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<a href="BioSQL-module.html">Package BioSQL</a> ::
Module Loader
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<h1 class="epydoc">Source Code for <a href="BioSQL.Loader-module.html">Module BioSQL.Loader</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2002 by Andrew Dalke. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Revisions 2007-2008 by Peter Cock.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Note that BioSQL (including the database schema and scripts) is</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># available and licensed separately. Please consult www.biosql.org</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""Load biopython objects into a BioSQL database for persistent storage.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">This code makes it possible to store biopython objects in a relational</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">database and then retrieve them back. You shouldn't use any of the</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">classes in this module directly. Rather, call the load() method on</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring">a database object.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"># standard modules</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-0', 'time', 'link-0');">time</a></tt> <tt class="py-keyword">import</tt> <tt class="py-name">gmtime</tt><tt class="py-op">,</tt> <tt class="py-name">strftime</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"># biopython</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-2', 'Alphabet', 'link-2');">Alphabet</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Package Bio.SeqUtils=Bio.SeqUtils-module.html"><a title="Bio.SeqUtils" class="py-name" href="#" onclick="return doclink('link-4', 'SeqUtils', 'link-4');">SeqUtils</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module Bio.SeqUtils.CheckSum=Bio.SeqUtils.CheckSum-module.html"><a title="Bio.SeqUtils.CheckSum" class="py-name" href="#" onclick="return doclink('link-5', 'CheckSum', 'link-5');">CheckSum</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Function Bio.SeqUtils.CheckSum.crc64()=Bio.SeqUtils.CheckSum-module.html#crc64"><a title="Bio.SeqUtils.CheckSum.crc64" class="py-name" href="#" onclick="return doclink('link-6', 'crc64', 'link-6');">crc64</a></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader"></a><div id="DatabaseLoader-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="DatabaseLoader-toggle" onclick="return toggle('DatabaseLoader');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html">DatabaseLoader</a><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DatabaseLoader-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a database with biopython objects.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="DatabaseLoader.__init__"></a><div id="DatabaseLoader.__init__-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="DatabaseLoader.__init__-toggle" onclick="return toggle('DatabaseLoader.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-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">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader.__init__-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize with connection information for the database.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> XXX Figure out what I need to load a database and document it.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Function Bio.Std.dbid()=Bio.Std-module.html#dbid"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-7', 'dbid', 'link-7');">dbid</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-8', 'dbid', 'link-7');">dbid</a></tt> </tt>
</div><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader.load_seqrecord"></a><div id="DatabaseLoader.load_seqrecord-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="DatabaseLoader.load_seqrecord-toggle" onclick="return toggle('DatabaseLoader.load_seqrecord');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#load_seqrecord">load_seqrecord</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader.load_seqrecord-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader.load_seqrecord-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a Biopython SeqRecord into the database.</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">bioentry_id</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 BioSQL.Loader.DatabaseLoader._load_bioentry_table()=BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_table"><a title="BioSQL.Loader.DatabaseLoader._load_bioentry_table" class="py-name" href="#" onclick="return doclink('link-9', '_load_bioentry_table', 'link-9');">_load_bioentry_table</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-10', 'record', 'link-10');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_bioentry_date()=BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_date"><a title="BioSQL.Loader.DatabaseLoader._load_bioentry_date" class="py-name" href="#" onclick="return doclink('link-11', '_load_bioentry_date', 'link-11');">_load_bioentry_date</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-12', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_biosequence()=BioSQL.Loader.DatabaseLoader-class.html#_load_biosequence"><a title="BioSQL.Loader.DatabaseLoader._load_biosequence" class="py-name" href="#" onclick="return doclink('link-13', '_load_biosequence', 'link-13');">_load_biosequence</a></tt><tt class="py-op">(</tt><tt id="link-14" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-14', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_comment()=BioSQL.Loader.DatabaseLoader-class.html#_load_comment"><a title="BioSQL.Loader.DatabaseLoader._load_comment" class="py-name" href="#" onclick="return doclink('link-15', '_load_comment', 'link-15');">_load_comment</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-16', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_dbxrefs()=BioSQL.Loader.DatabaseLoader-class.html#_load_dbxrefs"><a title="BioSQL.Loader.DatabaseLoader._load_dbxrefs" class="py-name" href="#" onclick="return doclink('link-17', '_load_dbxrefs', 'link-17');">_load_dbxrefs</a></tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-18', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">references</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-19', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-20', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-21', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'references'</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-22" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HeaderConsumer.reference()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#reference,Method Bio.Prosite.Prodoc._RecordConsumer.reference()=Bio.Prosite.Prodoc._RecordConsumer-class.html#reference,Variable Bio.expressions.embl.embl65.reference=Bio.expressions.embl.embl65-module.html#reference,Variable Bio.expressions.genbank.reference=Bio.expressions.genbank-module.html#reference,Variable Bio.expressions.swissprot.sprot38.reference=Bio.expressions.swissprot.sprot38-module.html#reference,Variable Martel.test.test_swissprot38.reference=Martel.test.test_swissprot38-module.html#reference,Variable Martel.test.testformats.swissprot38.reference=Martel.test.testformats.swissprot38-module.html#reference"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-22', 'reference', 'link-22');">reference</a></tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">references</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">references</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_reference()=BioSQL.Loader.DatabaseLoader-class.html#_load_reference"><a title="BioSQL.Loader.DatabaseLoader._load_reference" class="py-name" href="#" onclick="return doclink('link-23', '_load_reference', 'link-23');">_load_reference</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-24', 'reference', 'link-22');">reference</a></tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_annotations()=BioSQL.Loader.DatabaseLoader-class.html#_load_annotations"><a title="BioSQL.Loader.DatabaseLoader._load_annotations" class="py-name" href="#" onclick="return doclink('link-25', '_load_annotations', 'link-25');">_load_annotations</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-26', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seq_feature_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-27', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.GFF.Segment.features()=Bio.GFF.Segment-class.html#features,Variable BioSQL.BioSeq.DBSeqRecord.features=BioSQL.BioSeq.DBSeqRecord-class.html#features,Method Martel.Expression.Expression.features()=Martel.Expression.Expression-class.html#features,Method Martel.Expression.ExpressionList.features()=Martel.Expression.ExpressionList-class.html#features,Method Martel.Expression.FastFeature.features()=Martel.Expression.FastFeature-class.html#features,Method Martel.Expression.Group.features()=Martel.Expression.Group-class.html#features,Method Martel.Expression.HeaderFooter.features()=Martel.Expression.HeaderFooter-class.html#features,Method Martel.Expression.MaxRepeat.features()=Martel.Expression.MaxRepeat-class.html#features,Method Martel.Expression.ParseRecords.features()=Martel.Expression.ParseRecords-class.html#features,Method Martel.Expression.PassThrough.features()=Martel.Expression.PassThrough-class.html#features"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-28', 'features', 'link-28');">features</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">seq_feature</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-29', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-30', 'features', 'link-28');">features</a></tt><tt class="py-op">[</tt><tt class="py-name">seq_feature_num</tt><tt class="py-op">]</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_seqfeature()=BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature"><a title="BioSQL.Loader.DatabaseLoader._load_seqfeature" class="py-name" href="#" onclick="return doclink('link-31', '_load_seqfeature', 'link-31');">_load_seqfeature</a></tt><tt class="py-op">(</tt><tt class="py-name">seq_feature</tt><tt class="py-op">,</tt> <tt class="py-name">seq_feature_num</tt><tt class="py-op">,</tt> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_ontology_id"></a><div id="DatabaseLoader._get_ontology_id-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_ontology_id-toggle" onclick="return toggle('DatabaseLoader._get_ontology_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_ontology_id">_get_ontology_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">definition</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="DatabaseLoader._get_ontology_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_ontology_id-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the identifier for the named ontology.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> This looks through the onotology table for a the given entry name.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> If it is not found, a row is added for this ontology (using the</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> definition if supplied). In either case, the id corresponding to</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> the provided name is returned, so that you can reference it in</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> another table.</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-name">oids</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetch_col0"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-32', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">"SELECT ontology_id FROM ontology WHERE name = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-33" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-33', 'name', 'link-33');">name</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">oids</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">oids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-34', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO ontology(name, definition) VALUES (%s, %s)"</tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-35', 'name', 'link-33');">name</a></tt><tt class="py-op">,</tt> <tt id="link-36" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.definition()=Bio.GenBank._FeatureConsumer-class.html#definition,Method Bio.GenBank._RecordConsumer.definition()=Bio.GenBank._RecordConsumer-class.html#definition"><a title="Bio.GenBank._FeatureConsumer.definition
Bio.GenBank._RecordConsumer.definition" class="py-name" href="#" onclick="return doclink('link-36', 'definition', 'link-36');">definition</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</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">adaptor</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.last_id()=BioSQL.BioSeqDatabase.Adaptor-class.html#last_id,Method BioSQL.DBUtils.Generic_dbutils.last_id()=BioSQL.DBUtils.Generic_dbutils-class.html#last_id,Method BioSQL.DBUtils.Mysql_dbutils.last_id()=BioSQL.DBUtils.Mysql_dbutils-class.html#last_id,Method BioSQL.DBUtils.Pgdb_dbutils.last_id()=BioSQL.DBUtils.Pgdb_dbutils-class.html#last_id,Method BioSQL.DBUtils.Psycopg_dbutils.last_id()=BioSQL.DBUtils.Psycopg_dbutils-class.html#last_id"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-37', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"ontology"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_term_id"></a><div id="DatabaseLoader._get_term_id-def"><a name="L72"></a><tt class="py-lineno"> 72</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_term_id-toggle" onclick="return toggle('DatabaseLoader._get_term_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_term_id">_get_term_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-param">name</tt><tt class="py-op">,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-param">ontology_id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-param">identifier</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="DatabaseLoader._get_term_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_term_id-expanded"><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-docstring">"""Get the id that corresponds to a term.</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> This looks through the term table for a the given term. If it</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> is not found, a new id corresponding to this term is created.</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> In either case, the id corresponding to that term is returned, so</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> that you can reference it in another table.</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 class="py-docstring"> The ontology_id should be used to disambiguate the term.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># try to get the term id</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"SELECT term_id FROM term "</tt> \ </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-string">r"WHERE name = %s"</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-38" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-38', 'name', 'link-33');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ontology_id</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">+=</tt> <tt class="py-string">' AND ontology_id = %s'</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">fields</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-39', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ontology_id</tt><tt class="py-op">)</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">id_results</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_and_fetchall"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-40', 'execute_and_fetchall', 'link-40');">execute_and_fetchall</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-name">fields</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment"># something is wrong</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">id_results</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Multiple term ids for %s: %r"</tt> <tt class="py-op">%</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-41', 'name', 'link-33');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">id_results</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">id_results</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</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">id_results</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO term (name, definition,"</tt> \ </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-string">r" identifier, ontology_id)"</tt> \ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-string">r" VALUES (%s, %s, %s, %s)"</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-42', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-43', 'name', 'link-33');">name</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.GenBank._FeatureConsumer.definition
