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        <a href="BioSQL-module.html">Package&nbsp;BioSQL</a> ::
        Module&nbsp;BioSeq
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<h1 class="epydoc">Source Code for <a href="BioSQL.BioSeq-module.html">Module BioSQL.BioSeq</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 class="py-docstring">"""Implementations of Biopython-like Seq objects on top of BioSQL.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-docstring">This allows retrival of items stored in a BioSQL database using</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">a biopython-like Seq interface.</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</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-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html,Package Bio.builders.SeqRecord=Bio.builders.SeqRecord-module.html,Package Bio.writers.SeqRecord=Bio.writers.SeqRecord-module.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Module Bio.SeqFeature=Bio.SeqFeature-module.html,Class Bio.SeqFeature.SeqFeature=Bio.SeqFeature.SeqFeature-class.html"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-7', 'SeqFeature', 'link-7');">SeqFeature</a></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="DBSeq"></a><div id="DBSeq-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="DBSeq-toggle" onclick="return toggle('DBSeq');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-class.html">DBSeq</a><tt class="py-op">(</tt><tt class="py-base-class">Seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  <tt class="py-comment"># This implements the biopython Seq interface</tt> </tt>
</div><a name="DBSeq.__init__"></a><div id="DBSeq.__init__-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="DBSeq.__init__-toggle" onclick="return toggle('DBSeq.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-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">primary_id</tt><tt class="py-op">,</tt> <tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">length</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBSeq.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeq.__init__-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Variable Bio.expressions.swissprot.sprot38.primary_id=Bio.expressions.swissprot.sprot38-module.html#primary_id"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-8', 'primary_id', 'link-8');">primary_id</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-9', 'primary_id', 'link-8');">primary_id</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</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="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'alphabet', 'link-10');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'alphabet', 'link-10');">alphabet</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.MEME.Motif.Instance._length()=Bio.MEME.Motif.Instance-class.html#_length,Method Bio.MEME.Motif.Motif._length()=Bio.MEME.Motif.Motif-class.html#_length"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-12', '_length', 'link-12');">_length</a></tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-13', 'length', 'link-13');">length</a></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'start', 'link-14');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-15" 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-15', 'start', 'link-14');">start</a></tt> </tt>
</div><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"> </tt>
<a name="DBSeq.__len__"></a><div id="DBSeq.__len__-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="DBSeq.__len__-toggle" onclick="return toggle('DBSeq.__len__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBSeq.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeq.__len__-expanded"><a name="L28"></a><tt class="py-lineno"> 28</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-16" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-16', '_length', 'link-12');">_length</a></tt> </tt>
</div><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">     </tt>
<a name="DBSeq.__getitem__"></a><div id="DBSeq.__getitem__-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="DBSeq.__getitem__-toggle" onclick="return toggle('DBSeq.__getitem__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt>                 <tt class="py-comment"># Seq API requirement</tt> </tt>
</div><a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-comment">#Note since Python 2.0, __getslice__ is deprecated</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#and __getitem__ is used instead.</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#See http://docs.python.org/ref/sequence-methods.html</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</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-17" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-17', 'index', 'link-17');">index</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="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">            <tt class="py-comment">#Return a single letter as a string</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-18" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-18', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-19', 'index', 'link-17');">index</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-20" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-20', 'i', 'link-18');">i</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-op">-</tt><tt id="link-21" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-21', 'i', 'link-18');">i</a></tt> <tt class="py-op">&gt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-22', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">                    <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">                <tt id="link-24" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-24', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-25', 'i', 'link-18');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-26', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">            <tt class="py-keyword">elif</tt> <tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-18');">i</a></tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-28', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt>             </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string()=BioSQL.BioSeqDatabase.Adaptor-class.html#get_subseq_as_string"><a title="BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string" class="py-name" href="#" onclick="return doclink('link-30', 'get_subseq_as_string', 'link-30');">get_subseq_as_string</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-31', 'primary_id', 'link-8');">primary_id</a></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">self</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt id="link-33" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-33', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">                                                     <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt id="link-35" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-18');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</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 id="link-36" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-36', 'index', 'link-17');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">slice</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Unexpected index type"</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-comment">#Return the (sub)sequence as another DBSeq or Seq object</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#(see the Seq obect's __getitem__ method)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt id="link-37" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-37', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'start', 'link-14');">start</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">            <tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-18');">i</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">            <tt id="link-40" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-40', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-41', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt id="link-42" 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-42', 'start', 'link-14');">start</a></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-18');">i</a></tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">            <tt class="py-comment">#Map to equavilent positive index</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-op">-</tt><tt id="link-44" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-44', 'i', 'link-18');">i</a></tt> <tt class="py-op">&gt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-45', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">            <tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-18');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-49', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-18');">i</a></tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-51', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">            <tt class="py-comment">#Trivial case, should return empty string!</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-18');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-53', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-54" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-54', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt class="py-name">stop</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-55', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-56', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt class="py-name">stop</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">j</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">            <tt class="py-comment">#Map to equavilent positive index</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">if</tt> <tt class="py-op">-</tt><tt class="py-name">j</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-57', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">                <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">j</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-58', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">j</tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-59', '_length', 'link-12');">_length</a></tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">            <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-60', '_length', 'link-12');">_length</a></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-61" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-61', 'i', 'link-18');">i</a></tt> <tt class="py-op">&gt;=</tt> <tt class="py-name">j</tt><tt class="py-op">:</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">            <tt class="py-comment">#Trivial case, empty string.</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">return</tt> <tt id="link-62" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-62', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-63', 'alphabet', 'link-10');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-64" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-64', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt class="py-name">step</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt id="link-65" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-65', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt class="py-name">step</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">            <tt class="py-comment">#Easy case - can return a DBSeq with the start and end adjusted</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-66', 'primary_id', 'link-8');">primary_id</a></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 class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-67', 'alphabet', 'link-10');">alphabet</a></tt><tt class="py-op">,</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">                                  <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt id="link-69" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-69', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt> <tt class="py-op">-</tt> <tt id="link-70" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-70', 'i', 'link-18');">i</a></tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">            <tt class="py-comment">#Tricky.  