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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.EUtils-module.html">Package EUtils</a> ::
Module DBIdsClient
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<h1 class="epydoc">Source Code for <a href="Bio.EUtils.DBIdsClient-module.html">Module Bio.EUtils.DBIdsClient</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Search and retrieve information given a set of database identifiers.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">EUtils has two major modes. One uses history while the other uses</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">database identifiers. This is a high-level interface for working with</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">identifiers. You should use this module to get information about a</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">set of known database identifiers.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">See HistoryClient if you want to work with a large number of</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">identifiers or potentially large search results.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">>>> from Bio import EUtils</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">>>> from Bio.EUtils import DBIdsClient</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">>>> client = DBIdsClient.DBIdsClient()</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">>>> result = client.search("dalke", retmax = 100)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">>>> len(result)</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">30</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">>>> print result[0].efetch(retmode = "text", rettype = "abstract").read()</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring">1: Pac Symp Biocomput 1997;:85-96</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring">Using Tcl for molecular visualization and analysis.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring">Dalke A, Schulten K.</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring">Beckman Institute, Urbana, IL 61801, USA.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring">Reading and manipulating molecular structure data is a standard task in every</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">molecular visualization and analysis program, but is rarely available in a form</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">readily accessible to the user. Instead, the development of new methods for</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring">analysis, display, and interaction is often achieved by writing a new program,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">rather than building on pre-existing software. We present the Tcl-based script</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring">language used in our molecular modeling program, VMD, and show how it can access</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring">information about the molecular structure, perform analysis, and graphically</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring">display and animate the results. The commands are available to the user and make</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring">VMD a useful environment for studying biomolecules.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring">PMID: 9390282 [PubMed - indexed for MEDLINE]</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring">>>></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring">Find sequences similar to GI:4579714 which were published in 2002.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring">>>> protein = DBIdsClient.from_dbids(EUtils.DBIds("protein", "4579714"))</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring">>>> neighbors = protein.neighbor_links("protein",</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring">... daterange = EUtils.DateRange("2002/01/01", "2002/12/31", "pdat"))</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring">>>> dbids = neighbors.linksetdbs["protein_protein"].dbids</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring">>>> len(dbids)</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring">28</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring">>>> print dbids</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring">DBIds(u'protein', [u'4579714', u'25298947', u'24158913', u'24158914', u'24158915', u'17942993', u'17942994', u'17942995', u'20150921', u'20150922', u'20151159', u'25298949', u'19716034', u'20663737', u'20663738', u'20663741', u'24987328', u'25533128', u'25298946', u'25298948', u'23008597', u'20219020', u'21218340', u'21218344', u'19075395', u'21218338', u'21218342', u'21311795'])</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring">>>> </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring">>>> print client.from_dbids(dbids[:5]).efetch(retmode="text",</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring">... rettype="summary").read()</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring">1: BAA75200</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring">Bacteriorhodopsin [Halobacterium sp.]</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring">gi|4579714|dbj|BAA75200.1|[4579714]</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring">2: H84300</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring">bacteriorhodopsin [imported] - Halobacterium sp. NRC-1</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring">gi|25298947|pir||H84300[25298947]</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring">3: 1M0KA</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring">Chain A, Bacteriorhodopsin K Intermediate At 1.43 A Resolution</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring">gi|24158913|pdb|1M0K|A[24158913]</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring">4: 1M0LA</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring">Chain A, BacteriorhodopsinLIPID COMPLEX AT 1.47 A RESOLUTION</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring">gi|24158914|pdb|1M0L|A[24158914]</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring">5: 1M0MA</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring">Chain A, Bacteriorhodopsin M1 