclick="return toggle('_RecordConsumer.parse_block');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.LocusLink._RecordConsumer-class.html#parse_block">parse_block</a><tt class="py-op">(</tt> <tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">block</tt><tt class="py-op">,</tt> <tt class="py-param">block_key</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="_RecordConsumer.parse_block-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.parse_block-expanded"><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">block</tt><tt class="py-op">.</tt><tt class="py-name">splitlines</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">entry</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt> <a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">cols</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-113', 'split', 'link-81');">split</a></tt><tt class="py-op">(</tt> <tt class="py-string">':'</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt> <tt class="py-op">)</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt id="link-114" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-114', 'key', 'link-13');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">0</tt> <tt class="py-op">]</tt> </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt id="link-115" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-115', 'key', 'link-13');">key</a></tt> <tt class="py-op">=</tt> <tt id="link-116" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-116', 'key', 'link-13');">key</a></tt><tt class="py-op">.</tt><tt id="link-117" 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-117', 'strip', 'link-85');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">newval</tt> <tt class="py-op">=</tt> <tt class="py-name">cols</tt><tt class="py-op">[</tt> <tt class="py-number">1</tt> <tt class="py-op">]</tt> </tt> <a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">newval</tt> <tt class="py-op">=</tt> <tt class="py-name">newval</tt><tt class="py-op">.</tt><tt id="link-118" 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-118', 'strip', 'link-85');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">entry</tt><tt class="py-op">[</tt> <tt id="link-119" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-119', 'key', 'link-13');">key</a></tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">newval</tt> </tt> <a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt> <a name="L205"></a><tt class="py-lineno">205</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 id="link-120" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-120', 'data', 'link-55');">data</a></tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><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-121', 'has_key', 'link-89');">has_key</a></tt><tt class="py-op">(</tt> <tt class="py-name">block_key</tt> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-122', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt class="py-name">block_key</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-name">entry</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">val</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-123', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt class="py-name">block_key</tt> <tt class="py-op">]</tt> </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-124" 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-124', 'append', 'link-101');">append</a></tt><tt class="py-op">(</tt> <tt class="py-name">entry</tt> <tt class="py-op">)</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-125', 'data', 'link-55');">data</a></tt><tt class="py-op">[</tt> <tt class="py-name">block_key</tt> <tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt> </div></div><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt> <a name="RecordParser"></a><div id="RecordParser-def"><a name="L213"></a><tt class="py-lineno">213</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.LocusLink.RecordParser-class.html">RecordParser</a><tt class="py-op">:</tt> </tt> </div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse LocusLink files into Record objects</tt> </tt> <a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L216"></a><tt class="py-lineno">216</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.LocusLink.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-param">debug_level</tt> <tt class="py-op">=</tt> <tt class="py-number">0</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="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize the parser.</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"> o debug_level - An optional argument that specifies the amount of</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"> debugging information Martel should spit out. By default we have</tt> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> no debugging info (the fastest way to do things), but if you want</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> you can set this as high as two and see exactly where a parse fails.</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</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-126" 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-126', '_Scanner', 'link-126');">_Scanner</a></tt><tt class="py-op">(</tt><tt class="py-name">debug_level</tt><tt class="py-op">)</tt> </tt> </div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt> <a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L227"></a><tt class="py-lineno">227</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.LocusLink.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="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-docstring">"""Parse the specified handle into an NBRF record.</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</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-127" 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-127', '_RecordConsumer', 'link-127');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L231"></a><tt class="py-lineno">231</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-128" 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 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