Will have to create a Seq object because of the stride</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-71" class="py-name" targets="Method Bio.Restriction.Restriction.Analysis.full()=Bio.Restriction.Restriction.Analysis-class.html#full"><a title="Bio.Restriction.Restriction.Analysis.full" class="py-name" href="#" onclick="return doclink('link-71', 'full', 'link-71');">full</a></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-72" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string" class="py-name" href="#" onclick="return doclink('link-72', 'get_subseq_as_string', 'link-30');">get_subseq_as_string</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-73', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">                                                     <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt id="link-75" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-75', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">                                                     <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" 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-76', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">j</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-77" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-77', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Restriction.Restriction.Analysis.full" class="py-name" href="#" onclick="return doclink('link-78', 'full', 'link-71');">full</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt id="link-79" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-79', 'index', 'link-17');">index</a></tt><tt class="py-op">.</tt><tt class="py-name">step</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-80" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-80', 'alphabet', 'link-10');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">         </tt>
<a name="DBSeq.tostring"></a><div id="DBSeq.tostring-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="DBSeq.tostring-toggle" onclick="return toggle('DBSeq.tostring');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-class.html#tostring">tostring</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="DBSeq.tostring-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeq.tostring-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns the full sequence as a python string.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring">        Although not formally deprecated, you are now encouraged to use</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">        str(my_seq) instead of my_seq.tostring()."""</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</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-81" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string" class="py-name" href="#" onclick="return doclink('link-81', 'get_subseq_as_string', 'link-30');">get_subseq_as_string</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-82', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">                                                 <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" 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-83', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">                                                 <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" 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-84', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-85', '_length', 'link-12');">_length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="DBSeq.__str__"></a><div id="DBSeq.__str__-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="DBSeq.__str__-toggle" onclick="return toggle('DBSeq.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeq-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBSeq.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeq.__str__-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns the full sequence as a python string."""</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.get_subseq_as_string" class="py-name" href="#" onclick="return doclink('link-86', 'get_subseq_as_string', 'link-30');">get_subseq_as_string</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-87', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">                                                 <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" 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-88', 'start', 'link-14');">start</a></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">self</tt><tt class="py-op">.</tt><tt id="link-89" 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-89', 'start', 'link-14');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.MEME.Motif.Instance._length
Bio.MEME.Motif.Motif._length" class="py-name" href="#" onclick="return doclink('link-90', '_length', 'link-12');">_length</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt id="link-91" 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-91', 'data', 'link-91');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.property=Bio.Encodings.IUPACEncoding-module.html#property"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-92', 'property', 'link-92');">property</a></tt><tt class="py-op">(</tt><tt id="link-93" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-93', 'tostring', 'link-93');">tostring</a></tt><tt class="py-op">,</tt> <tt class="py-name">doc</tt><tt class="py-op">=</tt><tt class="py-string">"Sequence as string (DEPRECATED)"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_seq"></a><div id="_retrieve_seq-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="_retrieve_seq-toggle" onclick="return toggle('_retrieve_seq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_seq">_retrieve_seq</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_seq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_seq-expanded"><a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">    <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-94" 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-94', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-string">"SELECT alphabet, length(seq) FROM biosequence"</tt> \ </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-string">" WHERE bioentry_id = %s"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-95', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">seqs</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">        <tt class="py-name">moltype</tt><tt class="py-op">,</tt> <tt id="link-96" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-96', 'length', 'link-13');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">        <tt class="py-name">moltype</tt> <tt class="py-op">=</tt> <tt class="py-name">moltype</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#might be upper case in database</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">        <tt class="py-keyword">from</tt> <tt id="link-97" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-97', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-98" 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-98', 'Alphabet', 'link-98');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-99" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-99', 'IUPAC', 'link-99');">IUPAC</a></tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">moltype</tt> <tt class="py-op">==</tt> <tt class="py-string">"dna"</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">            <tt id="link-100" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-100', 'alphabet', 'link-10');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-101', 'IUPAC', 'link-99');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_dna=Bio.Alphabet.IUPAC-module.html#unambiguous_dna"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-102', 'unambiguous_dna', 'link-102');">unambiguous_dna</a></tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">moltype</tt> <tt class="py-op">==</tt> <tt class="py-string">"rna"</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">            <tt id="link-103" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-103', 'alphabet', 'link-10');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-104" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-104', 'IUPAC', 'link-99');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_rna=Bio.Alphabet.IUPAC-module.html#unambiguous_rna"><a title="Bio.Alphabet.IUPAC.unambiguous_rna" class="py-name" href="#" onclick="return doclink('link-105', 'unambiguous_rna', 'link-105');">unambiguous_rna</a></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">moltype</tt> <tt class="py-op">==</tt> <tt class="py-string">"protein"</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">            <tt id="link-106" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-106', 'alphabet', 'link-10');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-107" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-107', 'IUPAC', 'link-99');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name" targets="Variable Bio.Alphabet.IUPAC.protein=Bio.Alphabet.IUPAC-module.html#protein"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-108', 'protein', 'link-108');">protein</a></tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">(</tt><tt class="py-string">"Unknown moltype: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">moltype</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt id="link-109" 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-109', 'seq', 'link-109');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-110" class="py-name" targets="Class BioSQL.BioSeq.DBSeq=BioSQL.BioSeq.DBSeq-class.html"><a title="BioSQL.BioSeq.DBSeq" class="py-name" href="#" onclick="return doclink('link-110', 'DBSeq', 'link-110');">DBSeq</a></tt><tt class="py-op">(</tt><tt id="link-111" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-111', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-112" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-112', 'alphabet', 'link-10');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-113" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-113', 'length', 'link-13');">length</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-114" 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-114', 'seq', 'link-109');">seq</a></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_dbxrefs"></a><div id="_retrieve_dbxrefs-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="_retrieve_dbxrefs-toggle" onclick="return toggle('_retrieve_dbxrefs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_dbxrefs">_retrieve_dbxrefs</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_dbxrefs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_dbxrefs-expanded"><a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">    <tt class="py-docstring">"""Retrieve the database cross references for the sequence."""