Bio.GenBank._RecordConsumer.definition" class="py-name" href="#" onclick="return doclink('link-44', 'definition', 'link-36');">definition</a></tt><tt class="py-op">,</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt id="link-45" class="py-name" targets="Variable Bio.expressions.blocks.identifier=Bio.expressions.blocks-module.html#identifier"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-45', 'identifier', 'link-45');">identifier</a></tt><tt class="py-op">,</tt> <tt class="py-name">ontology_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</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">adaptor</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-46', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"term"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._add_dbxref"></a><div id="DatabaseLoader._add_dbxref-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="DatabaseLoader._add_dbxref-toggle" onclick="return toggle('DatabaseLoader._add_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_add_dbxref">_add_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbname</tt><tt class="py-op">,</tt> <tt class="py-param">accession</tt><tt class="py-op">,</tt> <tt class="py-param">version</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._add_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._add_dbxref-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-docstring">"""Insert a dbxref and return its id."""</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-47', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO dbxref(dbname, accession, version)"</tt> \ </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s)"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-48" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.accession()=Bio.GenBank._FeatureConsumer-class.html#accession,Method Bio.GenBank._RecordConsumer.accession()=Bio.GenBank._RecordConsumer-class.html#accession,Method Bio.Prosite.Prodoc._RecordConsumer.accession()=Bio.Prosite.Prodoc._RecordConsumer-class.html#accession,Method Bio.Prosite._RecordConsumer.accession()=Bio.Prosite._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._RecordConsumer.accession()=Bio.SwissProt.SProt._RecordConsumer-class.html#accession,Method Bio.SwissProt.SProt._SequenceConsumer.accession()=Bio.SwissProt.SProt._SequenceConsumer-class.html#accession,Variable Bio.expressions.embl.embl65.accession=Bio.expressions.embl.embl65-module.html#accession,Variable Bio.expressions.genbank.accession=Bio.expressions.genbank-module.html#accession"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-48', 'accession', 'link-48');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-49" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.version()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#version,Method Bio.Blast.NCBIStandalone._HeaderConsumer.version()=Bio.Blast.NCBIStandalone._HeaderConsumer-class.html#version,Method Bio.GenBank._FeatureConsumer.version()=Bio.GenBank._FeatureConsumer-class.html#version,Method Bio.GenBank._RecordConsumer.version()=Bio.GenBank._RecordConsumer-class.html#version,Variable Bio.MetaTool.metatool_format.version=Bio.MetaTool.metatool_format-module.html#version,Variable Bio.expressions.genbank.version=Bio.expressions.genbank-module.html#version"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-49', 'version', 'link-49');">version</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</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">adaptor</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-50', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"dbxref"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_taxon_id"></a><div id="DatabaseLoader._get_taxon_id-def"><a name="L117"></a><tt class="py-lineno">117</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_taxon_id-toggle" onclick="return toggle('DatabaseLoader._get_taxon_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_taxon_id">_get_taxon_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._get_taxon_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_taxon_id-expanded"><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-docstring">"""Get the taxon id for this record.</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> This searches the taxon/taxon_name tables using the</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> NCBI taxon ID, scientific name and common name to find</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> the matching taxon table entry's id.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> If the species isn't in the taxon table, and we have at</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> least the NCBI taxon ID, scientific name or common name,</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> a minimal stub entry is created in the table.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> If this information is not in the record's annotation,</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> then None is returned.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> See also the BioSQL script load_ncbi_taxonomy.pl which</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> will populate and update the taxon/taxon_name tables</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> with the latest information from the NCBI.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-comment"># To find the NCBI taxid, first check for a top level annotation</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ncbi_taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"ncbi_taxid"</tt> <tt class="py-keyword">in</tt> <tt id="link-51" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-51', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-52', 'annotations', 'link-20');">annotations</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment">#Could be a list of IDs.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-53" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-53', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-54', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt id="link-55" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-55', 'list', 'link-55');">list</a></tt><tt class="py-op">)</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">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-56', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-57', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">ncbi_taxon_id</tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-58', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-59', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">else</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">ncbi_taxon_id</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-60', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-61', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">]</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">ncbi_taxon_id</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># Secondly, look for a source feature</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt id="link-62" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-62', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.GFF.Segment.features
BioSQL.BioSeq.DBSeqRecord.features
Martel.Expression.Expression.features
Martel.Expression.ExpressionList.features
Martel.Expression.FastFeature.features
Martel.Expression.Group.features
Martel.Expression.HeaderFooter.features
Martel.Expression.MaxRepeat.features
Martel.Expression.ParseRecords.features
Martel.Expression.PassThrough.features" class="py-name" href="#" onclick="return doclink('link-63', 'features', 'link-28');">features</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-keyword">if</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-64', 'type', 'link-64');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'source'</tt><tt class="py-op">:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">quals</tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">f</tt><tt class="py-op">,</tt> <tt class="py-string">'qualifiers'</tt><tt class="py-op">,</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"db_xref"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">quals</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">db_xref</tt> <tt class="py-keyword">in</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt class="py-name">qualifiers</tt><tt class="py-op">[</tt><tt class="py-string">"db_xref"</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">db_xref</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">"taxon:"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">ncbi_taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">db_xref</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ncbi_taxon_id</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ncbi_taxon_id</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">taxa</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-65', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-string">"SELECT taxon_id FROM taxon WHERE ncbi_taxon_id = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">ncbi_taxon_id</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">taxa</tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-comment">#Good, we have mapped the NCBI taxid to a taxon table entry</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">taxa</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment">#Bad, this NCBI taxon id is not in the database!</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-comment"># Either we didn't find the NCBI taxid in the record, or it</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># isn't in the database yet. Next, we'll try and find a match</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># based on the species name (stored in GenBank files as the</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the organism and/or the source).</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">scientific_name</tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-66', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-67', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"organism"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">255</tt><tt class="py-op">]</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</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">scientific_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">common_name</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-68', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-69', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"source"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">255</tt><tt class="py-op">]</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt> <tt class="py-op">:</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">common_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-comment"># Note: The maximum length for taxon names in the schema is 255.</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Cropping it now should help in getting a match when searching,</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and avoids an error if we try and add these to the database.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ncbi_taxon_id</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> \ </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">common_name</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">scientific_name</tt> <tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment"># Nothing to go on... and there is no point adding</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># a new entry to the database. We'll just leave this</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># sequence's taxon as a NULL in the database.</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">scientific_name</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">taxa</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-70', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-string">"SELECT taxon_id FROM taxon_name"</tt> \ </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-string">" WHERE name_class = 'scientific name' AND name = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">scientific_name</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">taxa</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment">#Good, mapped the scientific name to a taxon table entry</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">taxa</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># Last chance...</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">common_name</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">taxa</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-71', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-string">"SELECT DISTINCT taxon_id FROM taxon_name"</tt> \ </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-string">" WHERE name = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">common_name</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment">#Its natural that several distinct taxa will have the same common</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#name - in which case we can't resolve the taxon uniquely.</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Taxa: %d species have name %r"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">taxa</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">common_name</tt><tt class="py-op">)</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">if</tt> <tt class="py-name">taxa</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-comment">#Good, mapped the common name to a taxon table entry</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">taxa</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-comment"># At this point, as far as we can tell, this species isn't</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># in the taxon table already. So we'll have to add it.</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-string">"""</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-string"> # Possible simplification of the scary code below; pending</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-string"> # discussion on the BioSQL mailing list...