Intermediate At 1.43 A Resolution</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring">gi|24158915|pdb|1M0M|A[24158915]</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">>>></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 class="py-docstring">"""</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">types</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</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 class="py-op">,</tt> <tt id="link-1" class="py-name" targets="Module Bio.EUtils.Mixins=Bio.EUtils.Mixins-module.html"><a title="Bio.EUtils.Mixins" class="py-name" href="#" onclick="return doclink('link-1', 'Mixins', 'link-1');">Mixins</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Module Bio.EUtils.Config=Bio.EUtils.Config-module.html"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-2', 'Config', 'link-2');">Config</a></tt><tt class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Module Bio.EUtils.ThinClient=Bio.EUtils.ThinClient-module.html,Class Bio.EUtils.ThinClient.ThinClient=Bio.EUtils.ThinClient.ThinClient-class.html"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-3', 'ThinClient', 'link-3');">ThinClient</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Module Bio.EUtils.Datatypes=Bio.EUtils.Datatypes-module.html"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-4', 'Datatypes', 'link-4');">Datatypes</a></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="DBIdsLookup"></a><div id="DBIdsLookup-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="DBIdsLookup-toggle" onclick="return toggle('DBIdsLookup');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html">DBIdsLookup</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBIdsLookup-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBIdsLookup-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Look up information about a DBIds</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> To get the list of dbids, as interpreted by fetching the</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> server's "uilist", use the "dbids" attribute.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="DBIdsLookup.__init__"></a><div id="DBIdsLookup.__init__-def"><a name="L94"></a><tt class="py-lineno"> 94</tt> <a class="py-toggle" href="#" id="DBIdsLookup.__init__-toggle" onclick="return toggle('DBIdsLookup.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-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">eutils</tt><tt class="py-op">,</tt> <tt class="py-param">records_dbids</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBIdsLookup.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsLookup.__init__-expanded"><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt class="py-name">eutils</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt> <tt class="py-op">=</tt> <tt class="py-name">records_dbids</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="DBIdsLookup.esummary"></a><div id="DBIdsLookup.esummary-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="DBIdsLookup.esummary-toggle" onclick="return toggle('DBIdsLookup.esummary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#esummary">esummary</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">'xml'</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</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="DBIdsLookup.esummary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsLookup.esummary-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""call esummary on this DBIds; returns the socket handle"""</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</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">eutils</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.esummary_using_dbids()=Bio.EUtils.ThinClient.ThinClient-class.html#esummary_using_dbids"><a title="Bio.EUtils.ThinClient.ThinClient.esummary_using_dbids" class="py-name" href="#" onclick="return doclink('link-5', 'esummary_using_dbids', 'link-5');">esummary_using_dbids</a></tt><tt class="py-op">(</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt id="link-6" class="py-name" targets="Variable Bio.EUtils.DBIdsClient.DBIdsLookup.dbids=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#dbids,Variable Bio.EUtils.Datatypes.CheckLinkSet.dbids=Bio.EUtils.Datatypes.CheckLinkSet-class.html#dbids,Variable Bio.EUtils.Datatypes.LinkSetDb.dbids=Bio.EUtils.Datatypes.LinkSetDb-class.html#dbids,Variable Bio.EUtils.HistoryClient.HistoryLookup.dbids=Bio.EUtils.HistoryClient.HistoryLookup-class.html#dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-6', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">)</tt> </tt>
</div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="DBIdsLookup.summary"></a><div id="DBIdsLookup.summary-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="DBIdsLookup.summary-toggle" onclick="return toggle('DBIdsLookup.summary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#summary">summary</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="DBIdsLookup.summary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsLookup.summary-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-docstring">"""get the summary for these DBIds, parsed into a Datatypes.Summary"""</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-7" 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-7', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Function Bio.EUtils.parse.parse_summary_xml()=Bio.EUtils.parse-module.html#parse_summary_xml"><a title="Bio.EUtils.parse.parse_summary_xml" class="py-name" href="#" onclick="return doclink('link-8', 'parse_summary_xml', 'link-8');">parse_summary_xml</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.esummary()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#esummary,Method Bio.EUtils.HistoryClient.HistoryLookup.esummary()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#esummary,Function Bio.Entrez.esummary()=Bio.Entrez-module.html#esummary"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.esummary
Bio.EUtils.HistoryClient.HistoryLookup.esummary
Bio.Entrez.esummary" class="py-name" href="#" onclick="return doclink('link-9', 'esummary', 'link-9');">esummary</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><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