</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-name">_dbxrefs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt id="link-115" 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-115', 'dbxrefs', 'link-115');">dbxrefs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-116', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">        <tt class="py-string">"SELECT dbname, accession, version"</tt> \ </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">        <tt class="py-string">" FROM bioentry_dbxref join dbxref using (dbxref_id)"</tt> \ </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-string">" WHERE bioentry_id = %s"</tt> \ </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-string">" ORDER BY rank"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-117" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-117', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-118" 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-118', 'accession', 'link-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-119" 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-119', 'version', 'link-119');">version</a></tt> <tt class="py-keyword">in</tt> <tt id="link-120" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-120', 'dbxrefs', 'link-115');">dbxrefs</a></tt><tt class="py-op">:</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-121" 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-121', 'version', 'link-119');">version</a></tt> <tt class="py-keyword">and</tt> <tt id="link-122" 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-122', 'version', 'link-119');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"0"</tt><tt class="py-op">:</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">            <tt id="link-123" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-123', 'v', 'link-123');">v</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s.%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><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-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-125" 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-125', 'version', 'link-119');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">            <tt id="link-126" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-126', 'v', 'link-123');">v</a></tt> <tt class="py-op">=</tt> <tt id="link-127" 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-127', 'accession', 'link-118');">accession</a></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-name">_dbxrefs</tt><tt class="py-op">.</tt><tt id="link-128" 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-128', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%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-129" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-129', 'v', 'link-123');">v</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">_dbxrefs</tt> </tt>
</div><a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_features"></a><div id="_retrieve_features-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="_retrieve_features-toggle" onclick="return toggle('_retrieve_features');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_features">_retrieve_features</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_features-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_features-expanded"><a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">    <tt class="py-name">sql</tt> <tt class="py-op">=</tt> <tt class="py-string">"SELECT seqfeature_id, type.name, rank"</tt> \ </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">          <tt class="py-string">" FROM seqfeature join term type on (type_term_id = type.term_id)"</tt> \ </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">          <tt class="py-string">" WHERE bioentry_id = %s"</tt> \ </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">          <tt class="py-string">" ORDER BY rank"</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-130', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</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-131" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-131', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">seq_feature_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">seqfeature_id</tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_type</tt><tt class="py-op">,</tt> <tt class="py-name">seqfeature_rank</tt> <tt class="py-keyword">in</tt> <tt class="py-name">results</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-comment"># Get qualifiers [except for db_xref which is stored separately]</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">qvs</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-132', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">            <tt class="py-string">"SELECT name, value"</tt> \ </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">            <tt class="py-string">" FROM seqfeature_qualifier_value  join term using (term_id)"</tt> \ </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">            <tt class="py-string">" WHERE seqfeature_id = %s"</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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">        <tt class="py-name">qualifiers</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">qv_name</tt><tt class="py-op">,</tt> <tt class="py-name">qv_value</tt> <tt class="py-keyword">in</tt> <tt class="py-name">qvs</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">qualifiers</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name" targets="Method Bio.Crystal.Crystal.setdefault()=Bio.Crystal.Crystal-class.html#setdefault"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-133', 'setdefault', 'link-133');">setdefault</a></tt><tt class="py-op">(</tt><tt class="py-name">qv_name</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 id="link-134" 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-134', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">qv_value</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">        <tt class="py-comment"># Get db_xrefs [special case of qualifiers]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">qvs</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_and_fetchall" class="py-name" href="#" onclick="return doclink('link-135', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">            <tt class="py-string">"SELECT dbxref.dbname, dbxref.accession"</tt> \ </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">            <tt class="py-string">" FROM dbxref join seqfeature_dbxref using (dbxref_id)"</tt> \ </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">            <tt class="py-string">" WHERE seqfeature_dbxref.seqfeature_id = %s"</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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">qv_name</tt><tt class="py-op">,</tt> <tt class="py-name">qv_value</tt> <tt class="py-keyword">in</tt> <tt class="py-name">qvs</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">            <tt id="link-136" 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-136', 'value', 'link-136');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s:%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">qv_name</tt><tt class="py-op">,</tt> <tt class="py-name">qv_value</tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            <tt class="py-name">qualifiers</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-137', 'setdefault', 'link-133');">setdefault</a></tt><tt class="py-op">(</tt><tt class="py-string">"db_xref"</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 id="link-138" 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-138', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt><tt id="link-139" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-139', 'value', 'link-136');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">        <tt class="py-comment"># Get locations</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-140', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt class="py-string">"SELECT location_id, start_pos, end_pos, strand"</tt> \ </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">            <tt class="py-string">" FROM location"</tt> \ </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">            <tt class="py-string">" WHERE seqfeature_id = %s"</tt> \ </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">            <tt class="py-string">" ORDER BY rank"</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-op">)</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">locations</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">        <tt class="py-comment"># convert to Python standard form</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">for</tt> <tt class="py-name">location_id</tt><tt class="py-op">,</tt> <tt id="link-141" 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-141', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-142" 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-142', 'end', 'link-142');">end</a></tt><tt class="py-op">,</tt> <tt id="link-143" 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-143', 'strand', 'link-143');">strand</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">results</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-144" 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-144', 'start', 'link-14');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">                <tt id="link-145" 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-145', 'start', 'link-14');">start</a></tt> <tt class="py-op">-=</tt> <tt class="py-number">1</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">            <tt class="py-name">locations</tt><tt class="py-op">.</tt><tt id="link-146" 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-146', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt> <tt class="py-op">(</tt><tt class="py-name">location_id</tt><tt class="py-op">,</tt> <tt id="link-147" 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-147', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-148" 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-148', 'end', 'link-142');">end</a></tt><tt class="py-op">,</tt> <tt id="link-149" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-149', 'strand', 'link-143');">strand</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-comment"># Get possible remote reference information</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">remote_results</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-150', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">            <tt class="py-string">"SELECT location_id, dbname, accession, version"</tt> \ </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">            <tt class="py-string">" FROM location join dbxref using (dbxref_id)"</tt> \ </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">            <tt class="py-string">" WHERE seqfeature_id = %s"</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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt id="link-151" class="py-name" targets="Method Bio.Mindy.BaseDB.OpenDB.lookup()=Bio.Mindy.BaseDB.OpenDB-class.html#lookup,Method BioSQL.BioSeqDatabase.BioSeqDatabase.lookup()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#lookup"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-151', 'lookup', 'link-151');">lookup</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">location_id</tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-152" 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-152', 'accession', 'link-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-153" 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-153', 'version', 'link-119');">version</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">remote_results</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt id="link-154" 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-154', 'version', 'link-119');">version</a></tt> <tt class="py-keyword">and</tt> <tt id="link-155" 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-155', 'version', 'link-119');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"0"</tt><tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">                <tt id="link-156" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-156', 'v', 'link-123');">v</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s.