</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-string"> #</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-string"> # We will record the bare minimum; as long as the NCBI taxon</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-string"> # id is present, then (re)running load_ncbi_taxonomy.pl should</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-string"> # fill in the taxonomomy lineage.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-string"> #</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-string"> # I am NOT going to try and record the lineage, even if it</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-string"> # is in the record annotation as a list of names, as we won't</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-string"> # know the NCBI taxon IDs for these parent nodes.</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-string"> self.adaptor.execute(</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-string"> "INSERT INTO taxon(parent_taxon_id, ncbi_taxon_id, node_rank,"\</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-string"> " left_value, right_value)" \</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-string"> " VALUES (%s, %s, %s, %s, %s)", (None,</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-string"> ncbi_taxon_id,</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-string"> "species",</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-string"> None,</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-string"> None))</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-string"> taxon_id = self.adaptor.last_id("taxon")</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-string"> if scientific_name:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-string"> self.adaptor.execute(</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-string"> "INSERT INTO taxon_name(taxon_id, name, name_class)" \</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-string"> "VALUES (%s, %s, 'scientific name')", (</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-string"> taxon_id, scientific_name))</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-string"> if common_name:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-string"> self.adaptor.execute(</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-string"> "INSERT INTO taxon_name(taxon_id, name, name_class)" \</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-string"> "VALUES (%s, %s, 'common name')", (</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-string"> taxon_id, common_name))</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-string"> return taxon_id</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-string"> """</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-comment"># OK, let's try inserting the species.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Chances are we don't have enough information ...</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Furthermore, it won't be in the hierarchy.</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">lineage</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-72" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-72', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-73', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-74', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"taxonomy"</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-75', 'append', 'link-39');">append</a></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-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lineage</tt><tt class="py-op">:</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"genus"</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-76', 'append', 'link-39');">append</a></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-string">"species"</tt><tt class="py-op">,</tt> <tt id="link-77" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-77', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-78', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"organism"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-comment"># XXX do we have them?</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-string">"subspecies"</tt> <tt class="py-keyword">in</tt> <tt id="link-79" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-79', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-80', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-81', 'append', 'link-39');">append</a></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-string">"subspecies"</tt><tt class="py-op">,</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt id="link-82" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-82', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-83', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"subspecies"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"variant"</tt> <tt class="py-keyword">in</tt> <tt id="link-84" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-84', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-85', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-86', 'append', 'link-39');">append</a></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-string">"varietas"</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt id="link-87" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-87', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-88', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"variant"</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">lineage</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">ncbi_taxon_id</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">left_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.execute_one()=BioSQL.BioSeqDatabase.Adaptor-class.html#execute_one"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_one" class="py-name" href="#" onclick="return doclink('link-89', 'execute_one', 'link-89');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-string">"SELECT MAX(left_value) FROM taxon"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">left_value</tt><tt class="py-op">:</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">left_value</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">left_value</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-comment"># XXX -- Brad: Fixing this for now in an ugly way because</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I am getting overlaps for right_values. I need to dig into this</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># more to actually understand how it works. I'm not sure it is</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># actually working right anyhow.</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">right_start_value</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_one" class="py-name" href="#" onclick="return doclink('link-90', 'execute_one', 'link-89');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">"SELECT MAX(right_value) FROM taxon"</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">right_start_value</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">right_start_value</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">right_value</tt> <tt class="py-op">=</tt> <tt class="py-name">right_start_value</tt> <tt class="py-op">+</tt> <tt class="py-number">2</tt> <tt class="py-op">*</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lineage</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">parent_taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">taxon</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lineage</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">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-91', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO taxon(parent_taxon_id, ncbi_taxon_id, node_rank,"</tt>\ </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-string">" left_value, right_value)"</tt> \ </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s, %s, %s)"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">parent_taxon_id</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">taxon</tt><tt class="py-op">[</tt><tt class="py-number">0</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 class="py-name">taxon</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">left_value</tt><tt class="py-op">,</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-name">right_value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-92', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"taxon"</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-93', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO taxon_name(taxon_id, name, name_class)"</tt> \ </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-string">"VALUES (%s, %s, 'scientific name')"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">taxon_id</tt><tt class="py-op">,</tt> <tt class="py-name">taxon</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">255</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-comment">#Note the name field is limited to 255, some SwissProt files</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#have a multi-species name which can be longer. So truncate this.</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">left_value</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">right_value</tt> <tt class="py-op">-=</tt> <tt class="py-number">1</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">parent_taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">taxon_id</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">common_name</tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-94', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO taxon_name(taxon_id, name, name_class)"</tt> \ </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-string">"VALUES (%s, %s, 'common name')"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-name">taxon_id</tt><tt class="py-op">,</tt> <tt class="py-name">common_name</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">taxon_id</tt> </tt>
</div><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_bioentry_table"></a><div id="DatabaseLoader._load_bioentry_table-def"><a name="L315"></a><tt class="py-lineno">315</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_bioentry_table-toggle" onclick="return toggle('DatabaseLoader._load_bioentry_table');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_table">_load_bioentry_table</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_bioentry_table-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_bioentry_table-expanded"><a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-docstring">"""Fill the bioentry table with sequence information.</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-docstring"> record - SeqRecord object to add to the database.</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment"># get the pertinent info and insert it</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-95" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-95', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-96', 'id', 'link-96');">id</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-97', 'find', 'link-97');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># try to get a version from the id</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt id="link-98" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-98', 'accession', 'link-48');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-99', 'version', 'link-49');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-100" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-100', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-101', 'id', 'link-96');">id</a></tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-102', 'split', 'link-102');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt id="link-103" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-103', 'version', 'link-49');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-104" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-104', 'version', 'link-49');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># otherwise just use a version of 0</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-105', 'accession', 'link-48');">accession</a></tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-106', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-107', 'id', 'link-96');">id</a></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-108', 'version', 'link-49');">version</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-comment">#Find the taxon id (this is not just the NCBI Taxon ID)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#NOTE - If the species isn't defined in the taxon table,</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#a new minimal entry is created.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_taxon_id()=BioSQL.Loader.DatabaseLoader-class.html#_get_taxon_id"><a title="BioSQL.Loader.DatabaseLoader._get_taxon_id" class="py-name" href="#" onclick="return doclink('link-109', '_get_taxon_id', 'link-109');">_get_taxon_id</a></tt><tt class="py-op">(</tt><tt id="link-110" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-110', 'record', 'link-10');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-111', 'identifier', 'link-45');">identifier</a></tt> <tt class="py-op">=</tt> <tt id="link-112" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-112', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-113', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-114', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'gi'</tt><tt class="py-op">)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt id="link-115" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-115', 'description', 'link-115');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt id="link-116" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-116', 'record', 'link-10');">record</a></tt><tt class="py-op">,</tt> <tt class="py-string">'description'</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-name">division</tt> <tt class="py-op">=</tt> <tt id="link-117" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-117', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-118', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-119', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"data_file_division"</tt><tt class="py-op">,</tt> <tt class="py-string">"UNK"</tt><tt class="py-op">)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"""</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-string"> INSERT INTO bioentry (</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-string"> biodatabase_id,</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-string"> taxon_id,</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-string"> name,</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-string"> accession,</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-string"> identifier,</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-string"> division,</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-string"> description,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-string"> version)</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-string"> VALUES (</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-string"> %s,</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-string"> %s)"""</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-120', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-121', 'dbid', 'link-7');">dbid</a></tt><tt class="py-op">,</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">taxon_id</tt><tt class="py-op">,</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt id="link-122" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-122', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-123', 'name', 'link-33');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt id="link-124" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-124', 'accession', 'link-48');">accession</a></tt><tt class="py-op">,</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-125', 'identifier', 'link-45');">identifier</a></tt><tt class="py-op">,</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-name">division</tt><tt class="py-op">,</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt id="link-126" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-126', 'description', 'link-115');">description</a></tt><tt class="py-op">,</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt id="link-127" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.version