<a name="DBIdsLookup.elink"></a><div id="DBIdsLookup.elink-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="DBIdsLookup.elink-toggle" onclick="return toggle('DBIdsLookup.elink');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#elink">elink</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</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="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-param">cmd</tt> <tt class="py-op">=</tt> <tt class="py-string">"neighbor"</tt><tt class="py-op">,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</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="L111"></a><tt class="py-lineno">111</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="L112"></a><tt class="py-lineno">112</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="DBIdsLookup.elink-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsLookup.elink-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-docstring">"""call elink on this DBIds; returns the socket handle"""</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</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">eutils</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.elink_using_dbids()=Bio.EUtils.ThinClient.ThinClient-class.html#elink_using_dbids"><a title="Bio.EUtils.ThinClient.ThinClient.elink_using_dbids" class="py-name" href="#" onclick="return doclink('link-10', 'elink_using_dbids', 'link-10');">elink_using_dbids</a></tt><tt class="py-op">(</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-11', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-12', 'dbids', 'link-6');">dbids</a></tt><tt class="py-op">,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt id="link-13" 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-13', 'db', 'link-13');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-14', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">cmd</tt> <tt class="py-op">=</tt> <tt class="py-name">cmd</tt><tt class="py-op">,</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</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="L119"></a><tt class="py-lineno">119</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="L120"></a><tt class="py-lineno">120</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="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="DBIdsLookup._get_dbids"></a><div id="DBIdsLookup._get_dbids-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="DBIdsLookup._get_dbids-toggle" onclick="return toggle('DBIdsLookup._get_dbids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#_get_dbids">_get_dbids</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="DBIdsLookup._get_dbids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsLookup._get_dbids-expanded"><a name="L124"></a><tt class="py-lineno">124</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" 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-15', 'efetch', 'link-15');">efetch</a></tt><tt class="py-op">(</tt><tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">"text"</tt><tt class="py-op">,</tt> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-string">"uilist"</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-16', 'ids', 'link-16');">ids</a></tt> <tt class="py-op">=</tt> <tt id="link-17" 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-17', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Function Bio.EUtils.parse.parse_fetch_identifiers()=Bio.EUtils.parse-module.html#parse_fetch_identifiers"><a title="Bio.EUtils.parse.parse_fetch_identifiers" class="py-name" href="#" onclick="return doclink('link-18', 'parse_fetch_identifiers', 'link-18');">parse_fetch_identifiers</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-19', 'Datatypes', 'link-4');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Class Bio.EUtils.Datatypes.DBIds=Bio.EUtils.Datatypes.DBIds-class.html"><a title="Bio.EUtils.Datatypes.DBIds" class="py-name" href="#" onclick="return doclink('link-20', 'DBIds', 'link-20');">DBIds</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</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-13');">db</a></tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-22', 'ids', 'link-16');">ids</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt id="link-23" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-23', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.property=Bio.Encodings.IUPACEncoding-module.html#property"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-24', 'property', 'link-24');">property</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup._get_dbids()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#_get_dbids,Method Bio.EUtils.Datatypes.CheckLinkSet._get_dbids()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#_get_dbids,Method Bio.EUtils.Datatypes.LinkSetDb._get_dbids()=Bio.EUtils.Datatypes.LinkSetDb-class.html#_get_dbids,Method Bio.EUtils.HistoryClient.HistoryLookup._get_dbids()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#_get_dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup._get_dbids
Bio.EUtils.Datatypes.CheckLinkSet._get_dbids
Bio.EUtils.Datatypes.LinkSetDb._get_dbids
Bio.EUtils.HistoryClient.HistoryLookup._get_dbids" class="py-name" href="#" onclick="return doclink('link-25', '_get_dbids', 'link-25');">_get_dbids</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-string">"The DBIds for this results set, validated from the server's 'uilist'"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt>
<a name="DBIdsRecord"></a><div id="DBIdsRecord-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="DBIdsRecord-toggle" onclick="return toggle('DBIdsRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsRecord-class.html">DBIdsRecord</a><tt class="py-op">(</tt><tt class="py-base-class">DBIdsLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBIdsRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBIdsRecord-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-docstring">"""A single record on the server"""</tt> </tt>