%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-157" 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-157', 'accession', 'link-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-158" 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-158', 'version', 'link-119');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">                <tt id="link-159" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-159', 'v', 'link-123');">v</a></tt> <tt class="py-op">=</tt> <tt id="link-160" 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-160', 'accession', 'link-118');">accession</a></tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">            <tt id="link-161" class="py-name"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-161', 'lookup', 'link-151');">lookup</a></tt><tt class="py-op">[</tt><tt class="py-name">location_id</tt><tt class="py-op">]</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-162" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-162', 'v', 'link-123');">v</a></tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">         </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">        <tt id="link-163" 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-163', 'feature', 'link-163');">feature</a></tt> <tt class="py-op">=</tt> <tt id="link-164" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-164', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-165" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-165', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">(</tt><tt id="link-166" 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-166', 'type', 'link-166');">type</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seqfeature_type</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt id="link-167" 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-167', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">qualifiers</tt> <tt class="py-op">=</tt> <tt class="py-name">qualifiers</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">locations</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="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</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">locations</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="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">            <tt class="py-name">location_id</tt><tt class="py-op">,</tt> <tt id="link-168" 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-168', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-169" 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-169', 'end', 'link-142');">end</a></tt><tt class="py-op">,</tt> <tt id="link-170" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-170', 'strand', 'link-143');">strand</a></tt> <tt class="py-op">=</tt> <tt class="py-name">locations</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">            <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-171" 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-171', 'version', 'link-119');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-172" class="py-name"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-172', 'lookup', 'link-151');">lookup</a></tt><tt class="py-op">.</tt><tt id="link-173" 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-173', 'get', 'link-173');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">location_id</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-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 id="link-174" 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-174', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt id="link-175" 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-175', 'location', 'link-175');">location</a></tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-176', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-177" class="py-name" targets="Class Bio.SeqFeature.FeatureLocation=Bio.SeqFeature.FeatureLocation-class.html"><a title="Bio.SeqFeature.FeatureLocation" class="py-name" href="#" onclick="return doclink('link-177', 'FeatureLocation', 'link-177');">FeatureLocation</a></tt><tt class="py-op">(</tt><tt id="link-178" 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-178', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-179" 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-179', 'end', 'link-142');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">            <tt id="link-180" 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-180', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-181', 'strand', 'link-143');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-182" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-182', 'strand', 'link-143');">strand</a></tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">            <tt id="link-183" 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-183', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">ref_db</tt> <tt class="py-op">=</tt> <tt class="py-name">dbname</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">            <tt id="link-184" 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-184', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt id="link-185" 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-185', 'version', 'link-119');">version</a></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">            <tt class="py-name">min_start</tt> <tt class="py-op">=</tt> <tt class="py-name">locations</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">1</tt><tt class="py-op">]</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">            <tt class="py-name">max_end</tt> <tt class="py-op">=</tt> <tt class="py-name">locations</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">2</tt><tt class="py-op">]</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">            <tt class="py-name">sub_feature_list</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt>       <tt class="py-comment"># (start, sub feature) for sorting</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">            <tt class="py-keyword">for</tt> <tt id="link-186" 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-186', 'location', 'link-175');">location</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">locations</tt><tt class="py-op">:</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">                <tt class="py-name">location_id</tt><tt class="py-op">,</tt> <tt id="link-187" 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-187', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-188" 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-188', 'end', 'link-142');">end</a></tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-189', 'strand', 'link-143');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-190" 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-190', 'location', 'link-175');">location</a></tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">                <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-191" 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-191', 'version', 'link-119');">version</a></tt> <tt class="py-op">=</tt> <tt id="link-192" class="py-name"><a title="Bio.Mindy.BaseDB.OpenDB.lookup
BioSQL.BioSeqDatabase.BioSeqDatabase.lookup" class="py-name" href="#" onclick="return doclink('link-192', 'lookup', 'link-151');">lookup</a></tt><tt class="py-op">.</tt><tt id="link-193" 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-193', 'get', 'link-173');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">location_id</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-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">                <tt class="py-name">min_start</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">min_start</tt><tt class="py-op">,</tt> <tt id="link-194" 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-194', 'start', 'link-14');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">                <tt class="py-name">max_end</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">max_end</tt><tt class="py-op">,</tt> <tt id="link-195" 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-195', 'end', 'link-142');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt> <tt class="py-op">=</tt> <tt id="link-196" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-196', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-197', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt id="link-198" 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-198', 'type', 'link-166');">type</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seqfeature_type</tt>  </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt class="py-name">location_operator</tt> <tt class="py-op">=</tt> <tt class="py-string">"join"</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt id="link-199" 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-199', 'location', 'link-175');">location</a></tt> <tt class="py-op">=</tt> <tt id="link-200" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-200', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.SeqFeature.FeatureLocation" class="py-name" href="#" onclick="return doclink('link-201', 'FeatureLocation', 'link-177');">FeatureLocation</a></tt><tt class="py-op">(</tt><tt id="link-202" 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-202', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-203" 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-203', 'end', 'link-142');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-204', 'strand', 'link-143');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-205" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-205', 'strand', 'link-143');">strand</a></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt class="py-name">ref_db</tt> <tt class="py-op">=</tt> <tt class="py-name">dbname</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">                <tt class="py-name">subfeature</tt><tt class="py-op">.</tt><tt class="py-name">ref</tt> <tt class="py-op">=</tt> <tt id="link-206" 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-206', 'version', 'link-119');">version</a></tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">                <tt class="py-name">sub_feature_list</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-128');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-208" 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-208', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt class="py-name">subfeature</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">            <tt class="py-name">sub_feature_list</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-209', 'sort', 'link-209');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">            <tt id="link-210" 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-210', 'feature', 'link-163');">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 class="py-name">sub_feature</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">                                    <tt class="py-keyword">for</tt> <tt class="py-name">sub_feature</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sub_feature_list</tt><tt class="py-op">]</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">            <tt id="link-211" 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-211', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt id="link-212" 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-212', 'location', 'link-175');">location</a></tt> <tt class="py-op">=</tt> <tt id="link-213" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-213', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="Bio.SeqFeature.FeatureLocation" class="py-name" href="#" onclick="return doclink('link-214', 'FeatureLocation', 'link-177');">FeatureLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">min_start</tt><tt class="py-op">,</tt> <tt class="py-name">max_end</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">            <tt id="link-215" 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-215', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-216', 'strand', 'link-143');">strand</a></tt> <tt class="py-op">=</tt> <tt id="link-217" 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-217', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt class="py-name">sub_features</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-218" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.strand
