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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        Module&nbsp;SeqRecord
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<h1 class="epydoc">Source Code for <a href="Bio.SeqRecord-module.html">Module Bio.SeqRecord</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Stores data about the sequence</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># NEEDS TO BE SYNCH WITH THE REST OF BIOPYTHON AND BIOPERL</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"># In particular, the SeqRecord and BioSQL.BioSeq.DBSeqRecord classes</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"># need to be in sync (this is the BioSQL "Database SeqRecord", see</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"># also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="SeqRecord"></a><div id="SeqRecord-def"><a name="L8"></a><tt class="py-lineno">  8</tt> <a class="py-toggle" href="#" id="SeqRecord-toggle" onclick="return toggle('SeqRecord');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-class.html">SeqRecord</a><tt class="py-op">:</tt> </tt>
</div><div id="SeqRecord-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SeqRecord-expanded"><a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line">    <tt class="py-docstring">"""A SeqRecord object holds a sequence and information about it.</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">    Main attributes:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">    id          - Identifier such as a locus tag (string)</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-docstring">    seq         - The sequence itself (Seq object)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-docstring">    Additional attributes:</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-docstring">    name        - Sequence name, e.g. gene name (string)</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-docstring">    description - Additional text (string)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-docstring">    dbxrefs     - List of database cross references (list of strings)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-docstring">    features    - Any (sub)features defined (list of SeqFeature objects)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-docstring">    annotations - Further information about the whole sequence (dictionary)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-docstring">                  Most entries are lists of strings.</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="SeqRecord.__init__"></a><div id="SeqRecord.__init__-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="SeqRecord.__init__-toggle" onclick="return toggle('SeqRecord.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-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">seq</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt> <tt class="py-op">=</tt> <tt class="py-string">"&lt;unknown id&gt;"</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt> <tt class="py-op">=</tt> <tt class="py-string">"&lt;unknown name&gt;"</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">                 <tt class="py-param">description</tt> <tt class="py-op">=</tt> <tt class="py-string">"&lt;unknown description&gt;"</tt><tt class="py-op">,</tt> <tt class="py-param">dbxrefs</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">                 <tt class="py-param">features</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SeqRecord.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqRecord.__init__-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-docstring">"""Create a SeqRecord.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">        Arguments:</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">        seq         - Sequence, required (Seq object)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring">        id          - Sequence identifier, recommended (string)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">        name        - Sequence name, optional (string)</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-docstring">        description - Sequence description, optional (string)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-docstring">        dbxrefs     - Database cross references, optional (list of strings)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-docstring">        features    - Any (sub)features, optional (list of SeqFeature objects)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-docstring">        Note that while an id is optional, we strongly recommend you supply a</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt class="py-docstring">        unique id string for each record.  This is especially important</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"><tt class="py-docstring">        if you wish to write your sequences to a file.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">        You can create a 'blank' SeqRecord object, and then populated the</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">        attributes later.  Note that currently the annotations dictionary</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">        cannot be specified when creating the SeqRecord."""</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-0" 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-0', 'seq', 'link-0');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-1" 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-1', 'seq', 'link-0');">seq</a></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-2" 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-2', 'id', 'link-2');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-3" 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-3', 'id', 'link-2');">id</a></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-4" 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-4', 'name', 'link-4');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-4');">name</a></tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" 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-6', 'description', 'link-6');">description</a></tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-7', 'description', 'link-6');">description</a></tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt id="link-8" 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-8', 'dbxrefs', 'link-8');">dbxrefs</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">            <tt id="link-9" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-9', 'dbxrefs', 'link-8');">dbxrefs</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-10', 'dbxrefs', 'link-8');">dbxrefs</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-11', 'dbxrefs', 'link-8');">dbxrefs</a></tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-comment"># annotations about the whole sequence</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'annotations', 'link-12');">annotations</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">         </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">        <tt class="py-comment"># annotations about parts of the sequence</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-keyword">if</tt> <tt id="link-13" 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-13', 'features', 'link-13');">features</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">            <tt id="link-14" 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-14', 'features', 'link-13');">features</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" 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-15', 'features', 'link-13');">features</a></tt> <tt class="py-op">=</tt> <tt id="link-16" 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-16', 'features', 'link-13');">features</a></tt> </tt>
</div><a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"> </tt>
<a name="SeqRecord.__str__"></a><div id="SeqRecord.__str__-def"><a name="L58"></a><tt class="py-lineno"> 58</tt> <a class="py-toggle" href="#" id="SeqRecord.__str__-toggle" onclick="return toggle('SeqRecord.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-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="SeqRecord.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqRecord.__str__-expanded"><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-docstring">"""A human readable summary of the record and its annotation."""</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'id', 'link-2');">id</a></tt> <tt class="py-op">:</tt> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-18" 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-18', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"ID: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-19', 'id', 'link-2');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-4');">name</a></tt> <tt class="py-op">:</tt> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"Name: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-23', 'description', 'link-6');">description</a></tt> <tt class="py-op">:</tt> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-24" 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-24', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"Description: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-25', 'description', 'link-6');">description</a></tt><tt class="py-op">)</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-26', 'dbxrefs', 'link-8');">dbxrefs</a></tt> <tt class="py-op">:</tt> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"Database cross-references: "</tt> \ </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">                                       <tt class="py-op">+</tt> <tt class="py-string">", "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-28', 'dbxrefs', 'link-8');">dbxrefs</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-29', 'annotations', 'link-12');">annotations</a></tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">            <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'append', 'link-18');">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">a</tt><tt class="py-op">,</tt> <tt class="py-name">str</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="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-31', 'annotations', 'link-12');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-name">a</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-comment">#Don't want to include the entire sequence,</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment">#and showing the alphabet is useful:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'append', 'link-18');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" 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-33', 'seq', 'link-0');">seq</a></tt><tt class="py-op">)</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">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="SeqRecord.