<a name="DBIdsRecord.summary"></a><div id="DBIdsRecord.summary-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="DBIdsRecord.summary-toggle" onclick="return toggle('DBIdsRecord.summary');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsRecord-class.html#summary">summary</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="DBIdsRecord.summary-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsRecord.summary-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-26" class="py-name" targets="Class Bio.EUtils.DBIdsClient.DBIdsLookup=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup" class="py-name" href="#" onclick="return doclink('link-26', 'DBIdsLookup', 'link-26');">DBIdsLookup</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsLookup.summary()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#summary,Method Bio.EUtils.DBIdsClient.DBIdsRecord.summary()=Bio.EUtils.DBIdsClient.DBIdsRecord-class.html#summary,Method Bio.EUtils.HistoryClient.HistoryLookup.summary()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#summary,Method Bio.EUtils.HistoryClient.HistoryRecord.summary()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#summary"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.summary
Bio.EUtils.DBIdsClient.DBIdsRecord.summary
Bio.EUtils.HistoryClient.HistoryLookup.summary
Bio.EUtils.HistoryClient.HistoryRecord.summary" class="py-name" href="#" onclick="return doclink('link-27', 'summary', 'link-27');">summary</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="SequenceDBIdsFetchMixin"></a><div id="SequenceDBIdsFetchMixin-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="SequenceDBIdsFetchMixin-toggle" onclick="return toggle('SequenceDBIdsFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html">SequenceDBIdsFetchMixin</a><tt class="py-op">:</tt> </tt>
</div><div id="SequenceDBIdsFetchMixin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceDBIdsFetchMixin-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-docstring">"""Support 'efetch' for sequence records"""</tt> </tt>
<a name="SequenceDBIdsFetchMixin.efetch"></a><div id="SequenceDBIdsFetchMixin.efetch-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="SequenceDBIdsFetchMixin.efetch-toggle" onclick="return toggle('SequenceDBIdsFetchMixin.efetch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin-class.html#efetch">efetch</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">'xml'</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-param">seq_start</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">seq_stop</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">strand</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-param">complexity</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="SequenceDBIdsFetchMixin.efetch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequenceDBIdsFetchMixin.efetch-expanded"><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-28" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.strand()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#strand,Variable Bio.expressions.blast.ncbiblast.strand=Bio.expressions.blast.ncbiblast-module.html#strand"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-28', 'strand', 'link-28');">strand</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Strand can only be 1 (plus, default) or 2 (minus)"</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</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">eutils</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.efetch_using_dbids()=Bio.EUtils.ThinClient.ThinClient-class.html#efetch_using_dbids"><a title="Bio.EUtils.ThinClient.ThinClient.efetch_using_dbids" class="py-name" href="#" onclick="return doclink('link-29', 'efetch_using_dbids', 'link-29');">efetch_using_dbids</a></tt><tt class="py-op">(</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-30', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">,</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-name">retmode</tt><tt class="py-op">,</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">rettype</tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">seq_start</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_start</tt><tt class="py-op">,</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">seq_stop</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_stop</tt><tt class="py-op">,</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-31', 'strand', 'link-28');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-32', 'strand', 'link-28');">strand</a></tt><tt class="py-op">,</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">complexity</tt> <tt class="py-op">=</tt> <tt class="py-name">complexity</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="SequenceDBIdsRecord"></a><div id="SequenceDBIdsRecord-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="SequenceDBIdsRecord-toggle" onclick="return toggle('SequenceDBIdsRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html">SequenceDBIdsRecord</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">SequenceFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-base-class">SequenceDBIdsFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-base-class">DBIdsRecord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceDBIdsRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceDBIdsRecord-expanded"><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-docstring">"""a single sequence record, referenced by database identifier"""</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> </tt>
<a name="PublicationDBIdsFetchMixin"></a><div id="PublicationDBIdsFetchMixin-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="PublicationDBIdsFetchMixin-toggle" onclick="return toggle('PublicationDBIdsFetchMixin');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html">PublicationDBIdsFetchMixin</a><tt class="py-op">:</tt> </tt>
</div><div id="PublicationDBIdsFetchMixin-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationDBIdsFetchMixin-expanded"><a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-docstring">"""Support 'efetch' for publication records"""</tt> </tt>