Bio.expressions.blast.ncbiblast.strand" class="py-name" href="#" onclick="return doclink('link-218', 'strand', 'link-143');">strand</a></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">        <tt class="py-name">seq_feature_list</tt><tt class="py-op">.</tt><tt id="link-219" 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-219', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">            <tt class="py-op">(</tt><tt class="py-name">seqfeature_rank</tt><tt class="py-op">,</tt> <tt id="link-220" 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-220', 'feature', 'link-163');">feature</a></tt><tt class="py-op">.</tt><tt id="link-221" 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-221', 'location', 'link-175');">location</a></tt><tt class="py-op">.</tt><tt id="link-222" 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-222', 'start', 'link-14');">start</a></tt><tt class="py-op">.</tt><tt class="py-name">position</tt><tt class="py-op">,</tt> <tt id="link-223" 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-223', 'feature', 'link-163');">feature</a></tt><tt class="py-op">)</tt> <tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-comment"># Primary sort is on the feature's rank</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  .. then on the start position</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#  .. then arbitrary on the feature's id (SeqFeature has no __cmp__)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">seq_feature_list</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-224', 'sort', 'link-209');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line">    <tt class="py-comment"># Get just the SeqFeature</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-225" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-225', 'x', 'link-225');">x</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-226" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-226', 'x', 'link-225');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_feature_list</tt><tt class="py-op">]</tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_annotations"></a><div id="_retrieve_annotations-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="_retrieve_annotations-toggle" onclick="return toggle('_retrieve_annotations');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_annotations">_retrieve_annotations</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">,</tt> <tt class="py-param">taxon_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_annotations-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_annotations-expanded"><a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">    <tt id="link-227" 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-227', 'annotations', 'link-227');">annotations</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">    <tt id="link-228" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-228', 'annotations', 'link-227');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-229" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-229', 'update', 'link-229');">update</a></tt><tt class="py-op">(</tt><tt id="link-230" class="py-name" targets="Function BioSQL.BioSeq._retrieve_qualifier_value()=BioSQL.BioSeq-module.html#_retrieve_qualifier_value"><a title="BioSQL.BioSeq._retrieve_qualifier_value" class="py-name" href="#" onclick="return doclink('link-230', '_retrieve_qualifier_value', 'link-230');">_retrieve_qualifier_value</a></tt><tt class="py-op">(</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-231" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-231', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">    <tt id="link-232" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-232', 'annotations', 'link-227');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-233" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-233', 'update', 'link-229');">update</a></tt><tt class="py-op">(</tt><tt id="link-234" class="py-name" targets="Function BioSQL.BioSeq._retrieve_reference()=BioSQL.BioSeq-module.html#_retrieve_reference"><a title="BioSQL.BioSeq._retrieve_reference" class="py-name" href="#" onclick="return doclink('link-234', '_retrieve_reference', 'link-234');">_retrieve_reference</a></tt><tt class="py-op">(</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-235" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-235', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt id="link-236" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-236', 'annotations', 'link-227');">annotations</a></tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-237', 'update', 'link-229');">update</a></tt><tt class="py-op">(</tt><tt id="link-238" class="py-name" targets="Function BioSQL.BioSeq._retrieve_taxon()=BioSQL.BioSeq-module.html#_retrieve_taxon"><a title="BioSQL.BioSeq._retrieve_taxon" class="py-name" href="#" onclick="return doclink('link-238', '_retrieve_taxon', 'link-238');">_retrieve_taxon</a></tt><tt class="py-op">(</tt><tt class="py-name">adaptor</tt><tt class="py-op">,</tt> <tt id="link-239" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-239', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt> <tt class="py-name">taxon_id</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-240" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-240', 'annotations', 'link-227');">annotations</a></tt> </tt>
</div><a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_qualifier_value"></a><div id="_retrieve_qualifier_value-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="_retrieve_qualifier_value-toggle" onclick="return toggle('_retrieve_qualifier_value');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_qualifier_value">_retrieve_qualifier_value</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_qualifier_value-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_qualifier_value-expanded"><a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">    <tt class="py-name">qvs</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-241', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</a></tt><tt class="py-op">(</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-string">"SELECT name, value"</tt> \ </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt class="py-string">" FROM bioentry_qualifier_value JOIN term USING (term_id)"</tt> \ </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">        <tt class="py-string">" WHERE bioentry_id = %s"</tt> \ </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">        <tt class="py-string">" ORDER BY rank"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-242" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-242', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">    <tt class="py-name">qualifiers</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt id="link-243" 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-243', 'name', 'link-243');">name</a></tt><tt class="py-op">,</tt> <tt id="link-244" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-244', 'value', 'link-136');">value</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">qvs</tt><tt class="py-op">:</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-245" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-245', 'name', 'link-243');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"keyword"</tt><tt class="py-op">:</tt> <tt id="link-246" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-246', 'name', 'link-243');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"keywords"</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-247" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-247', 'name', 'link-243');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"date_changed"</tt><tt class="py-op">:</tt> <tt id="link-248" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-248', 'name', 'link-243');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"dates"</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt id="link-249" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-249', 'name', 'link-243');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"secondary_accession"</tt><tt class="py-op">:</tt> <tt id="link-250" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-250', 'name', 'link-243');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"accessions"</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line">        <tt class="py-name">qualifiers</tt><tt class="py-op">.</tt><tt id="link-251" class="py-name"><a title="Bio.Crystal.Crystal.setdefault" class="py-name" href="#" onclick="return doclink('link-251', 'setdefault', 'link-133');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-252" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-252', 'name', 'link-243');">name</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-253" 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-253', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt><tt id="link-254" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-254', 'value', 'link-136');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">qualifiers</tt> </tt>
</div><a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_reference"></a><div id="_retrieve_reference-def"><a name="L261"></a><tt class="py-lineno">261</tt> <a class="py-toggle" href="#" id="_retrieve_reference-toggle" onclick="return toggle('_retrieve_reference');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_reference">_retrieve_reference</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_reference-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_reference-expanded"><a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">    <tt class="py-comment"># XXX dbxref_qualifier_value</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"><tt class="py-comment"></tt>  </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">    <tt class="py-name">refs</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetchall" class="py-name" href="#" onclick="return doclink('link-255', 'execute_and_fetchall', 'link-94');">execute_and_fetchall</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-string">"SELECT start_pos, end_pos, "</tt> \ </tt>
<a name="L266"></a><tt class="py-lineno">266</tt>  <tt class="py-line">        <tt class="py-string">" location, title, authors,"</tt> \ </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line">        <tt class="py-string">" dbname, accession"</tt> \ </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">        <tt class="py-string">" FROM bioentry_reference"</tt> \ </tt>
<a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line">        <tt class="py-string">" JOIN reference USING (reference_id)"</tt> \ </tt>
<a name="L270"></a><tt class="py-lineno">270</tt>  <tt class="py-line">        <tt class="py-string">" LEFT JOIN dbxref USING (dbxref_id)"</tt> \ </tt>