Bio.Blast.NCBIStandalone._HeaderConsumer.version
Bio.GenBank._FeatureConsumer.version
Bio.GenBank._RecordConsumer.version
Bio.MetaTool.metatool_format.version
Bio.expressions.genbank.version" class="py-name" href="#" onclick="return doclink('link-127', 'version', 'link-49');">version</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-comment"># now retrieve the id for the bioentry</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">bioentry_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-128', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'bioentry'</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bioentry_id</tt> </tt>
</div><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_bioentry_date"></a><div id="DatabaseLoader._load_bioentry_date-def"><a name="L370"></a><tt class="py-lineno">370</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_bioentry_date-toggle" onclick="return toggle('DatabaseLoader._load_bioentry_date');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_bioentry_date">_load_bioentry_date</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_bioentry_date-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_bioentry_date-expanded"><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-docstring">"""Add the effective date of the entry into the database.</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object with an annotated date</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-docstring"> bioentry_id - corresponding database identifier</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-comment"># dates are GenBank style, like:</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 14-SEP-2000</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-129" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-129', 'date', 'link-129');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-130', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-131', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-132', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"date"</tt><tt class="py-op">,</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">strftime</tt><tt class="py-op">(</tt><tt class="py-string">"%d-%b-%Y"</tt><tt class="py-op">,</tt> <tt class="py-name">gmtime</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">annotation_tags_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_ontology_id()=BioSQL.Loader.DatabaseLoader-class.html#_get_ontology_id"><a title="BioSQL.Loader.DatabaseLoader._get_ontology_id" class="py-name" href="#" onclick="return doclink('link-133', '_get_ontology_id', 'link-133');">_get_ontology_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"Annotation Tags"</tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">date_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_term_id()=BioSQL.Loader.DatabaseLoader-class.html#_get_term_id"><a title="BioSQL.Loader.DatabaseLoader._get_term_id" class="py-name" href="#" onclick="return doclink('link-134', '_get_term_id', 'link-134');">_get_term_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"date_changed"</tt><tt class="py-op">,</tt> <tt class="py-name">annotation_tags_id</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO bioentry_qualifier_value"</tt> \ </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-string">r" (bioentry_id, term_id, value, rank)"</tt> \ </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-string">r" VALUES (%s, %s, %s, 1)"</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-135', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">date_id</tt><tt class="py-op">,</tt> <tt id="link-136" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-136', 'date', 'link-129');">date</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_biosequence"></a><div id="DatabaseLoader._load_biosequence-def"><a name="L387"></a><tt class="py-lineno">387</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_biosequence-toggle" onclick="return toggle('DatabaseLoader._load_biosequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_biosequence">_load_biosequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_biosequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_biosequence-expanded"><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-docstring">"""Record a SeqRecord's sequence and alphabet in the database.</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object with a seq property</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-docstring"> bioentry_id - corresponding database identifier</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-comment"># determine the string representation of the alphabet</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-137', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-138" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-138', 'seq', 'link-138');">seq</a></tt><tt class="py-op">.</tt><tt id="link-139" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-139', 'alphabet', 'link-139');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-140" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-140', 'Alphabet', 'link-2');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Class Bio.Alphabet.DNAAlphabet=Bio.Alphabet.DNAAlphabet-class.html"><a title="Bio.Alphabet.DNAAlphabet" class="py-name" href="#" onclick="return doclink('link-141', 'DNAAlphabet', 'link-141');">DNAAlphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt id="link-142" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-142', 'alphabet', 'link-139');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"dna"</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-143', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-144', 'seq', 'link-138');">seq</a></tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-145', 'alphabet', 'link-139');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-146" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-146', 'Alphabet', 'link-2');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-147" class="py-name" targets="Class Bio.Alphabet.RNAAlphabet=Bio.Alphabet.RNAAlphabet-class.html"><a title="Bio.Alphabet.RNAAlphabet" class="py-name" href="#" onclick="return doclink('link-147', 'RNAAlphabet', 'link-147');">RNAAlphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt id="link-148" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-148', 'alphabet', 'link-139');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"rna"</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-149', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-150', 'seq', 'link-138');">seq</a></tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-151', 'alphabet', 'link-139');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-152" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-152', 'Alphabet', 'link-2');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Class Bio.Alphabet.ProteinAlphabet=Bio.Alphabet.ProteinAlphabet-class.html"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-153', 'ProteinAlphabet', 'link-153');">ProteinAlphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt id="link-154" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-154', 'alphabet', 'link-139');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"protein"</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt id="link-155" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-155', 'alphabet', 'link-139');">alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"unknown"</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO biosequence (bioentry_id, version, "</tt> \ </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-string">r"length, seq, alphabet) "</tt> \ </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-string">r"VALUES (%s, 0, %s, %s, %s)"</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-156', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-157', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-158', 'seq', 'link-138');">seq</a></tt><tt class="py-op">.</tt><tt id="link-159" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-159', 'data', 'link-159');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-160', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-161', 'seq', 'link-138');">seq</a></tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-162', 'data', 'link-159');">data</a></tt><tt class="py-op">,</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt id="link-163" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-163', 'alphabet', 'link-139');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_comment"></a><div id="DatabaseLoader._load_comment-def"><a name="L411"></a><tt class="py-lineno">411</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_comment-toggle" onclick="return toggle('DatabaseLoader._load_comment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_comment">_load_comment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_comment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_comment-expanded"><a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-docstring">"""Record a SeqRecord's annotated comment in the database.</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object with an annotated comment</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"> bioentry_id - corresponding database identifier</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-comment"># Assume annotations['comment'] is not a list</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-164" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.comment()=Bio.EUtils.POM.ElementNode-class.html#comment,Method Bio.Enzyme._RecordConsumer.comment()=Bio.Enzyme._RecordConsumer-class.html#comment,Method Bio.GenBank._FeatureConsumer.comment()=Bio.GenBank._FeatureConsumer-class.html#comment,Method Bio.GenBank._RecordConsumer.comment()=Bio.GenBank._RecordConsumer-class.html#comment,Method Bio.IntelliGenetics._RecordConsumer.comment()=Bio.IntelliGenetics._RecordConsumer-class.html#comment,Method Bio.NBRF._RecordConsumer.comment()=Bio.NBRF._RecordConsumer-class.html#comment,Method Bio.PopGen.GenePop._RecordConsumer.comment()=Bio.PopGen.GenePop._RecordConsumer-class.html#comment,Method Bio.Prosite._RecordConsumer.comment()=Bio.Prosite._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._RecordConsumer.comment()=Bio.SwissProt.SProt._RecordConsumer-class.html#comment,Method Bio.SwissProt.SProt._SequenceConsumer.comment()=Bio.SwissProt.SProt._SequenceConsumer-class.html#comment,Variable Bio.expressions.swissprot.sprot38.comment=Bio.expressions.swissprot.sprot38-module.html#comment,Variable Martel.test.test_swissprot38.comment=Martel.test.test_swissprot38-module.html#comment,Variable Martel.test.testformats.swissprot38.comment=Martel.test.testformats.swissprot38-module.html#comment"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-164', 'comment', 'link-164');">comment</a></tt> <tt class="py-op">=</tt> <tt id="link-165" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-165', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-166', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-167" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-167', 'get', 'link-21');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'comment'</tt><tt class="py-op">)</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-168" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-168', 'comment', 'link-164');">comment</a></tt><tt class="py-op">:</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt id="link-169" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-169', 'comment', 'link-164');">comment</a></tt> <tt class="py-op">=</tt> <tt id="link-170" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-170', 'comment', 'link-164');">comment</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"INSERT INTO comment (bioentry_id, comment_text, rank)"</tt> \ </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s)"</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-171', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt id="link-172" class="py-name"><a title="Bio.EUtils.POM.ElementNode.comment
Bio.Enzyme._RecordConsumer.comment
Bio.GenBank._FeatureConsumer.comment
Bio.GenBank._RecordConsumer.comment
Bio.IntelliGenetics._RecordConsumer.comment
Bio.NBRF._RecordConsumer.comment
Bio.PopGen.GenePop._RecordConsumer.comment
Bio.Prosite._RecordConsumer.comment
Bio.SwissProt.SProt._RecordConsumer.comment
Bio.SwissProt.SProt._SequenceConsumer.comment
Bio.expressions.swissprot.sprot38.comment
Martel.test.test_swissprot38.comment
Martel.test.testformats.swissprot38.comment" class="py-name" href="#" onclick="return doclink('link-172', 'comment', 'link-164');">comment</a></tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_annotations"></a><div id="DatabaseLoader._load_annotations-def"><a name="L427"></a><tt class="py-lineno">427</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_annotations-toggle" onclick="return toggle('DatabaseLoader._load_annotations');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_annotations">_load_annotations</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_annotations-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_annotations-expanded"><a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-docstring">"""Record a SeqRecord's misc annotations in the database.</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt class="py-docstring"> The annotation strings are recorded in the bioentry_qualifier_value</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-docstring"> table, except for special cases like the reference, comment and</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-docstring"> taxonomy which are handled with their own tables.