<a name="PublicationDBIdsFetchMixin.efetch"></a><div id="PublicationDBIdsFetchMixin.efetch-def"><a name="L160"></a><tt class="py-lineno">160</tt> <a class="py-toggle" href="#" id="PublicationDBIdsFetchMixin.efetch-toggle" onclick="return toggle('PublicationDBIdsFetchMixin.efetch');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin-class.html#efetch">efetch</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">retmode</tt> <tt class="py-op">=</tt> <tt class="py-string">"xml"</tt><tt class="py-op">,</tt> <tt class="py-param">rettype</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="PublicationDBIdsFetchMixin.efetch-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PublicationDBIdsFetchMixin.efetch-expanded"><a name="L161"></a><tt class="py-lineno">161</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">eutils</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.EUtils.ThinClient.ThinClient.efetch_using_dbids" class="py-name" href="#" onclick="return doclink('link-33', 'efetch_using_dbids', 'link-29');">efetch_using_dbids</a></tt><tt class="py-op">(</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt id="link-34" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-34', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">,</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">retmode</tt> <tt class="py-op">=</tt> <tt class="py-name">retmode</tt><tt class="py-op">,</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">rettype</tt> <tt class="py-op">=</tt> <tt class="py-name">rettype</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> </tt>
<a name="PublicationDBIdsRecord"></a><div id="PublicationDBIdsRecord-def"><a name="L166"></a><tt class="py-lineno">166</tt> <a class="py-toggle" href="#" id="PublicationDBIdsRecord-toggle" onclick="return toggle('PublicationDBIdsRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html">PublicationDBIdsRecord</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">PublicationFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-base-class">PublicationDBIdsFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-base-class">DBIdsRecord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationDBIdsRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationDBIdsRecord-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-docstring">"""a single publication record, referenced by database identifier"""</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="BaseDBIdsRecordSet"></a><div id="BaseDBIdsRecordSet-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="BaseDBIdsRecordSet-toggle" onclick="return toggle('BaseDBIdsRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html">BaseDBIdsRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">DBIdsLookup</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseDBIdsRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BaseDBIdsRecordSet-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for dealing with a set of records, reference by identifier"""</tt> </tt>
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Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
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-36', '__init__', 'link-36');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">records_dbids</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">metadata</tt> <tt class="py-op">=</tt> <tt class="py-name">metadata</tt> </tt>
</div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="BaseDBIdsRecordSet.__len__"></a><div id="BaseDBIdsRecordSet.__len__-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="BaseDBIdsRecordSet.__len__-toggle" onclick="return toggle('BaseDBIdsRecordSet.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__len__">__len__</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="BaseDBIdsRecordSet.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseDBIdsRecordSet.__len__-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-docstring">"""Number of records referenced by this RecordSet"""</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</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="BaseDBIdsRecordSet.__getitem__"></a><div id="BaseDBIdsRecordSet.__getitem__-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="BaseDBIdsRecordSet.__getitem__-toggle" onclick="return toggle('BaseDBIdsRecordSet.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BaseDBIdsRecordSet.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BaseDBIdsRecordSet.__getitem__-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-docstring">"""Return subset of the records"""</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-37', 'i', 'link-37');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">types</tt><tt class="py-op">.</tt><tt class="py-name">SliceType</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># Metadata is not passed downwards</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-38" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-38', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">step</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</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">__class__</tt><tt class="py-op">(</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-40', 'start', 'link-40');">start</a></tt><tt class="py-op">:</tt><tt id="link-41" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-41', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">stop</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</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">__class__</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 class="py-name">eutils</tt><tt class="py-op">,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-43', 'start', 'link-40');">start</a></tt><tt class="py-op">:</tt><tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-44', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">stop</tt><tt class="py-op">:</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-45', 'i', 'link-37');">i</a></tt><tt class="py-op">.</tt><tt class="py-name">step</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="L194"></a><tt class="py-lineno">194</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">_record_class</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_dbids</tt><tt class="py-op">.</tt><tt id="link-46" 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-46', 'item', 'link-46');">item</a></tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-37');">i</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> </tt>