<a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">        <tt class="py-string">" WHERE bioentry_id = %s"</tt> \ </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">        <tt class="py-string">" ORDER BY rank"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-256', 'primary_id', 'link-8');">primary_id</a></tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line">    <tt class="py-name">references</tt> <tt class="py-op">=</tt> <tt class="py-op">[</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">for</tt> <tt id="link-257" 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-257', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-258" 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-258', 'end', 'link-142');">end</a></tt><tt class="py-op">,</tt> <tt id="link-259" 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-259', 'location', 'link-175');">location</a></tt><tt class="py-op">,</tt> <tt id="link-260" 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-260', 'title', 'link-260');">title</a></tt><tt class="py-op">,</tt> <tt id="link-261" 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-261', 'authors', 'link-261');">authors</a></tt><tt class="py-op">,</tt> <tt class="py-name">dbname</tt><tt class="py-op">,</tt> <tt id="link-262" 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-262', 'accession', 'link-118');">accession</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">refs</tt><tt class="py-op">:</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">        <tt id="link-263" 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-263', 'reference', 'link-263');">reference</a></tt> <tt class="py-op">=</tt> <tt id="link-264" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-264', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-265" class="py-name" targets="Class Bio.GenBank.Record.Reference=Bio.GenBank.Record.Reference-class.html,Class Bio.Prosite.Prodoc.Reference=Bio.Prosite.Prodoc.Reference-class.html,Class Bio.SeqFeature.Reference=Bio.SeqFeature.Reference-class.html,Class Bio.SwissProt.SProt.Reference=Bio.SwissProt.SProt.Reference-class.html"><a title="Bio.GenBank.Record.Reference
Bio.Prosite.Prodoc.Reference
Bio.SeqFeature.Reference
Bio.SwissProt.SProt.Reference" class="py-name" href="#" onclick="return doclink('link-265', 'Reference', 'link-265');">Reference</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-266" 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-266', 'start', 'link-14');">start</a></tt><tt class="py-op">:</tt> <tt id="link-267" 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-267', 'start', 'link-14');">start</a></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 id="link-268" 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-268', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-269" 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-269', 'location', 'link-175');">location</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-270" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-270', 'SeqFeature', 'link-7');">SeqFeature</a></tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.SeqFeature.FeatureLocation" class="py-name" href="#" onclick="return doclink('link-271', 'FeatureLocation', 'link-177');">FeatureLocation</a></tt><tt class="py-op">(</tt><tt id="link-272" 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-272', 'start', 'link-14');">start</a></tt><tt class="py-op">,</tt> <tt id="link-273" 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-273', 'end', 'link-142');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line">        <tt id="link-274" 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-274', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-275', 'authors', 'link-261');">authors</a></tt> <tt class="py-op">=</tt> <tt id="link-276" class="py-name"><a title="Bio.GenBank._FeatureConsumer.authors
Bio.GenBank._RecordConsumer.authors" class="py-name" href="#" onclick="return doclink('link-276', 'authors', 'link-261');">authors</a></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">        <tt class="py-comment">#Don't replace the default "" with None.</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt id="link-277" 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-277', 'title', 'link-260');">title</a></tt> <tt class="py-op">:</tt> <tt id="link-278" 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-278', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-279" 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-279', 'title', 'link-260');">title</a></tt> <tt class="py-op">=</tt> <tt id="link-280" 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-280', 'title', 'link-260');">title</a></tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">        <tt id="link-281" 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-281', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-282" 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-282', 'journal', 'link-282');">journal</a></tt> <tt class="py-op">=</tt> <tt id="link-283" 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-283', 'location', 'link-175');">location</a></tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dbname</tt> <tt class="py-op">==</tt> <tt class="py-string">'PUBMED'</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">            <tt id="link-284" 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-284', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-285" 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-285', 'pubmed_id', 'link-285');">pubmed_id</a></tt> <tt class="py-op">=</tt> <tt id="link-286" 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-286', 'accession', 'link-118');">accession</a></tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">dbname</tt> <tt class="py-op">==</tt> <tt class="py-string">'MEDLINE'</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">            <tt id="link-287" 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-287', 'reference', 'link-263');">reference</a></tt><tt class="py-op">.</tt><tt id="link-288" 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-288', 'medline_id', 'link-288');">medline_id</a></tt> <tt class="py-op">=</tt> <tt id="link-289" 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-289', 'accession', 'link-118');">accession</a></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">        <tt class="py-name">references</tt><tt class="py-op">.</tt><tt id="link-290" 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-290', 'append', 'link-128');">append</a></tt><tt class="py-op">(</tt><tt id="link-291" 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-291', 'reference', 'link-263');">reference</a></tt><tt class="py-op">)</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">{</tt><tt class="py-string">'references'</tt><tt class="py-op">:</tt> <tt class="py-name">references</tt><tt class="py-op">}</tt> </tt>
</div><a name="L288"></a><tt class="py-lineno">288</tt>  <tt class="py-line"> </tt>
<a name="_retrieve_taxon"></a><div id="_retrieve_taxon-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="_retrieve_taxon-toggle" onclick="return toggle('_retrieve_taxon');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq-module.html#_retrieve_taxon">_retrieve_taxon</a><tt class="py-op">(</tt><tt class="py-param">adaptor</tt><tt class="py-op">,</tt> <tt class="py-param">primary_id</tt><tt class="py-op">,</tt> <tt class="py-param">taxon_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_retrieve_taxon-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_retrieve_taxon-expanded"><a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">    <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">    <tt class="py-name">common_names</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-292" 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-292', 'execute_and_fetch_col0', 'link-292');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">        <tt class="py-string">"SELECT name FROM taxon_name WHERE taxon_id = %s"</tt> \ </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">        <tt class="py-string">" AND name_class = 'genbank common 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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">common_names</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">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-name">common_names</tt><tt class="py-op">[</tt><tt class="py-number">0</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">scientific_names</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-293', 'execute_and_fetch_col0', 'link-292');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">        <tt class="py-string">"SELECT name FROM taxon_name WHERE taxon_id = %s"</tt> \ </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">        <tt class="py-string">" AND name_class = '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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">scientific_names</tt><tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">        <tt class="py-name">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-name">scientific_names</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">    <tt class="py-name">ncbi_taxids</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_and_fetch_col0" class="py-name" href="#" onclick="return doclink('link-294', 'execute_and_fetch_col0', 'link-292');">execute_and_fetch_col0</a></tt><tt class="py-op">(</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt>  <tt class="py-line">        <tt class="py-string">"SELECT ncbi_taxon_id FROM taxon WHERE taxon_id = %s"</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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">ncbi_taxids</tt> <tt class="py-keyword">and</tt> <tt class="py-name">ncbi_taxids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">ncbi_taxids</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-string">"0"</tt><tt class="py-op">:</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt>  <tt class="py-line">        <tt class="py-name">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-name">ncbi_taxids</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line"> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt>  <tt class="py-line">    <tt class="py-comment">#Old code used the left/right values in the taxon table to get the</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#taxonomy lineage in one SQL command.  This was actually very slow,</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#and would fail if the (optional) left/right values were missing.</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#The following code is based on a contribution from Eric Gibert, and</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#relies on the taxon table's parent_taxon_id field only (ignoring the</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#optional left/right values).  This means that it has to make a</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#separate SQL query for each entry in the lineage, but it does still</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#appear to be *much* faster.  See Bug 2494. </tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-295" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.taxonomy()=Bio.GenBank._FeatureConsumer-class.html#taxonomy,Method Bio.GenBank._RecordConsumer.taxonomy()=Bio.GenBank._RecordConsumer-class.html#taxonomy,Variable Bio.expressions.genbank.taxonomy=Bio.expressions.genbank-module.html#taxonomy"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-295', 'taxonomy', 'link-295');">taxonomy</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">taxon_id</tt> <tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line">        <tt id="link-296" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-296', 'name', 'link-243');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">rank</tt><tt class="py-op">,</tt> <tt class="py-name">parent_taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">adaptor</tt><tt class="py-op">.</tt><tt id="link-297" 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-297', 'execute_one', 'link-297');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line">        <tt class="py-string">"SELECT taxon_name.name, taxon.node_rank, taxon.parent_taxon_id"</tt> \ </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line">        <tt class="py-string">" FROM taxon, taxon_name"</tt> \ </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line">        <tt class="py-string">" WHERE taxon.taxon_id=taxon_name.taxon_id"</tt> \ </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line">        <tt class="py-string">" AND taxon_name.name_class='scientific name'"</tt> \ </tt>