__repr__"></a><div id="SeqRecord.__repr__-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="SeqRecord.__repr__-toggle" onclick="return toggle('SeqRecord.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-class.html#__repr__">__repr__</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="SeqRecord.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqRecord.__repr__-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-docstring">"""A concise summary of the record for debugging."""</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> \ </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">         <tt class="py-op">+</tt> <tt class="py-string">"(seq=%s, id=%s, name=%s, description=%s, dbxrefs=%s)"</tt> \ </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">         <tt class="py-op">%</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-34', 'map', 'link-34');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">repr</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-35" 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-35', 'seq', 'link-0');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'id', 'link-2');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-37', 'name', 'link-4');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">                            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-38', 'description', 'link-6');">description</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-39', 'dbxrefs', 'link-8');">dbxrefs</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">     </tt>
<a name="SeqRecord.__len__"></a><div id="SeqRecord.__len__-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="SeqRecord.__len__-toggle" onclick="return toggle('SeqRecord.__len__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-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="SeqRecord.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqRecord.__len__-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns the length of the sequence."""</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'seq', 'link-0');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"> </tt>
<a name="SeqRecord.__nonzero__"></a><div id="SeqRecord.__nonzero__-def"><a name="L84"></a><tt class="py-lineno"> 84</tt> <a class="py-toggle" href="#" id="SeqRecord.__nonzero__-toggle" onclick="return toggle('SeqRecord.__nonzero__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqRecord.SeqRecord-class.html#__nonzero__">__nonzero__</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="SeqRecord.__nonzero__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SeqRecord.__nonzero__-expanded"><a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">        <tt class="py-docstring">"""Returns True regardless of the length of the sequence.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"><tt class="py-docstring">        This behaviour is for backwards compatibility, since until the</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"><tt class="py-docstring">        __len__ method was added, a SeqRecord always evaluated as True.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"><tt class="py-docstring">        Note that in comparison, a Seq object will evaluate to False if it</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring">        has a zero length sequence.</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">        WARNING: The SeqRecord may in future evaluate to False when its</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">        sequence is of zero length (in order to better match the Seq</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">        object behaviour)!</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-41" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-41', 'True', 'link-41');">True</a></tt> </tt>
</div></div><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt> <tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">    <tt class="py-comment">#The following is a very quick example of how to create a SeqRecord object</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-keyword">from</tt> <tt id="link-42" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-42', 'Bio', 'link-42');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-43" 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-43', 'Seq', 'link-43');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-44" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-44', 'Seq', 'link-43');">Seq</a></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-45" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-45', 'Bio', 'link-42');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-46" 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-46', 'Alphabet', 'link-46');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-47" class="py-name" targets="Variable Bio.Alphabet.generic_protein=Bio.Alphabet-module.html#generic_protein"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-47', 'generic_protein', 'link-47');">generic_protein</a></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">    <tt id="link-48" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-48', 'record', 'link-48');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-49" 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-49', 'SeqRecord', 'link-49');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-50', 'Seq', 'link-43');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKAT"</tt> \ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                          <tt class="py-op">+</tt><tt class="py-string">"GEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQ"</tt> \ </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">                          <tt class="py-op">+</tt><tt class="py-string">"SGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQ"</tt> \ </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">                          <tt class="py-op">+</tt><tt class="py-string">"PQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF"</tt><tt class="py-op">,</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                           <tt id="link-51" class="py-name"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-51', 'generic_protein', 'link-47');">generic_protein</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">                       <tt id="link-52" 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-52', 'id', 'link-2');">id</a></tt><tt class="py-op">=</tt><tt class="py-string">"NP_418483.1"</tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-53', 'name', 'link-4');">name</a></tt><tt class="py-op">=</tt><tt class="py-string">"b4059"</tt><tt class="py-op">,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                       <tt id="link-54" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-54', 'description', 'link-6');">description</a></tt><tt class="py-op">=</tt><tt class="py-string">"ssDNA-binding protein"</tt><tt class="py-op">,</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">                       <tt id="link-55" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-55', 'dbxrefs', 'link-8');">dbxrefs</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-string">"ASAP:13298"</tt><tt class="py-op">,</tt> <tt class="py-string">"GI:16131885"</tt><tt class="py-op">,</tt> <tt class="py-string">"GeneID:948570"</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>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">    <tt class="py-comment">#Note that annotations must be added AFTER creating the record</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-56" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-56', 'record', 'link-48');">record</a></tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-57', 'annotations', 'link-12');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"note"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"This annotation was added later"</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-58', 'record', 'link-48');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-59', 'record', 'link-48');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-number">178</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-60', 'record', 'link-48');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">    <tt class="py-comment">#One way to create a minimal record.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt id="link-61" class="py-name" targets="Variable Martel.test.test_swissprot38.record2=Martel.test.test_swissprot38-module.html#record2"><a title="Martel.test.test_swissprot38.record2" class="py-name" href="#" onclick="return doclink('link-61', 'record2', 'link-61');">record2</a></tt> <tt class="py-op">=</tt> <tt id="link-62" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-62', 'SeqRecord', 'link-49');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-63" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-63', 'Seq', 'link-43');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt id="link-64" class="py-name"><a title="Martel.test.test_swissprot38.record2" class="py-name" href="#" onclick="return doclink('link-64', 'record2', 'link-61');">record2</a></tt> <tt class="py-comment">#True eeven though length is zero</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Martel.test.test_swissprot38.record2" class="py-name" href="#" onclick="return doclink('link-65', 'record2', 'link-61');">record2</a></tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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