</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object with an annotations dictionary</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-docstring"> bioentry_id - corresponding database identifier</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">mono_sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"INSERT INTO bioentry_qualifier_value"</tt> \ </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-string">"(bioentry_id, term_id, value)"</tt> \ </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s)"</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-name">many_sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"INSERT INTO bioentry_qualifier_value"</tt> \ </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-string">"(bioentry_id, term_id, value, rank)"</tt> \ </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s, %s)"</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">tag_ontology_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-173" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_ontology_id" class="py-name" href="#" onclick="return doclink('link-173', '_get_ontology_id', 'link-133');">_get_ontology_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'Annotation Tags'</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-174" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-174', 'key', 'link-174');">key</a></tt><tt class="py-op">,</tt> <tt id="link-175" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-175', 'value', 'link-175');">value</a></tt> <tt class="py-keyword">in</tt> <tt id="link-176" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-176', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-177', 'annotations', 'link-20');">annotations</a></tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-178" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-178', 'key', 'link-174');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">"references"</tt><tt class="py-op">,</tt> <tt class="py-string">"comment"</tt><tt class="py-op">,</tt> <tt class="py-string">"ncbi_taxid"</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-comment">#Handled separately</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">continue</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-name">term_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-179" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_term_id" class="py-name" href="#" onclick="return doclink('link-179', '_get_term_id', 'link-134');">_get_term_id</a></tt><tt class="py-op">(</tt><tt id="link-180" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-180', 'key', 'link-174');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">ontology_id</tt><tt class="py-op">=</tt><tt class="py-name">tag_ontology_id</tt><tt class="py-op">)</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</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-181" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-181', 'value', 'link-175');">value</a></tt><tt class="py-op">,</tt> <tt id="link-182" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-182', 'list', 'link-55');">list</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-name">rank</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt id="link-183" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-183', 'value', 'link-175');">value</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">entry</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">entry</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-comment">#Easy case</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rank</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-184', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">many_sql</tt><tt class="py-op">,</tt> \ </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">term_id</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">entry</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-comment">#print "Ignoring annotation '%s' sub-entry of type '%s'" \</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># % (key, str(type(entry)))</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-185" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-185', 'value', 'link-175');">value</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-186" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-186', 'value', 'link-175');">value</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-comment">#Have a simple single entry, leave rank as the DB default</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-187', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">mono_sql</tt><tt class="py-op">,</tt> \ </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">term_id</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-188', 'value', 'link-175');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-comment">#print "Ignoring annotation '%s' entry of type '%s'" \</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># % (key, type(value))</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_reference"></a><div id="DatabaseLoader._load_reference-def"><a name="L471"></a><tt class="py-lineno">471</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_reference-toggle" onclick="return toggle('DatabaseLoader._load_reference');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_reference">_load_reference</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">reference</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_reference-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_reference-expanded"><a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-docstring">"""Record a SeqRecord's annotated references in the database.</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt class="py-docstring"> record - a SeqRecord object with annotated references</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"><tt class="py-docstring"> bioentry_id - corresponding database identifier</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">refs</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-189" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-189', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-190" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.medline_id()=Bio.GenBank._FeatureConsumer-class.html#medline_id,Method Bio.GenBank._RecordConsumer.medline_id()=Bio.GenBank._RecordConsumer-class.html#medline_id"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-190', 'medline_id', 'link-190');">medline_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">refs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-191', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-string">"SELECT reference_id"</tt> \ </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-string">" FROM reference JOIN dbxref USING (dbxref_id)"</tt> \ </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-string">" WHERE dbname = 'MEDLINE' AND accession = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-192', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-193', 'medline_id', 'link-190');">medline_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">refs</tt> <tt class="py-keyword">and</tt> <tt id="link-194" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-194', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-195" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.pubmed_id()=Bio.GenBank._FeatureConsumer-class.html#pubmed_id,Method Bio.GenBank._RecordConsumer.pubmed_id()=Bio.GenBank._RecordConsumer-class.html#pubmed_id,Method Bio.Medline._RecordConsumer.pubmed_id()=Bio.Medline._RecordConsumer-class.html#pubmed_id"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-195', 'pubmed_id', 'link-195');">pubmed_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">refs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-196', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-string">"SELECT reference_id"</tt> \ </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-string">" FROM reference JOIN dbxref USING (dbxref_id)"</tt> \ </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt class="py-string">" WHERE dbname = 'PUBMED' AND accession = %s"</tt><tt class="py-op">,</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-197" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-197', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-198', 'pubmed_id', 'link-195');">pubmed_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">refs</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt id="link-199" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-199', 's', 'link-199');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt id="link-200" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-200', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-201" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.authors()=Bio.GenBank._FeatureConsumer-class.html#authors,Method Bio.GenBank._RecordConsumer.authors()=Bio.GenBank._RecordConsumer-class.html#authors"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-201', 'authors', 'link-201');">authors</a></tt><tt class="py-op">,</tt> <tt id="link-202" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-202', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-203', 'title', 'link-203');">title</a></tt><tt class="py-op">,</tt> <tt id="link-204" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-204', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-205" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.journal()=Bio.GenBank._FeatureConsumer-class.html#journal,Method Bio.GenBank._RecordConsumer.journal()=Bio.GenBank._RecordConsumer-class.html#journal"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-205', 'journal', 'link-205');">journal</a></tt><tt class="py-op">:</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt id="link-206" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-206', 's', 'link-199');">s</a></tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-207', 'append', 'link-39');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">f</tt> <tt class="py-keyword">or</tt> <tt class="py-string">"<undef>"</tt><tt class="py-op">)</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-name">crc</tt> <tt class="py-op">=</tt> <tt id="link-208" class="py-name"><a title="Bio.SeqUtils.CheckSum.crc64" class="py-name" href="#" onclick="return doclink('link-208', 'crc64', 'link-6');">crc64</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-209" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-209', 's', 'link-199');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-name">refs</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-210', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-string">"SELECT reference_id FROM reference"</tt> \ </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-string">r" WHERE crc = %s"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">crc</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">refs</tt><tt class="py-op">:</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-211" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-211', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-212', 'medline_id', 'link-190');">medline_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._add_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_add_dbxref"><a title="BioSQL.Loader.DatabaseLoader._add_dbxref" class="py-name" href="#" onclick="return doclink('link-213', '_add_dbxref', 'link-213');">_add_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-string">"MEDLINE"</tt><tt class="py-op">,</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt id="link-214" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-214', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.GenBank._FeatureConsumer.medline_id
Bio.GenBank._RecordConsumer.medline_id" class="py-name" href="#" onclick="return doclink('link-215', 'medline_id', 'link-190');">medline_id</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-216" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-216', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-217" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-217', 'pubmed_id', 'link-195');">pubmed_id</a></tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-218" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._add_dbxref" class="py-name" href="#" onclick="return doclink('link-218', '_add_dbxref', 'link-213');">_add_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-string">"PUBMED"</tt><tt class="py-op">,</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt id="link-219" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-219', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-220" class="py-name"><a title="Bio.GenBank._FeatureConsumer.pubmed_id
Bio.GenBank._RecordConsumer.pubmed_id
Bio.Medline._RecordConsumer.pubmed_id" class="py-name" href="#" onclick="return doclink('link-220', 'pubmed_id', 'link-195');">pubmed_id</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt id="link-221" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-221', 'authors', 'link-201');">authors</a></tt> <tt class="py-op">=</tt> <tt id="link-222" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-222', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-223" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-223', 'authors', 'link-201');">authors</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">None</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-224', 'title', 'link-203');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-225" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-225', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-226', 'title', 'link-203');">title</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">None</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-comment">#The location/journal field cannot be Null, so default</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#to an empty string rather than None:</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-227" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-227', 'journal', 'link-205');">journal</a></tt> <tt class="py-op">=</tt> <tt id="link-228" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-228', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-229" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-229', 'journal', 'link-205');">journal</a></tt> <tt class="py-keyword">or</tt> <tt class="py-string">""</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-230', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-string">"INSERT INTO reference (dbxref_id, location,"</tt> \ </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-string">" title, authors, crc)"</tt> \ </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s, %s, %s)"</tt><tt class="py-op">,</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt id="link-231" class="py-name"><a title="Bio.GenBank._FeatureConsumer.journal
Bio.GenBank._RecordConsumer.journal" class="py-name" href="#" onclick="return doclink('link-231', 'journal', 'link-205');">journal</a></tt><tt class="py-op">,</tt> <tt id="link-232" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-232', 'title', 'link-203');">title</a></tt><tt class="py-op">,</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt id="link-233" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-233', 'authors', 'link-201');">authors</a></tt><tt class="py-op">,</tt> <tt class="py-name">crc</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-name">reference_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-234', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">"reference"</tt><tt class="py-op">)</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">reference_id</tt> <tt class="py-op">=</tt> <tt class="py-name">refs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-235" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-235', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-236" class="py-name" targets="Method Bio.GFF.Feature.location()=Bio.GFF.Feature-class.html#location,Method Bio.GFF.FeatureAggregate.location()=Bio.GFF.FeatureAggregate-class.html#location,Method Bio.GenBank._FeatureConsumer.location()=Bio.GenBank._FeatureConsumer-class.html#location,Method Bio.GenBank._RecordConsumer.location()=Bio.GenBank._RecordConsumer-class.html#location,Variable Bio.expressions.genbank.location=Bio.expressions.genbank-module.html#location"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-236', 'location', 'link-236');">location</a></tt><tt class="py-op">:</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt id="link-237" 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-237', 'start', 'link-237');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> <tt class="py-op">+</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-238" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-238', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-239', 'location', 'link-236');">location</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-240" 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-240', 'start', 'link-237');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt id="link-241" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-241', 'end', 'link-241');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-242" class="py-name"><a title="Bio.Blast.NCBIStandalone._HeaderConsumer.reference