<a name="L322"></a><tt class="py-lineno">322</tt>  <tt class="py-line">        <tt class="py-string">" AND taxon.taxon_id = %s"</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-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">taxon_id</tt> <tt class="py-op">==</tt> <tt class="py-name">parent_taxon_id</tt> <tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line">            <tt class="py-comment"># If the taxon table has been populated by the BioSQL script</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># load_ncbi_taxonomy.pl this is how top parent nodes are stored.</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-comment"># Personally, I would have used a NULL parent_taxon_id here.</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt class="py-keyword">break</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">rank</tt> <tt class="py-op">&lt;&gt;</tt> <tt class="py-string">"no rank"</tt> <tt class="py-op">:</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">            <tt class="py-comment">#For consistency with older versions of Biopython, we are only</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">#interested in taxonomy entries with a stated rank.</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">#Add this to the start of the lineage list.</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line"><tt class="py-comment"></tt>            <tt id="link-298" class="py-name"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-298', 'taxonomy', 'link-295');">taxonomy</a></tt><tt class="py-op">.</tt><tt id="link-299" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-299', 'insert', 'link-299');">insert</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-300" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-300', 'name', 'link-243');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">        <tt class="py-name">taxon_id</tt> <tt class="py-op">=</tt> <tt class="py-name">parent_taxon_id</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line"> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-301" class="py-name"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-301', 'taxonomy', 'link-295');">taxonomy</a></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">a</tt><tt class="py-op">[</tt><tt class="py-string">'taxonomy'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-302" class="py-name"><a title="Bio.GenBank._FeatureConsumer.taxonomy
Bio.GenBank._RecordConsumer.taxonomy
Bio.expressions.genbank.taxonomy" class="py-name" href="#" onclick="return doclink('link-302', 'taxonomy', 'link-295');">taxonomy</a></tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">a</tt> </tt>
</div><a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord"></a><div id="DBSeqRecord-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="DBSeqRecord-toggle" onclick="return toggle('DBSeqRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html">DBSeqRecord</a><tt class="py-op">(</tt><tt class="py-base-class">SeqRecord</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBSeqRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DBSeqRecord-expanded"><a name="L340"></a><tt class="py-lineno">340</tt>  <tt class="py-line">    <tt class="py-docstring">"""BioSQL equivalent of the biopython SeqRecord object.</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord.__init__"></a><div id="DBSeqRecord.__init__-def"><a name="L343"></a><tt class="py-lineno">343</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__init__-toggle" onclick="return toggle('DBSeqRecord.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-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">primary_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DBSeqRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeqRecord.__init__-expanded"><a name="L344"></a><tt class="py-lineno">344</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="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt> <tt class="py-op">=</tt> <tt id="link-303" class="py-name"><a title="Bio.expressions.swissprot.sprot38.primary_id" class="py-name" href="#" onclick="return doclink('link-303', 'primary_id', 'link-8');">primary_id</a></tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line"> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line">        <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_biodatabase_id</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</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-304" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-304', 'name', 'link-243');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt>  <tt class="py-line">         <tt id="link-305" 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-305', 'accession', 'link-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-306" 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-306', 'version', 'link-119');">version</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_identifier</tt><tt class="py-op">,</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">         <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_division</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-307" 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-307', 'description', 'link-307');">description</a></tt><tt class="py-op">)</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-308" class="py-name"><a title="BioSQL.BioSeqDatabase.Adaptor.execute_one" class="py-name" href="#" onclick="return doclink('link-308', 'execute_one', 'link-297');">execute_one</a></tt><tt class="py-op">(</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">            <tt class="py-string">"SELECT biodatabase_id, taxon_id, name, accession, version,"</tt> \ </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">            <tt class="py-string">" identifier, division, description"</tt> \ </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">            <tt class="py-string">" FROM bioentry"</tt> \ </tt>
<a name="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">            <tt class="py-string">" WHERE bioentry_id = %s"</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt><tt class="py-op">,</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-309" 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-309', 'version', 'link-119');">version</a></tt> <tt class="py-keyword">and</tt> <tt id="link-310" 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-310', 'version', 'link-119');">version</a></tt> <tt class="py-op">!=</tt> <tt class="py-string">"0"</tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-311" 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-311', 'id', 'link-311');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"%s.%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-312" 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-312', 'accession', 'link-118');">accession</a></tt><tt class="py-op">,</tt> <tt id="link-313" 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-313', 'version', 'link-119');">version</a></tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</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 id="link-314" 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-314', 'id', 'link-311');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-315" 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-315', 'accession', 'link-118');">accession</a></tt> </tt>
</div><a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord.__get_seq"></a><div id="DBSeqRecord.__get_seq-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__get_seq-toggle" onclick="return toggle('DBSeqRecord.__get_seq');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_seq">__get_seq</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="DBSeqRecord.__get_seq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeqRecord.__get_seq-expanded"><a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"_seq"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt> <tt class="py-op">=</tt> <tt id="link-316" class="py-name" targets="Function BioSQL.BioSeq._retrieve_seq()=BioSQL.BioSeq-module.html#_retrieve_seq"><a title="BioSQL.BioSeq._retrieve_seq" class="py-name" href="#" onclick="return doclink('link-316', '_retrieve_seq', 'link-316');">_retrieve_seq</a></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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt><tt class="py-op">)</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</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">_seq</tt> </tt>
</div><a name="DBSeqRecord.__set_seq"></a><div id="DBSeqRecord.__set_seq-def"><a name="L363"></a><tt class="py-lineno">363</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__set_seq-toggle" onclick="return toggle('DBSeqRecord.__set_seq');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_seq">__set_seq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt> <tt class="py-op">=</tt> <tt id="link-317" 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-317', 'seq', 'link-109');">seq</a></tt> </tt>
</div><a name="DBSeqRecord.__del_seq"></a><div id="DBSeqRecord.__del_seq-def"><a name="L364"></a><tt class="py-lineno">364</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__del_seq-toggle" onclick="return toggle('DBSeqRecord.__del_seq');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_seq">__del_seq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>      <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt> </tt>
</div><a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">    <tt id="link-318" 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-318', 'seq', 'link-109');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-319" class="py-name"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-319', 'property', 'link-92');">property</a></tt><tt class="py-op">(</tt><tt id="link-320" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__get_seq()=BioSQL.BioSeq.DBSeqRecord-class.html#__get_seq"><a title="BioSQL.BioSeq.DBSeqRecord.__get_seq" class="py-name" href="#" onclick="return doclink('link-320', '__get_seq', 'link-320');">__get_seq</a></tt><tt class="py-op">,</tt> <tt id="link-321" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__set_seq()=BioSQL.BioSeq.DBSeqRecord-class.html#__set_seq"><a title="BioSQL.BioSeq.DBSeqRecord.__set_seq" class="py-name" href="#" onclick="return doclink('link-321', '__set_seq', 'link-321');">__set_seq</a></tt><tt class="py-op">,</tt> <tt id="link-322" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__del_seq()=BioSQL.BioSeq.DBSeqRecord-class.html#__del_seq"><a title="BioSQL.BioSeq.DBSeqRecord.__del_seq" class="py-name" href="#" onclick="return doclink('link-322', '__del_seq', 'link-322');">__del_seq</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Seq object"</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord.__get_dbxrefs"></a><div id="DBSeqRecord.__get_dbxrefs-def"><a name="L367"></a><tt class="py-lineno">367</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__get_dbxrefs-toggle" onclick="return toggle('DBSeqRecord.__get_dbxrefs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_dbxrefs">__get_dbxrefs</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="DBSeqRecord.__get_dbxrefs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeqRecord.__get_dbxrefs-expanded"><a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-string">"_dbxrefs"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_dbxrefs</tt> <tt class="py-op">=</tt> <tt id="link-323" class="py-name" targets="Function BioSQL.BioSeq._retrieve_dbxrefs()=BioSQL.BioSeq-module.html#_retrieve_dbxrefs"><a title="BioSQL.BioSeq._retrieve_dbxrefs" class="py-name" href="#" onclick="return doclink('link-323', '_retrieve_dbxrefs', 'link-323');">_retrieve_dbxrefs</a></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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt><tt class="py-op">)</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</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">_dbxrefs</tt> </tt>
