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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module Mixins
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.Mixins-module.html">Module Bio.EUtils.Mixins</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""implements functionality shared between HistoryClient and DBIdsClient"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># These are mixins and use methods implemented by the main classes.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" 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-0', 'parse', 'link-0');">parse</a></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
<a name="LinkMixin"></a><div id="LinkMixin-def"><a name="L6"></a><tt class="py-lineno"> 6</tt> <a class="py-toggle" href="#" id="LinkMixin-toggle" onclick="return toggle('LinkMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html">LinkMixin</a><tt class="py-op">:</tt> </tt>
</div><div id="LinkMixin-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="LinkMixin-expanded"><a name="LinkMixin.prlinks"></a><div id="LinkMixin.prlinks-def"><a name="L7"></a><tt class="py-lineno"> 7</tt> <a class="py-toggle" href="#" id="LinkMixin.prlinks-toggle" onclick="return toggle('LinkMixin.prlinks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html#prlinks">prlinks</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> <tt class="py-param">daterange</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="LinkMixin.prlinks-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="LinkMixin.prlinks-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-docstring">"""get the prlinks as a Datatypes.LinksLinkSet"""</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.elink()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#elink,Method Bio.EUtils.HistoryClient.HistoryLookup.elink()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#elink,Function Bio.Entrez.elink()=Bio.Entrez-module.html#elink,Function Bio.WWW.NCBI.elink()=Bio.WWW.NCBI-module.html#elink"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-1', 'elink', 'link-1');">elink</a></tt><tt class="py-op">(</tt><tt id="link-2" class="py-name" targets="Variable Bio.LocusLink.locus_format.db=Bio.LocusLink.locus_format-module.html#db,Variable Bio.config.DBRegistry.db=Bio.config.DBRegistry-module.html#db"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-2', 'db', 'link-2');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-3" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-3', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"prlinks"</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-4" class="py-name"><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-4', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt class="py-name">parse_prlinks</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </tt>
<a name="LinkMixin.llinks"></a><div id="LinkMixin.llinks-def"><a name="L20"></a><tt class="py-lineno">20</tt> <a class="py-toggle" href="#" id="LinkMixin.llinks-toggle" onclick="return toggle('LinkMixin.llinks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html#llinks">llinks</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-param">daterange</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="LinkMixin.llinks-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="LinkMixin.llinks-expanded"><a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-docstring">"""get the llinks as a Datatypes.LinksLinkSet"""</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-5', 'elink', 'link-1');">elink</a></tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-6', 'db', 'link-2');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-7', 'db', 'link-2');">db</a></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">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"llinks"</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</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">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-8" class="py-name"><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-8', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function Bio.EUtils.parse.parse_llinks()=Bio.EUtils.parse-module.html#parse_llinks"><a title="Bio.EUtils.parse.parse_llinks" class="py-name" href="#" onclick="return doclink('link-9', 'parse_llinks', 'link-9');">parse_llinks</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt>
<a name="LinkMixin.lcheck"></a><div id="LinkMixin.lcheck-def"><a name="L33"></a><tt class="py-lineno">33</tt> <a class="py-toggle" href="#" id="LinkMixin.lcheck-toggle" onclick="return toggle('LinkMixin.lcheck');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html#lcheck">lcheck</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-param">daterange</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="LinkMixin.lcheck-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="LinkMixin.lcheck-expanded"><a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-10', 'elink', 'link-1');">elink</a></tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-11', 'db', 'link-2');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-12', 'db', 'link-2');">db</a></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">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"lcheck"</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</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">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-13" class="py-name"><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-13', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Function Bio.EUtils.parse.parse_lcheck()=Bio.EUtils.parse-module.html#parse_lcheck"><a title="Bio.EUtils.parse.parse_lcheck" class="py-name" href="#" onclick="return doclink('link-14', 'parse_lcheck', 'link-14');">parse_lcheck</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
<a name="LinkMixin.ncheck"></a><div id="LinkMixin.ncheck-def"><a name="L45"></a><tt class="py-lineno">45</tt> <a class="py-toggle" href="#" id="LinkMixin.ncheck-toggle" onclick="return toggle('LinkMixin.ncheck');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html#ncheck">ncheck</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-param">daterange</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="LinkMixin.ncheck-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="LinkMixin.ncheck-expanded"><a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-15', 'elink', 'link-1');">elink</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-16', 'db', 'link-2');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-17', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"ncheck"</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-18" class="py-name"><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-18', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt class="py-name">parse_ncheck</tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> </tt>