<a name="SequenceDBIdsRecordSet"></a><div id="SequenceDBIdsRecordSet-def"><a name="L196"></a><tt class="py-lineno">196</tt> <a class="py-toggle" href="#" id="SequenceDBIdsRecordSet-toggle" onclick="return toggle('SequenceDBIdsRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html">SequenceDBIdsRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">SequenceFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-base-class">SequenceDBIdsFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-base-class">BaseDBIdsRecordSet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequenceDBIdsRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequenceDBIdsRecordSet-expanded"><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-docstring">"""a set of sequence records, referenced by database identifier"""</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">_record_class</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name" targets="Class Bio.EUtils.DBIdsClient.SequenceDBIdsRecord=Bio.EUtils.DBIdsClient.SequenceDBIdsRecord-class.html"><a title="Bio.EUtils.DBIdsClient.SequenceDBIdsRecord" class="py-name" href="#" onclick="return doclink('link-48', 'SequenceDBIdsRecord', 'link-48');">SequenceDBIdsRecord</a></tt> </tt>
</div><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> </tt>
<a name="PublicationDBIdsRecordSet"></a><div id="PublicationDBIdsRecordSet-def"><a name="L202"></a><tt class="py-lineno">202</tt> <a class="py-toggle" href="#" id="PublicationDBIdsRecordSet-toggle" onclick="return toggle('PublicationDBIdsRecordSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html">PublicationDBIdsRecordSet</a><tt class="py-op">(</tt><tt class="py-base-class">Mixins</tt><tt class="py-op">.</tt><tt class="py-base-class">PublicationFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-base-class">PublicationDBIdsFetchMixin</tt><tt class="py-op">,</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-base-class">BaseDBIdsRecordSet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="PublicationDBIdsRecordSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PublicationDBIdsRecordSet-expanded"><a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-docstring">"""a set of publication records, referenced by database identifier"""</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-name">_record_class</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name" targets="Class Bio.EUtils.DBIdsClient.PublicationDBIdsRecord=Bio.EUtils.DBIdsClient.PublicationDBIdsRecord-class.html"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsRecord" class="py-name" href="#" onclick="return doclink('link-49', 'PublicationDBIdsRecord', 'link-49');">PublicationDBIdsRecord</a></tt> </tt>
</div><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="_get_recordset_constructor"></a><div id="_get_recordset_constructor-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="_get_recordset_constructor-toggle" onclick="return toggle('_get_recordset_constructor');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient-module.html#_get_recordset_constructor">_get_recordset_constructor</a><tt class="py-op">(</tt><tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">dbtype</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_get_recordset_constructor-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_get_recordset_constructor-expanded"><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-docstring">"""get the right DataSet constructor for a database"""</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">dbtype</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-50', 'Config', 'link-2');">Config</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Variable Bio.EUtils.Config.databases=Bio.EUtils.Config-module.html#databases"><a title="Bio.EUtils.Config.databases" class="py-name" href="#" onclick="return doclink('link-51', 'databases', 'link-51');">databases</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name" targets="Method Bio.EUtils.Config.DatabaseDict.gettype()=Bio.EUtils.Config.DatabaseDict-class.html#gettype"><a title="Bio.EUtils.Config.DatabaseDict.gettype" class="py-name" href="#" onclick="return doclink('link-52', 'gettype', 'link-52');">gettype</a></tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-53', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dbtype</tt> <tt class="py-op">==</tt> <tt id="link-54" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-54', 'Config', 'link-2');">Config</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Variable Bio.EUtils.Config.SEQUENCE_TYPE=Bio.EUtils.Config-module.html#SEQUENCE_TYPE"><a title="Bio.EUtils.Config.SEQUENCE_TYPE" class="py-name" href="#" onclick="return doclink('link-55', 'SEQUENCE_TYPE', 'link-55');">SEQUENCE_TYPE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-56" class="py-name" targets="Class Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet=Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet-class.html"><a title="Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet" class="py-name" href="#" onclick="return doclink('link-56', 'SequenceDBIdsRecordSet', 'link-56');">SequenceDBIdsRecordSet</a></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">dbtype</tt> <tt class="py-op">==</tt> <tt id="link-57" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-57', 'Config', 'link-2');">Config</a></tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Variable Bio.EUtils.Config.PUBLICATION_TYPE=Bio.EUtils.Config-module.html#PUBLICATION_TYPE"><a title="Bio.EUtils.Config.PUBLICATION_TYPE" class="py-name" href="#" onclick="return doclink('link-58', 'PUBLICATION_TYPE', 'link-58');">PUBLICATION_TYPE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-59" class="py-name" targets="Class Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet=Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet-class.html"><a title="Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet" class="py-name" href="#" onclick="return doclink('link-59', 'PublicationDBIdsRecordSet', 'link-59');">PublicationDBIdsRecordSet</a></tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown database type: %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">dbtype</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