</div><a name="DBSeqRecord.__set_dbxrefs"></a><div id="DBSeqRecord.__set_dbxrefs-def"><a name="L371"></a><tt class="py-lineno">371</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__set_dbxrefs-toggle" onclick="return toggle('DBSeqRecord.__set_dbxrefs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_dbxrefs">__set_dbxrefs</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-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_dbxrefs</tt> <tt class="py-op">=</tt> <tt id="link-324" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-324', 'dbxrefs', 'link-115');">dbxrefs</a></tt> </tt>
</div><a name="DBSeqRecord.__del_dbxrefs"></a><div id="DBSeqRecord.__del_dbxrefs-def"><a name="L372"></a><tt class="py-lineno">372</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__del_dbxrefs-toggle" onclick="return toggle('DBSeqRecord.__del_dbxrefs');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_dbxrefs">__del_dbxrefs</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>      <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_dbxrefs</tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">    <tt id="link-325" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-325', 'dbxrefs', 'link-115');">dbxrefs</a></tt> <tt class="py-op">=</tt> <tt id="link-326" class="py-name"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-326', 'property', 'link-92');">property</a></tt><tt class="py-op">(</tt><tt id="link-327" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__get_dbxrefs()=BioSQL.BioSeq.DBSeqRecord-class.html#__get_dbxrefs"><a title="BioSQL.BioSeq.DBSeqRecord.__get_dbxrefs" class="py-name" href="#" onclick="return doclink('link-327', '__get_dbxrefs', 'link-327');">__get_dbxrefs</a></tt><tt class="py-op">,</tt> <tt id="link-328" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__set_dbxrefs()=BioSQL.BioSeq.DBSeqRecord-class.html#__set_dbxrefs"><a title="BioSQL.BioSeq.DBSeqRecord.__set_dbxrefs" class="py-name" href="#" onclick="return doclink('link-328', '__set_dbxrefs', 'link-328');">__set_dbxrefs</a></tt><tt class="py-op">,</tt> <tt id="link-329" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__del_dbxrefs()=BioSQL.BioSeq.DBSeqRecord-class.html#__del_dbxrefs"><a title="BioSQL.BioSeq.DBSeqRecord.__del_dbxrefs" class="py-name" href="#" onclick="return doclink('link-329', '__del_dbxrefs', 'link-329');">__del_dbxrefs</a></tt><tt class="py-op">,</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">                       <tt class="py-string">"Database cross references"</tt><tt class="py-op">)</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord.__get_features"></a><div id="DBSeqRecord.__get_features-def"><a name="L376"></a><tt class="py-lineno">376</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__get_features-toggle" onclick="return toggle('DBSeqRecord.__get_features');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_features">__get_features</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="DBSeqRecord.__get_features-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeqRecord.__get_features-expanded"><a name="L377"></a><tt class="py-lineno">377</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"_features"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_features</tt> <tt class="py-op">=</tt> <tt id="link-330" class="py-name" targets="Function BioSQL.BioSeq._retrieve_features()=BioSQL.BioSeq-module.html#_retrieve_features"><a title="BioSQL.BioSeq._retrieve_features" class="py-name" href="#" onclick="return doclink('link-330', '_retrieve_features', 'link-330');">_retrieve_features</a></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>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">                                                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt><tt class="py-op">)</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</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">_features</tt> </tt>
</div><a name="DBSeqRecord.__set_features"></a><div id="DBSeqRecord.__set_features-def"><a name="L381"></a><tt class="py-lineno">381</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__set_features-toggle" onclick="return toggle('DBSeqRecord.__set_features');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_features">__set_features</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">features</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_features</tt> <tt class="py-op">=</tt> <tt id="link-331" 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-331', 'features', 'link-331');">features</a></tt> </tt>
</div><a name="DBSeqRecord.__del_features"></a><div id="DBSeqRecord.__del_features-def"><a name="L382"></a><tt class="py-lineno">382</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__del_features-toggle" onclick="return toggle('DBSeqRecord.__del_features');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_features">__del_features</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>      <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_features</tt> </tt>
</div><a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">    <tt id="link-332" 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-332', 'features', 'link-331');">features</a></tt> <tt class="py-op">=</tt> <tt id="link-333" class="py-name"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-333', 'property', 'link-92');">property</a></tt><tt class="py-op">(</tt><tt id="link-334" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__get_features()=BioSQL.BioSeq.DBSeqRecord-class.html#__get_features"><a title="BioSQL.BioSeq.DBSeqRecord.__get_features" class="py-name" href="#" onclick="return doclink('link-334', '__get_features', 'link-334');">__get_features</a></tt><tt class="py-op">,</tt> <tt id="link-335" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__set_features()=BioSQL.BioSeq.DBSeqRecord-class.html#__set_features"><a title="BioSQL.BioSeq.DBSeqRecord.__set_features" class="py-name" href="#" onclick="return doclink('link-335', '__set_features', 'link-335');">__set_features</a></tt><tt class="py-op">,</tt> <tt id="link-336" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__del_features()=BioSQL.BioSeq.DBSeqRecord-class.html#__del_features"><a title="BioSQL.BioSeq.DBSeqRecord.__del_features" class="py-name" href="#" onclick="return doclink('link-336', '__del_features', 'link-336');">__del_features</a></tt><tt class="py-op">,</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">                        <tt class="py-string">"Features"</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line"> </tt>
<a name="DBSeqRecord.__get_annotations"></a><div id="DBSeqRecord.__get_annotations-def"><a name="L386"></a><tt class="py-lineno">386</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__get_annotations-toggle" onclick="return toggle('DBSeqRecord.__get_annotations');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_annotations">__get_annotations</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="DBSeqRecord.__get_annotations-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DBSeqRecord.__get_annotations-expanded"><a name="L387"></a><tt class="py-lineno">387</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">"_annotations"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt> <tt class="py-op">=</tt> <tt id="link-337" class="py-name" targets="Function BioSQL.BioSeq._retrieve_annotations()=BioSQL.BioSeq-module.html#_retrieve_annotations"><a title="BioSQL.BioSeq._retrieve_annotations" class="py-name" href="#" onclick="return doclink('link-337', '_retrieve_annotations', 'link-337');">_retrieve_annotations</a></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>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">                                                      <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_primary_id</tt><tt class="py-op">,</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">                                                      <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_taxon_id</tt><tt class="py-op">)</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_identifier</tt><tt class="py-op">:</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt><tt class="py-op">[</tt><tt class="py-string">"gi"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_identifier</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_division</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line">                <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt><tt class="py-op">[</tt><tt class="py-string">"data_file_division"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_division</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</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">_annotations</tt> </tt>
</div><a name="DBSeqRecord.__set_annotations"></a><div id="DBSeqRecord.__set_annotations-def"><a name="L396"></a><tt class="py-lineno">396</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__set_annotations-toggle" onclick="return toggle('DBSeqRecord.__set_annotations');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_annotations">__set_annotations</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">annotations</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt> <tt class="py-op">=</tt> <tt id="link-338" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-338', 'annotations', 'link-227');">annotations</a></tt> </tt>
</div><a name="DBSeqRecord.__del_annotations"></a><div id="DBSeqRecord.__del_annotations-def"><a name="L397"></a><tt class="py-lineno">397</tt> <a class="py-toggle" href="#" id="DBSeqRecord.__del_annotations-toggle" onclick="return toggle('DBSeqRecord.__del_annotations');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_annotations">__del_annotations</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt> </tt>
</div><a name="L398"></a><tt class="py-lineno">398</tt>  <tt class="py-line">    <tt id="link-339" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-339', 'annotations', 'link-227');">annotations</a></tt> <tt class="py-op">=</tt> <tt id="link-340" class="py-name"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-340', 'property', 'link-92');">property</a></tt><tt class="py-op">(</tt><tt id="link-341" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__get_annotations()=BioSQL.BioSeq.DBSeqRecord-class.html#__get_annotations"><a title="BioSQL.BioSeq.DBSeqRecord.__get_annotations" class="py-name" href="#" onclick="return doclink('link-341', '__get_annotations', 'link-341');">__get_annotations</a></tt><tt class="py-op">,</tt> <tt id="link-342" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__set_annotations()=BioSQL.BioSeq.DBSeqRecord-class.html#__set_annotations"><a title="BioSQL.BioSeq.DBSeqRecord.__set_annotations" class="py-name" href="#" onclick="return doclink('link-342', '__set_annotations', 'link-342');">__set_annotations</a></tt><tt class="py-op">,</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt>  <tt class="py-line">                           <tt id="link-343" class="py-name" targets="Method BioSQL.BioSeq.DBSeqRecord.__del_annotations()=BioSQL.BioSeq.DBSeqRecord-class.html#__del_annotations"><a title="BioSQL.BioSeq.DBSeqRecord.__del_annotations" class="py-name" href="#" onclick="return doclink('link-343', '__del_annotations', 'link-343');">__del_annotations</a></tt><tt class="py-op">,</tt> <tt class="py-string">"Annotations"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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