Bio.Prosite.Prodoc._RecordConsumer.reference
Bio.expressions.embl.embl65.reference
Bio.expressions.genbank.reference
Bio.expressions.swissprot.sprot38.reference
Martel.test.test_swissprot38.reference
Martel.test.testformats.swissprot38.reference" class="py-name" href="#" onclick="return doclink('link-242', 'reference', 'link-22');">reference</a></tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-243', 'location', 'link-236');">location</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-244" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-244', 'end', 'link-241');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt id="link-245" 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-245', 'start', 'link-237');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt id="link-246" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-246', 'end', 'link-241');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"INSERT INTO bioentry_reference (bioentry_id, reference_id,"</tt> \ </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt class="py-string">" start_pos, end_pos, rank)"</tt> \ </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-string">" VALUES (%s, %s, %s, %s, %s)"</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-247', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">reference_id</tt><tt class="py-op">,</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt id="link-248" 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-248', 'start', 'link-237');">start</a></tt><tt class="py-op">,</tt> <tt id="link-249" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-249', 'end', 'link-241');">end</a></tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_seqfeature"></a><div id="DatabaseLoader._load_seqfeature-def"><a name="L536"></a><tt class="py-lineno">536</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_seqfeature-toggle" onclick="return toggle('DatabaseLoader._load_seqfeature');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature">_load_seqfeature</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">feature</tt><tt class="py-op">,</tt> <tt class="py-param">feature_rank</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_seqfeature-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_seqfeature-expanded"><a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-docstring">"""Load a biopython SeqFeature into the database.</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-name">seqfeature_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_seqfeature_basic()=BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_basic"><a title="BioSQL.Loader.DatabaseLoader._load_seqfeature_basic" class="py-name" href="#" onclick="return doclink('link-250', '_load_seqfeature_basic', 'link-250');">_load_seqfeature_basic</a></tt><tt class="py-op">(</tt><tt id="link-251" class="py-name" targets="Function Bio.Std.feature()=Bio.Std-module.html#feature,Variable Bio.expressions.embl.embl65.feature=Bio.expressions.embl.embl65-module.html#feature,Variable Bio.expressions.genbank.feature=Bio.expressions.genbank-module.html#feature"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-251', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt id="link-252" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-252', 'type', 'link-64');">type</a></tt><tt class="py-op">,</tt> <tt class="py-name">feature_rank</tt><tt class="py-op">,</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">bioentry_id</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-253" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_seqfeature_locations()=BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_locations"><a title="BioSQL.Loader.DatabaseLoader._load_seqfeature_locations" class="py-name" href="#" onclick="return doclink('link-253', '_load_seqfeature_locations', 'link-253');">_load_seqfeature_locations</a></tt><tt class="py-op">(</tt><tt id="link-254" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-254', 'feature', 'link-251');">feature</a></tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_id</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_seqfeature_qualifiers()=BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_qualifiers"><a title="BioSQL.Loader.DatabaseLoader._load_seqfeature_qualifiers" class="py-name" href="#" onclick="return doclink('link-255', '_load_seqfeature_qualifiers', 'link-255');">_load_seqfeature_qualifiers</a></tt><tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-256', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">qualifiers</tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_seqfeature_basic"></a><div id="DatabaseLoader._load_seqfeature_basic-def"><a name="L544"></a><tt class="py-lineno">544</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_seqfeature_basic-toggle" onclick="return toggle('DatabaseLoader._load_seqfeature_basic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_basic">_load_seqfeature_basic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">feature_type</tt><tt class="py-op">,</tt> <tt class="py-param">feature_rank</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_seqfeature_basic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_seqfeature_basic-expanded"><a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-docstring">"""Load the first tables of a seqfeature and returns the id.</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"><tt class="py-docstring"> This loads the "key" of the seqfeature (ie. CDS, gene) and</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"><tt class="py-docstring"> the basic seqfeature table itself.</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-name">ontology_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_ontology_id" class="py-name" href="#" onclick="return doclink('link-257', '_get_ontology_id', 'link-133');">_get_ontology_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'SeqFeature Keys'</tt><tt class="py-op">)</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-name">seqfeature_key_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_term_id" class="py-name" href="#" onclick="return doclink('link-258', '_get_term_id', 'link-134');">_get_term_id</a></tt><tt class="py-op">(</tt><tt class="py-name">feature_type</tt><tt class="py-op">,</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-name">ontology_id</tt> <tt class="py-op">=</tt> <tt class="py-name">ontology_id</tt><tt class="py-op">)</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-comment"># XXX source is always EMBL/GenBank/SwissProt here; it should depend on</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the record (how?)</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">source_cat_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_ontology_id" class="py-name" href="#" onclick="return doclink('link-259', '_get_ontology_id', 'link-133');">_get_ontology_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'SeqFeature Sources'</tt><tt class="py-op">)</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-name">source_term_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_term_id" class="py-name" href="#" onclick="return doclink('link-260', '_get_term_id', 'link-134');">_get_term_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'EMBL/GenBank/SwissProt'</tt><tt class="py-op">,</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-name">ontology_id</tt> <tt class="py-op">=</tt> <tt class="py-name">source_cat_id</tt><tt class="py-op">)</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO seqfeature (bioentry_id, type_term_id, "</tt> \ </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-string">r"source_term_id, rank) VALUES (%s, %s, %s, %s)"</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-261', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_key_id</tt><tt class="py-op">,</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-name">source_term_id</tt><tt class="py-op">,</tt> <tt class="py-name">feature_rank</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-name">seqfeature_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.last_id
BioSQL.DBUtils.Generic_dbutils.last_id
BioSQL.DBUtils.Mysql_dbutils.last_id
BioSQL.DBUtils.Pgdb_dbutils.last_id
BioSQL.DBUtils.Psycopg_dbutils.last_id" class="py-name" href="#" onclick="return doclink('link-262', 'last_id', 'link-37');">last_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'seqfeature'</tt><tt class="py-op">)</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">seqfeature_id</tt> </tt>
</div><a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_seqfeature_locations"></a><div id="DatabaseLoader._load_seqfeature_locations-def"><a name="L568"></a><tt class="py-lineno">568</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_seqfeature_locations-toggle" onclick="return toggle('DatabaseLoader._load_seqfeature_locations');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_locations">_load_seqfeature_locations</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">feature</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_seqfeature_locations-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_seqfeature_locations-expanded"><a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-docstring">"""Load all of the locations for a SeqFeature into tables.</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-docstring"> This adds the locations related to the SeqFeature into the</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-docstring"> seqfeature_location table. Fuzzies are not handled right now.</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-docstring"> For a simple location, ie (1..2), we have a single table row</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"><tt class="py-docstring"> with seq_start = 1, seq_end = 2, location_rank = 1.</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"><tt class="py-docstring"> For split locations, ie (1..2, 3..4, 5..6) we would have three</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"><tt class="py-docstring"> row tables with:</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-docstring"> start = 1, end = 2, rank = 1</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"><tt class="py-docstring"> start = 3, end = 4, rank = 2</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-docstring"> start = 5, end = 6, rank = 3</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-comment"># two cases, a simple location or a split location</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-263" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-263', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">sub_features</tt><tt class="py-op">:</tt> <tt class="py-comment"># simple location</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._insert_seqfeature_location()=BioSQL.Loader.DatabaseLoader-class.html#_insert_seqfeature_location"><a title="BioSQL.Loader.DatabaseLoader._insert_seqfeature_location" class="py-name" href="#" onclick="return doclink('link-264', '_insert_seqfeature_location', 'link-264');">_insert_seqfeature_location</a></tt><tt class="py-op">(</tt><tt id="link-265" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-265', 'feature', 'link-251');">feature</a></tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_id</tt><tt class="py-op">)</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># split location</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rank</tt><tt class="py-op">,</tt> <tt class="py-name">cur_feature</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-266" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-266', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">sub_features</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._insert_seqfeature_location" class="py-name" href="#" onclick="return doclink('link-267', '_insert_seqfeature_location', 'link-264');">_insert_seqfeature_location</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_feature</tt><tt class="py-op">,</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">rank</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-name">seqfeature_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._insert_seqfeature_location"></a><div id="DatabaseLoader._insert_seqfeature_location-def"><a name="L591"></a><tt class="py-lineno">591</tt> <a class="py-toggle" href="#" id="DatabaseLoader._insert_seqfeature_location-toggle" onclick="return toggle('DatabaseLoader._insert_seqfeature_location');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_insert_seqfeature_location">_insert_seqfeature_location</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">feature</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._insert_seqfeature_location-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._insert_seqfeature_location-expanded"><a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a location of a SeqFeature to the seqfeature_location table.</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO location (seqfeature_id, "</tt> \ </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-string">r"start_pos, end_pos, strand, rank) "</tt> \ </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-string">r"VALUES (%s, %s, %s, %s, %s)"</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-comment"># convert biopython locations to the 1-based location system</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># used in bioSQL</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># XXX This could also handle fuzzies</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-268" 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-268', 'start', 'link-237');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-269" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-269', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt id="link-270" class="py-name"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-270', 'location', 'link-236');">location</a></tt><tt class="py-op">.</tt><tt class="py-name">nofuzzy_start</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt id="link-271" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-271', 'end', 'link-241');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-272', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="Bio.GFF.Feature.location
Bio.GFF.FeatureAggregate.location
Bio.GenBank._FeatureConsumer.location
Bio.GenBank._RecordConsumer.location