<a name="from_dbids"></a><div id="from_dbids-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="from_dbids-toggle" onclick="return toggle('from_dbids');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient-module.html#from_dbids">from_dbids</a><tt class="py-op">(</tt><tt class="py-param">dbids</tt><tt class="py-op">,</tt> <tt class="py-param">dbtype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">eutils</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="from_dbids-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="from_dbids-expanded"><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-docstring">"""create a RecordSet interface for the set of database identifiers</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-docstring"> Parameters are:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-docstring"> dbids -- a DBIds</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"> dbtype -- the dbtype to use (EUtils.Config.{SEQUENCE,PUBLIATION}_TYPE)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> in case dbids.db isn't in the list of know NCBI databases.</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> Defaults to None.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"> eutils -- the ThinClient to use, defaults to creating a new</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> ThinClient.ThinClient()</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-keyword">return</tt> <tt id="link-60" class="py-name" targets="Module Bio.EUtils.DBIdsClient=Bio.EUtils.DBIdsClient-module.html,Class Bio.EUtils.DBIdsClient.DBIdsClient=Bio.EUtils.DBIdsClient.DBIdsClient-class.html"><a title="Bio.EUtils.DBIdsClient
Bio.EUtils.DBIdsClient.DBIdsClient" class="py-name" href="#" onclick="return doclink('link-60', 'DBIdsClient', 'link-60');">DBIdsClient</a></tt><tt class="py-op">(</tt><tt class="py-name">eutils</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.from_dbids()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#from_dbids,Function Bio.EUtils.DBIdsClient.from_dbids()=Bio.EUtils.DBIdsClient-module.html#from_dbids"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.from_dbids
Bio.EUtils.DBIdsClient.from_dbids" class="py-name" href="#" onclick="return doclink('link-61', 'from_dbids', 'link-61');">from_dbids</a></tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-62', 'dbids', 'link-6');">dbids</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
</div><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> </tt>
<a name="DBIdsClient"></a><div id="DBIdsClient-def"><a name="L232"></a><tt class="py-lineno">232</tt> <a class="py-toggle" href="#" id="DBIdsClient-toggle" onclick="return toggle('DBIdsClient');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsClient-class.html">DBIdsClient</a><tt class="py-op">:</tt> </tt>
</div><div id="DBIdsClient-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBIdsClient-expanded"><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-docstring">"""Create a RecordSet either from a search or a set of dbids</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"> The constructor takes an optional ThinClient to use for</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> connecting to NCBI.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="DBIdsClient.__init__"></a><div id="DBIdsClient.__init__-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="DBIdsClient.__init__-toggle" onclick="return toggle('DBIdsClient.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsClient-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">eutils</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="DBIdsClient.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsClient.__init__-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">eutils</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-63', 'ThinClient', 'link-3');">ThinClient</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.EUtils.ThinClient
Bio.EUtils.ThinClient.ThinClient" class="py-name" href="#" onclick="return doclink('link-64', 'ThinClient', 'link-3');">ThinClient</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt> <tt class="py-op">=</tt> <tt class="py-name">eutils</tt> </tt>
</div><a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> </tt>
<a name="DBIdsClient.from_dbids"></a><div id="DBIdsClient.from_dbids-def"><a name="L243"></a><tt class="py-lineno">243</tt> <a class="py-toggle" href="#" id="DBIdsClient.from_dbids-toggle" onclick="return toggle('DBIdsClient.from_dbids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsClient-class.html#from_dbids">from_dbids</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbids</tt><tt class="py-op">,</tt> <tt class="py-param">dbtype</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="DBIdsClient.from_dbids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsClient.from_dbids-expanded"><a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-docstring">"""Return a RecordSet given the DBIds</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"> This RecordSet can be used to fetch data from NCBI</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> related to the given DBIds.</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">set_klass</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name" targets="Function Bio.EUtils.DBIdsClient._get_recordset_constructor()=Bio.EUtils.DBIdsClient-module.html#_get_recordset_constructor,Function Bio.EUtils.HistoryClient._get_recordset_constructor()=Bio.EUtils.HistoryClient-module.html#_get_recordset_constructor"><a title="Bio.EUtils.DBIdsClient._get_recordset_constructor
Bio.EUtils.HistoryClient._get_recordset_constructor" class="py-name" href="#" onclick="return doclink('link-65', '_get_recordset_constructor', 'link-65');">_get_recordset_constructor</a></tt><tt class="py-op">(</tt><tt id="link-66" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-66', 'dbids', 'link-6');">dbids</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-67', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">set_klass</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt id="link-68" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-68', 'dbids', 'link-6');">dbids</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div><a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="DBIdsClient.search"></a><div id="DBIdsClient.search-def"><a name="L252"></a><tt class="py-lineno">252</tt> <a class="py-toggle" href="#" id="DBIdsClient.search-toggle" onclick="return toggle('DBIdsClient.search');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search">search</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-param">term</tt><tt