<a name="LinkMixin.neighbor_links"></a><div id="LinkMixin.neighbor_links-def"><a name="L57"></a><tt class="py-lineno">57</tt> <a class="py-toggle" href="#" id="LinkMixin.neighbor_links-toggle" onclick="return toggle('LinkMixin.neighbor_links');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.LinkMixin-class.html#neighbor_links">neighbor_links</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-param">db</tt> <tt class="py-op">=</tt> <tt class="py-string">"pubmed"</tt><tt class="py-op">,</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-param">term</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-param">field</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-param">daterange</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="LinkMixin.neighbor_links-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="LinkMixin.neighbor_links-expanded"><a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.elink
Bio.EUtils.HistoryClient.HistoryLookup.elink
Bio.Entrez.elink
Bio.WWW.NCBI.elink" class="py-name" href="#" onclick="return doclink('link-19', 'elink', 'link-1');">elink</a></tt><tt class="py-op">(</tt><tt id="link-20" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-20', 'db', 'link-2');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-21', 'db', 'link-2');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"neighbor"</tt><tt class="py-op">,</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">term</tt> <tt class="py-op">=</tt> <tt class="py-name">term</tt><tt class="py-op">,</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-name">field</tt> <tt class="py-op">=</tt> <tt class="py-name">field</tt><tt class="py-op">,</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-name">daterange</tt> <tt class="py-op">=</tt> <tt class="py-name">daterange</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-22" class="py-name"><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-22', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Function Bio.EUtils.parse.parse_neighbor_links()=Bio.EUtils.parse-module.html#parse_neighbor_links"><a title="Bio.EUtils.parse.parse_neighbor_links" class="py-name" href="#" onclick="return doclink('link-23', 'parse_neighbor_links', 'link-23');">parse_neighbor_links</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> </tt>
<a name="SequenceFetchMixin"></a><div id="SequenceFetchMixin-def"><a name="L69"></a><tt class="py-lineno">69</tt> <a class="py-toggle" href="#" id="SequenceFetchMixin-toggle" onclick="return toggle('SequenceFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.SequenceFetchMixin-class.html">SequenceFetchMixin</a><tt class="py-op">(</tt><tt class="py-base-class">LinkMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceFetchMixin-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SequenceFetchMixin-expanded"><a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"><tt class="py-comment">## Should turn this into a Bio.SeqRecord object</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## Could do that using the XML code, but GenBank/GenPept is better.</tt> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## def fetch(self,</tt> </tt>
<a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## seq_start = None, seq_stop = None, strand = None,</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## complexity = None):</tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return parse.parse_fetch_xml(self.efetch(seq_start = seq_start,</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## seq_stop = seq_stop,</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## strand = strand,</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## complexity = complexity))</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="PublicationFetchMixin"></a><div id="PublicationFetchMixin-def"><a name="L83"></a><tt class="py-lineno">83</tt> <a class="py-toggle" href="#" id="PublicationFetchMixin-toggle" onclick="return toggle('PublicationFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.PublicationFetchMixin-class.html">PublicationFetchMixin</a><tt class="py-op">(</tt><tt class="py-base-class">LinkMixin</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationFetchMixin-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="PublicationFetchMixin-expanded"><a name="PublicationFetchMixin.fetch"></a><div id="PublicationFetchMixin.fetch-def"><a name="L84"></a><tt class="py-lineno">84</tt> <a class="py-toggle" href="#" id="PublicationFetchMixin.fetch-toggle" onclick="return toggle('PublicationFetchMixin.fetch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.Mixins.PublicationFetchMixin-class.html#fetch">fetch</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="PublicationFetchMixin.fetch-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="PublicationFetchMixin.fetch-expanded"><a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-24" class="py-name"><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-24', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Function Bio.EUtils.parse.parse_fetch_publication_xml()=Bio.EUtils.parse-module.html#parse_fetch_publication_xml"><a title="Bio.EUtils.parse.parse_fetch_publication_xml" class="py-name" href="#" onclick="return doclink('link-25', 'parse_fetch_publication_xml', 'link-25');">parse_fetch_publication_xml</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch()=Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin-class.html#efetch,Method Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch()=Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin-class.html#efetch,Function Bio.Entrez.efetch()=Bio.Entrez-module.html#efetch,Function Bio.WWW.NCBI.efetch()=Bio.WWW.NCBI-module.html#efetch"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin.efetch
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin.efetch
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin.efetch
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin.efetch
Bio.Entrez.efetch
Bio.WWW.NCBI.efetch" class="py-name" href="#" onclick="return doclink('link-26', 'efetch', 'link-26');">efetch</a></tt><tt class="py-op">(</tt><tt class="py-string">"xml"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> </tt><script type="text/javascript">
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