Bio.expressions.genbank.location" class="py-name" href="#" onclick="return doclink('link-273', 'location', 'link-236');">location</a></tt><tt class="py-op">.</tt><tt class="py-name">nofuzzy_end</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-comment"># Biopython uses None when we don't know strand information but</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># BioSQL requires something (non null) and sets this as zero</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># So we'll use the strand or 0 if Biopython spits out None</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-274" 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-274', 'strand', 'link-274');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-275" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-275', 'feature', 'link-251');">feature</a></tt><tt class="py-op">.</tt><tt id="link-276" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-276', 'strand', 'link-274');">strand</a></tt> <tt class="py-keyword">or</tt> <tt class="py-number">0</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-277', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt id="link-278" 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-278', 'start', 'link-237');">start</a></tt><tt class="py-op">,</tt> <tt id="link-279" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-279', 'end', 'link-241');">end</a></tt><tt class="py-op">,</tt> <tt id="link-280" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-280', 'strand', 'link-274');">strand</a></tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_seqfeature_qualifiers"></a><div id="DatabaseLoader._load_seqfeature_qualifiers-def"><a name="L610"></a><tt class="py-lineno">610</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_seqfeature_qualifiers-toggle" onclick="return toggle('DatabaseLoader._load_seqfeature_qualifiers');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_qualifiers">_load_seqfeature_qualifiers</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">qualifiers</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_seqfeature_qualifiers-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_seqfeature_qualifiers-expanded"><a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-docstring">"""Insert the (key, value) pair qualifiers relating to a feature.</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"><tt class="py-docstring"> Qualifiers should be a dictionary of the form:</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"><tt class="py-docstring"> {key : [value1, value2]}</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-name">tag_ontology_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_ontology_id" class="py-name" href="#" onclick="return doclink('link-281', '_get_ontology_id', 'link-133');">_get_ontology_id</a></tt><tt class="py-op">(</tt><tt class="py-string">'Annotation Tags'</tt><tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">qualifier_key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">qualifiers</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-282', 'keys', 'link-282');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-comment"># Treat db_xref qualifiers differently to sequence annotation</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># qualifiers by populating the seqfeature_dbxref and dbxref</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># tables. Other qualifiers go into the seqfeature_qualifier_value</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and (if new) term tables.</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">qualifier_key</tt> <tt class="py-op">!=</tt> <tt class="py-string">'db_xref'</tt><tt class="py-op">:</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-name">qualifier_key_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-283" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_term_id" class="py-name" href="#" onclick="return doclink('link-283', '_get_term_id', 'link-134');">_get_term_id</a></tt><tt class="py-op">(</tt><tt class="py-name">qualifier_key</tt><tt class="py-op">,</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-name">ontology_id</tt><tt class="py-op">=</tt><tt class="py-name">tag_ontology_id</tt><tt class="py-op">)</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-comment"># now add all of the values to their table</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-name">qualifiers</tt><tt class="py-op">[</tt><tt class="py-name">qualifier_key</tt><tt class="py-op">]</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">entries</tt><tt class="py-op">,</tt> <tt id="link-284" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-284', 'list', 'link-55');">list</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-comment"># Could be a plain string, or an int or a float.</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># However, we exect a list of strings here.</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">entries</tt><tt class="py-op">]</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">qual_value_rank</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">entries</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-name">qualifier_value</tt> <tt class="py-op">=</tt> <tt class="py-name">entries</tt><tt class="py-op">[</tt><tt class="py-name">qual_value_rank</tt><tt class="py-op">]</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"INSERT INTO seqfeature_qualifier_value "</tt>\ </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-string">r" (seqfeature_id, term_id, rank, value) VALUES"</tt>\ </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-string">r" (%s, %s, %s, %s)"</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-285', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-name">qualifier_key_id</tt><tt class="py-op">,</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt class="py-name">qual_value_rank</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-name">qualifier_value</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-comment"># The dbxref_id qualifier/value sets go into the dbxref table</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># as dbname, accession, version tuples, with dbxref.dbxref_id</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># being automatically assigned, and into the seqfeature_dbxref</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># table as seqfeature_id, dbxref_id, and rank tuples</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-286" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._load_seqfeature_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_dbxref"><a title="BioSQL.Loader.DatabaseLoader._load_seqfeature_dbxref" class="py-name" href="#" onclick="return doclink('link-286', '_load_seqfeature_dbxref', 'link-286');">_load_seqfeature_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">qualifiers</tt><tt class="py-op">[</tt><tt class="py-name">qualifier_key</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-name">seqfeature_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_seqfeature_dbxref"></a><div id="DatabaseLoader._load_seqfeature_dbxref-def"><a name="L649"></a><tt class="py-lineno">649</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_seqfeature_dbxref-toggle" onclick="return toggle('DatabaseLoader._load_seqfeature_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_seqfeature_dbxref">_load_seqfeature_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dbxrefs</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_seqfeature_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_seqfeature_dbxref-expanded"><a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-docstring">"""Add the database crossreferences of a SeqFeature to the database.</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"><tt class="py-docstring"> o dbxrefs List, dbxref data from the source file in the</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"><tt class="py-docstring"> format <database>:<accession></tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"><tt class="py-docstring"> o seqfeature_id Int, the identifier for the seqfeature in the</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"><tt class="py-docstring"> seqfeature table</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-docstring"> Insert dbxref qualifier data for a seqfeature into the</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-docstring"> seqfeature_dbxref and, if required, dbxref tables.</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"><tt class="py-docstring"> The dbxref_id qualifier/value sets go into the dbxref table</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"><tt class="py-docstring"> as dbname, accession, version tuples, with dbxref.dbxref_id</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"><tt class="py-docstring"> being automatically assigned, and into the seqfeature_dbxref</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"><tt class="py-docstring"> table as seqfeature_id, dbxref_id, and rank tuples</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-comment"># NOTE - In older versions of Biopython, we would map the GenBank</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># db_xref "name", for example "GI" to "GeneIndex", and give a warning</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for any unknown terms. This was a long term maintainance problem,</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and differed from BioPerl and BioJava's implementation. See bug 2405</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">rank</tt><tt class="py-op">,</tt> <tt id="link-287" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-287', 'value', 'link-175');">value</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-288" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.dbxrefs=BioSQL.BioSeq.DBSeqRecord-class.html#dbxrefs"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-288', 'dbxrefs', 'link-288');">dbxrefs</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-comment"># Split the DB:accession format string at colons. We have to</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># account for multiple-line and multiple-accession entries</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-name">dbxref_data</tt> <tt class="py-op">=</tt> <tt id="link-289" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-289', 'value', 'link-175');">value</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-290" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-290', 'split', 'link-102');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">':'</tt><tt class="py-op">)</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt id="link-291" 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-291', 'db', 'link-291');">db</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dbxref_data</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-name">accessions</tt> <tt class="py-op">=</tt> <tt class="py-name">dbxref_data</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Parsing of db_xref failed: '%s'"</tt> <tt class="py-op">%</tt> <tt id="link-292" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-292', 'value', 'link-175');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-comment"># Loop over all the grabbed accessions, and attempt to fill the</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># table</tt> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-293" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-293', 'accession', 'link-48');">accession</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">accessions</tt><tt class="py-op">:</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-comment"># Get the dbxref_id value for the dbxref data</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_dbxref_id()=BioSQL.Loader.DatabaseLoader-class.html#_get_dbxref_id"><a title="BioSQL.Loader.DatabaseLoader._get_dbxref_id" class="py-name" href="#" onclick="return doclink('link-294', '_get_dbxref_id', 'link-294');">_get_dbxref_id</a></tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-295', 'db', 'link-291');">db</a></tt><tt class="py-op">,</tt> <tt id="link-296" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-296', 'accession', 'link-48');">accession</a></tt><tt class="py-op">)</tt> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-comment"># Insert the seqfeature_dbxref data</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_seqfeature_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_get_seqfeature_dbxref"><a title="BioSQL.Loader.DatabaseLoader._get_seqfeature_dbxref" class="py-name" href="#" onclick="return doclink('link-297', '_get_seqfeature_dbxref', 'link-297');">_get_seqfeature_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_dbxref_id"></a><div id="DatabaseLoader._get_dbxref_id-def"><a name="L686"></a><tt class="py-lineno">686</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_dbxref_id-toggle" onclick="return toggle('DatabaseLoader._get_dbxref_id');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_dbxref_id">_get_dbxref_id</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">db</tt><tt class="py-op">,</tt> <tt class="py-param">accession</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._get_dbxref_id-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_dbxref_id-expanded"><a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-docstring">""" _get_dbxref_id(self, db, accession) -> Int</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"><tt class="py-docstring"> o db String, the name of the external database containing</tt> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"><tt class="py-docstring"> the accession number</tt> </tt>
<a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt class="py-docstring"> o accession String, the accession of the dbxref data</tt> </tt>
<a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-docstring"> Finds and returns the dbxref_id for the passed data. The method</tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"><tt class="py-docstring"> attempts to find an existing record first, and inserts the data</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"><tt class="py-docstring"> if there is no record.</tt> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"> <tt class="py-comment"># Check for an existing record</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r'SELECT dbxref_id FROM dbxref WHERE dbname = %s '</tt> \ </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"> <tt class="py-string">r'AND accession = %s'</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-298', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-299" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-299', 'db', 'link-291');">db</a></tt><tt class="py-op">,</tt> <tt id="link-300" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-300', 'accession', 'link-48');">accession</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"> <tt class="py-comment"># If there was a record, return the dbxref_id, else create the</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># record and return the created dbxref_id</tt> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">:</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-301" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._add_dbxref" class="py-name" href="#" onclick="return doclink('link-301', '_add_dbxref', 'link-213');">_add_dbxref</a></tt><tt class="py-op">(</tt><tt id="link-302" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-302', 'db', 'link-291');">db</a></tt><tt class="py-op">,</tt> <tt id="link-303" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-303', 'accession', 'link-48');">accession</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
</div><a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_seqfeature_dbxref"></a><div id="DatabaseLoader._get_seqfeature_dbxref-def"><a name="L708"></a><tt class="py-lineno">708</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_seqfeature_dbxref-toggle" onclick="return toggle('DatabaseLoader._get_seqfeature_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_seqfeature_dbxref">_get_seqfeature_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-param">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._get_seqfeature_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_seqfeature_dbxref-expanded"><a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> <tt class="py-docstring">""" Check for a pre-existing seqfeature_dbxref entry with the passed</tt> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"><tt class="py-docstring"> seqfeature_id and dbxref_id. If one does not exist, insert new</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-docstring"> data</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-comment"># Check for an existing record</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"SELECT seqfeature_id, dbxref_id FROM seqfeature_dbxref "</tt> \ </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt class="py-string">r"WHERE seqfeature_id = '%s' AND dbxref_id = '%s'"</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-304" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-304', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-comment"># If there was a record, return without executing anything, else create</tt> </tt>