class="py-op">,</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</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="L255"></a><tt class="py-lineno">255</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="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-param">retstart</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-param">retmax</tt> <tt class="py-op">=</tt> <tt class="py-number">20</tt><tt class="py-op">,</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="L260"></a><tt class="py-lineno">260</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>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-param">dbtype</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBIdsClient.search-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBIdsClient.search-expanded"><a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-docstring">"""do an Entrez search</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> The parameters are:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> 'term' -- the query string in the Entrez query language; see</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> http://www.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> 'db' -- the database to search</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> 'field' -- the field to use for unqualified words</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> Eg, "dalke[au] AND gene" with field==None becomes</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> dalke[au] AND (genes[MeSH Terms] OR gene[Text Word]</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> and "dalke[au] AND gene" with field=="au" becomes</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-docstring"> dalke[au] AND genes[Author]</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-docstring"> (Yes, I think the first "au" should be "Author" too)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-docstring"> 'retstart' -- include identifiers in the output, starting with</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"> position 'retstart' (normally starts with 0)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-docstring"> 'retmax' -- return at most 'retmax' identifiers in the output</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-docstring"> (if not specified, NCBI returns 20 identifiers)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> 'daterange' -- a date restriction; either WithinNDays or DateRange</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-docstring"> 'dbtype' -- (optional) the database type (Config.PUBLICATION_TYPE</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-docstring"> or SEQUENCE_TYPE). Overrides the type based on the 'db'</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">set_klass</tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="Bio.EUtils.DBIdsClient._get_recordset_constructor
Bio.EUtils.HistoryClient._get_recordset_constructor" class="py-name" href="#" onclick="return doclink('link-69', '_get_recordset_constructor', 'link-65');">_get_recordset_constructor</a></tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-70', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbtype</tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</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 class="py-name">eutils</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name" targets="Method Bio.EUtils.ThinClient.ThinClient.esearch()=Bio.EUtils.ThinClient.ThinClient-class.html#esearch,Function Bio.Entrez.esearch()=Bio.Entrez-module.html#esearch,Function Bio.WWW.NCBI.esearch()=Bio.WWW.NCBI-module.html#esearch"><a title="Bio.EUtils.ThinClient.ThinClient.esearch
Bio.Entrez.esearch
Bio.WWW.NCBI.esearch" class="py-name" href="#" onclick="return doclink('link-71', 'esearch', 'link-71');">esearch</a></tt><tt class="py-op">(</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</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="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt id="link-72" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-72', 'db', 'link-13');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-73', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</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="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">retstart</tt> <tt class="py-op">=</tt> <tt class="py-name">retstart</tt><tt class="py-op">,</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">retmax</tt> <tt class="py-op">=</tt> <tt class="py-name">retmax</tt><tt class="py-op">,</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</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="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">searchinfo</tt> <tt class="py-op">=</tt> <tt id="link-74" 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-74', 'parse', 'link-0');">parse</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name" targets="Function Bio.EUtils.parse.parse_search()=Bio.EUtils.parse-module.html#parse_search"><a title="Bio.EUtils.parse.parse_search" class="py-name" href="#" onclick="return doclink('link-75', 'parse_search', 'link-75');">parse_search</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-76', 'dbids', 'link-6');">dbids</a></tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="Bio.EUtils.Datatypes" class="py-name" href="#" onclick="return doclink('link-77', 'Datatypes', 'link-4');">Datatypes</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds" class="py-name" href="#" onclick="return doclink('link-78', 'DBIds', 'link-20');">DBIds</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-79', 'db', 'link-13');">db</a></tt><tt class="py-op">,</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-80', 'ids', 'link-16');">ids</a></tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">set_klass</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">eutils</tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsLookup.dbids
Bio.EUtils.Datatypes.CheckLinkSet.dbids
Bio.EUtils.Datatypes.LinkSetDb.dbids
Bio.EUtils.HistoryClient.HistoryLookup.dbids" class="py-name" href="#" onclick="return doclink('link-81', 'dbids', 'link-6');">dbids</a></tt><tt class="py-op">,</tt> <tt class="py-name">searchinfo</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> </tt><script type="text/javascript">
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