<a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the record and return</tt> </tt>
<a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt><tt class="py-op">:</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-305" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._add_seqfeature_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_add_seqfeature_dbxref"><a title="BioSQL.Loader.DatabaseLoader._add_seqfeature_dbxref" class="py-name" href="#" onclick="return doclink('link-305', '_add_seqfeature_dbxref', 'link-305');">_add_seqfeature_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt> </tt>
</div><a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._add_seqfeature_dbxref"></a><div id="DatabaseLoader._add_seqfeature_dbxref-def"><a name="L725"></a><tt class="py-lineno">725</tt> <a class="py-toggle" href="#" id="DatabaseLoader._add_seqfeature_dbxref-toggle" onclick="return toggle('DatabaseLoader._add_seqfeature_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_add_seqfeature_dbxref">_add_seqfeature_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-param">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._add_seqfeature_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._add_seqfeature_dbxref-expanded"><a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-docstring">""" Insert a seqfeature_dbxref row and return the seqfeature_id and</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-docstring"> dbxref_id</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r'INSERT INTO seqfeature_dbxref '</tt> \ </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-string">'(seqfeature_id, dbxref_id, rank) VALUES'</tt> \ </tt>
<a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-string">r'(%s, %s, %s)'</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-306" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-306', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">)</tt> </tt>
</div><a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._load_dbxrefs"></a><div id="DatabaseLoader._load_dbxrefs-def"><a name="L735"></a><tt class="py-lineno">735</tt> <a class="py-toggle" href="#" id="DatabaseLoader._load_dbxrefs-toggle" onclick="return toggle('DatabaseLoader._load_dbxrefs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_load_dbxrefs">_load_dbxrefs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._load_dbxrefs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._load_dbxrefs-expanded"><a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-docstring">"""Load any sequence level cross references into the database.</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"><tt class="py-docstring"> See table bioentry_dbxref"""</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rank</tt><tt class="py-op">,</tt> <tt id="link-307" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-307', 'value', 'link-175');">value</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-308" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-308', 'record', 'link-10');">record</a></tt><tt class="py-op">.</tt><tt id="link-309" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-309', 'dbxrefs', 'link-288');">dbxrefs</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-comment"># Split the DB:accession string at first colon.</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># We have to cope with things like:</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># "MGD:MGI:892" (db="MGD", accession="MGI:892")</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># "GO:GO:123" (db="GO", accession="GO:123")</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Annoyingly I have seen the NCBI use both the style</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># "GO:GO:123" and "GO:123" in different vintages.</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-310" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-310', 'value', 'link-175');">value</a></tt><tt class="py-op">.</tt><tt id="link-311" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-311', 'count', 'link-311');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt id="link-312" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-312', 'db', 'link-291');">db</a></tt><tt class="py-op">,</tt> <tt id="link-313" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-313', 'accession', 'link-48');">accession</a></tt> <tt class="py-op">=</tt> <tt id="link-314" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-314', 'value', 'link-175');">value</a></tt><tt class="py-op">.</tt><tt id="link-315" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-315', 'split', 'link-102');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">':'</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt id="link-316" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-316', 'db', 'link-291');">db</a></tt> <tt class="py-op">=</tt> <tt id="link-317" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-317', 'db', 'link-291');">db</a></tt><tt class="py-op">.</tt><tt id="link-318" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-318', 'strip', 'link-318');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt id="link-319" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-319', 'accession', 'link-48');">accession</a></tt> <tt class="py-op">=</tt> <tt id="link-320" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-320', 'accession', 'link-48');">accession</a></tt><tt class="py-op">.</tt><tt id="link-321" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-321', 'strip', 'link-318');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Parsing of dbxrefs list failed: '%s'"</tt> <tt class="py-op">%</tt> <tt id="link-322" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-322', 'value', 'link-175');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> <tt class="py-comment"># Get the dbxref_id value for the dbxref data</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dbxref_id</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-323" class="py-name"><a title="BioSQL.Loader.DatabaseLoader._get_dbxref_id" class="py-name" href="#" onclick="return doclink('link-323', '_get_dbxref_id', 'link-294');">_get_dbxref_id</a></tt><tt class="py-op">(</tt><tt id="link-324" class="py-name"><a title="Bio.LocusLink.locus_format.db
Bio.config.DBRegistry.db" class="py-name" href="#" onclick="return doclink('link-324', 'db', 'link-291');">db</a></tt><tt class="py-op">,</tt> <tt id="link-325" class="py-name"><a title="Bio.GenBank._FeatureConsumer.accession
Bio.GenBank._RecordConsumer.accession
Bio.Prosite.Prodoc._RecordConsumer.accession
Bio.Prosite._RecordConsumer.accession
Bio.SwissProt.SProt._RecordConsumer.accession
Bio.SwissProt.SProt._SequenceConsumer.accession
Bio.expressions.embl.embl65.accession
Bio.expressions.genbank.accession" class="py-name" href="#" onclick="return doclink('link-325', 'accession', 'link-48');">accession</a></tt><tt class="py-op">)</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"> <tt class="py-comment"># Insert the bioentry_dbxref data</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-326" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._get_bioentry_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_get_bioentry_dbxref"><a title="BioSQL.Loader.DatabaseLoader._get_bioentry_dbxref" class="py-name" href="#" onclick="return doclink('link-326', '_get_bioentry_dbxref', 'link-326');">_get_bioentry_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._get_bioentry_dbxref"></a><div id="DatabaseLoader._get_bioentry_dbxref-def"><a name="L759"></a><tt class="py-lineno">759</tt> <a class="py-toggle" href="#" id="DatabaseLoader._get_bioentry_dbxref-toggle" onclick="return toggle('DatabaseLoader._get_bioentry_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_get_bioentry_dbxref">_get_bioentry_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-param">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._get_bioentry_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._get_bioentry_dbxref-expanded"><a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt class="py-docstring">""" Check for a pre-existing bioentry_dbxref entry with the passed</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"><tt class="py-docstring"> seqfeature_id and dbxref_id. If one does not exist, insert new</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"><tt class="py-docstring"> data</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-comment"># Check for an existing record</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"SELECT bioentry_id, dbxref_id FROM bioentry_dbxref "</tt> \ </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt class="py-string">r"WHERE bioentry_id = '%s' AND dbxref_id = '%s'"</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-327" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-327', 'execute_and_fetch_col0', 'link-32');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-name">dbxref_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-comment"># If there was a record, return without executing anything, else create</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the record and return</tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">result</tt><tt class="py-op">:</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-328" class="py-name" targets="Method BioSQL.Loader.DatabaseLoader._add_bioentry_dbxref()=BioSQL.Loader.DatabaseLoader-class.html#_add_bioentry_dbxref"><a title="BioSQL.Loader.DatabaseLoader._add_bioentry_dbxref" class="py-name" href="#" onclick="return doclink('link-328', '_add_bioentry_dbxref', 'link-328');">_add_bioentry_dbxref</a></tt><tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt> </tt>
</div><a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> </tt>
<a name="DatabaseLoader._add_bioentry_dbxref"></a><div id="DatabaseLoader._add_bioentry_dbxref-def"><a name="L776"></a><tt class="py-lineno">776</tt> <a class="py-toggle" href="#" id="DatabaseLoader._add_bioentry_dbxref-toggle" onclick="return toggle('DatabaseLoader._add_bioentry_dbxref');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseLoader-class.html#_add_bioentry_dbxref">_add_bioentry_dbxref</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-param">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-param">rank</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseLoader._add_bioentry_dbxref-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseLoader._add_bioentry_dbxref-expanded"><a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-docstring">""" Insert a bioentry_dbxref row and return the seqfeature_id and</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"><tt class="py-docstring"> dbxref_id</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r'INSERT INTO bioentry_dbxref '</tt> \ </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-string">'(bioentry_id,dbxref_id,rank) VALUES '</tt> \ </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-string">'(%s, %s, %s)'</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-329', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">bioentry_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbxref_id</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> </tt>
<a name="DatabaseRemover"></a><div id="DatabaseRemover-def"><a name="L786"></a><tt class="py-lineno">786</tt> <a class="py-toggle" href="#" id="DatabaseRemover-toggle" onclick="return toggle('DatabaseRemover');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseRemover-class.html">DatabaseRemover</a><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseRemover-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DatabaseRemover-expanded"><a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-docstring">"""Complement the Loader functionality by fully removing a database.</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"><tt class="py-docstring"> This probably isn't really useful for normal purposes, since you</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"><tt class="py-docstring"> can just do a:</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"><tt class="py-docstring"> DROP DATABASE db_name</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"><tt class="py-docstring"> and then recreate the database. But, it's really useful for testing</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"><tt class="py-docstring"> purposes.</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"><tt class="py-docstring"> YB: now use the cascaded deletions</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="DatabaseRemover.__init__"></a><div id="DatabaseRemover.__init__-def"><a name="L797"></a><tt class="py-lineno">797</tt> <a class="py-toggle" href="#" id="DatabaseRemover.__init__-toggle" onclick="return toggle('DatabaseRemover.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseRemover-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">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">dbid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DatabaseRemover.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseRemover.__init__-expanded"><a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize with a database id and adaptor connection.</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-330', 'dbid', 'link-7');">dbid</a></tt> <tt class="py-op">=</tt> <tt id="link-331" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-331', 'dbid', 'link-7');">dbid</a></tt> </tt>
</div><a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> </tt>
<a name="DatabaseRemover.remove"></a><div id="DatabaseRemover.remove-def"><a name="L803"></a><tt class="py-lineno">803</tt> <a class="py-toggle" href="#" id="DatabaseRemover.remove-toggle" onclick="return toggle('DatabaseRemover.remove');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.Loader.DatabaseRemover-class.html#remove">remove</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="DatabaseRemover.remove-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DatabaseRemover.remove-expanded"><a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> <tt class="py-docstring">"""Remove everything related to the given database id.</tt> </tt>
<a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"DELETE FROM bioentry WHERE biodatabase_id = %s"</tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-332" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-332', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-333" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-333', 'dbid', 'link-7');">dbid</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">r"DELETE FROM biodatabase WHERE biodatabase_id = %s"</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute" class="py-name" href="#" onclick="return doclink('link-334', 'execute', 'link-34');">execute</a></tt><tt class="py-op">(</tt><tt class="py-name">sql</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-335" class="py-name"><a title="Bio.Std.dbid" class="py-name" href="#" onclick="return doclink('link-335', 'dbid', 'link-7');">dbid</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> </tt><script type="text/javascript">
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