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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignIO-module.html">Package AlignIO</a> ::
Module StockholmIO
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<h1 class="epydoc">Source Code for <a href="Bio.AlignIO.StockholmIO-module.html">Module Bio.AlignIO.StockholmIO</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 2006-2008 by Peter Cock. 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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</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"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</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="Package Bio.Align=Bio.Align-module.html"><a title="Bio.Align" class="py-name" href="#" onclick="return doclink('link-1', 'Align', 'link-1');">Align</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Align.Generic=Bio.Align.Generic-module.html"><a title="Bio.Align.Generic" class="py-name" href="#" onclick="return doclink('link-2', 'Generic', 'link-2');">Generic</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-3', 'Alignment', 'link-3');">Alignment</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Module Bio.AlignIO.Interfaces=Bio.AlignIO.Interfaces-module.html,Module Bio.SeqIO.Interfaces=Bio.SeqIO.Interfaces-module.html"><a title="Bio.AlignIO.Interfaces
Bio.SeqIO.Interfaces" class="py-name" href="#" onclick="return doclink('link-4', 'Interfaces', 'link-4');">Interfaces</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.AlignIO.Interfaces.AlignmentIterator=Bio.AlignIO.Interfaces.AlignmentIterator-class.html"><a title="Bio.AlignIO.Interfaces.AlignmentIterator" class="py-name" href="#" onclick="return doclink('link-5', 'AlignmentIterator', 'link-5');">AlignmentIterator</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Class Bio.AlignIO.Interfaces.SequentialAlignmentWriter=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html"><a title="Bio.AlignIO.Interfaces.SequentialAlignmentWriter" class="py-name" href="#" onclick="return doclink('link-6', 'SequentialAlignmentWriter', 'link-6');">SequentialAlignmentWriter</a></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="StockholmWriter"></a><div id="StockholmWriter-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="StockholmWriter-toggle" onclick="return toggle('StockholmWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html">StockholmWriter</a><tt class="py-op">(</tt><tt class="py-base-class">SequentialAlignmentWriter</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StockholmWriter-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> <tt class="py-docstring">"""Stockholm/PFAM alignment writer."""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-comment">#These dictionaries should be kept in sync with those</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#defined in the StockholmIterator class.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-7" class="py-name" targets="Variable Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#pfam_gr_mapping,Variable Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping=Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gr_mapping,Variable Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#pfam_gr_mapping,Variable Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#pfam_gr_mapping"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-7', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"secondary_structure"</tt> <tt class="py-op">:</tt> <tt class="py-string">"SS"</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-string">"surface_accessibility"</tt> <tt class="py-op">:</tt> <tt class="py-string">"SA"</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-string">"transmembrane"</tt> <tt class="py-op">:</tt> <tt class="py-string">"TM"</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-string">"posterior_probability"</tt> <tt class="py-op">:</tt> <tt class="py-string">"PP"</tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-string">"ligand_binding"</tt> <tt class="py-op">:</tt> <tt class="py-string">"LI"</tt><tt class="py-op">,</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-string">"active_site"</tt> <tt class="py-op">:</tt> <tt class="py-string">"AS"</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-string">"intron"</tt> <tt class="py-op">:</tt> <tt class="py-string">"IN"</tt><tt class="py-op">}</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-comment">#Following dictionary deliberately does not cover AC, DE or DR</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-8" class="py-name" targets="Variable Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#pfam_gs_mapping,Variable Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping=Bio.AlignIO.StockholmIO.StockholmWriter-class.html#pfam_gs_mapping,Variable Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#pfam_gs_mapping,Variable Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#pfam_gs_mapping"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-8', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"organism"</tt> <tt class="py-op">:</tt> <tt class="py-string">"OS"</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-string">"organism_classification"</tt> <tt class="py-op">:</tt> <tt class="py-string">"OC"</tt><tt class="py-op">,</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-string">"look"</tt> <tt class="py-op">:</tt> <tt class="py-string">"LO"</tt><tt class="py-op">}</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
<a name="StockholmWriter.write_alignment"></a><div id="StockholmWriter.write_alignment-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="StockholmWriter.write_alignment-toggle" onclick="return toggle('StockholmWriter.write_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#write_alignment">write_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">alignment</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmWriter.write_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmWriter.write_alignment-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write (another) single alignment to an open file.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> Note that sequences and their annotation are recorded</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> together (rather than having a block of annotation followed</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> by a block of aligned sequences).</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-9', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_all_seqs()=Bio.Align.Generic.Alignment-class.html#get_all_seqs"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-10', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt id="link-11" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-11', 'count', 'link-11');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">records</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_length_of_sequences</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-12', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_alignment_length()=Bio.Align.Generic.Alignment-class.html#get_alignment_length"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-13', 'get_alignment_length', 'link-13');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ids_written</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-comment">#NOTE - For now, the alignment object does not hold any per column</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#or per alignment annotation - only per sequence.</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-14" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-14', 'count', 'link-11');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Must have at least one sequence"</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</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">_length_of_sequences</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Non-empty sequences are required"</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-16', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# STOCKHOLM 1.0\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-17', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-18', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GF SQ %i\n"</tt> <tt class="py-op">%</tt> <tt id="link-19" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-19', 'count', 'link-11');">count</a></tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-20" 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-20', 'record', 'link-20');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt> <tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.AlignIO.StockholmIO.StockholmWriter._write_record()=Bio.AlignIO.StockholmIO.StockholmWriter-class.html#_write_record"><a title="Bio.AlignIO.StockholmIO.StockholmWriter._write_record" class="py-name" href="#" onclick="return doclink('link-21', '_write_record', 'link-21');">_write_record</a></tt><tt class="py-op">(</tt><tt id="link-22" 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-22', 'record', 'link-20');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-23', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-24', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"//\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="StockholmWriter._write_record"></a><div id="StockholmWriter._write_record-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="StockholmWriter._write_record-toggle" onclick="return toggle('StockholmWriter._write_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmWriter-class.html#_write_record">_write_record</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StockholmWriter._write_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmWriter._write_record-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-docstring">"""Write a single SeqRecord to the file"""</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</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">_length_of_sequences</tt> <tt class="py-op"><></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-25" 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-25', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'seq', 'link-26');">seq</a></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-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Sequences must all be the same length"</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-comment">#For the case for stockholm to stockholm, try and use record.name</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">seq_name</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-27', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'id', 'link-28');">id</a></tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-29" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-29', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'name', 'link-30');">name</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"accession"</tt> <tt class="py-keyword">in</tt> <tt id="link-31" 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-31', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'annotations', 'link-32');">annotations</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 id="link-33" 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-33', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt id="link-35" 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-35', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-36', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">seq_name</tt> <tt class="py-op">=</tt> <tt id="link-37" 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-37', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-38', 'name', 'link-30');">name</a></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment">#In the Stockholm file format, spaces are not allowed in the id</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">seq_name</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_name</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"start"</tt> <tt class="py-keyword">in</tt> <tt id="link-39" 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-39', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-40', 'annotations', 'link-32');">annotations</a></tt> \ </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-string">"end"</tt> <tt class="py-keyword">in</tt> <tt id="link-41" 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-41', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-42', 'annotations', 'link-32');">annotations</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt id="link-43" class="py-name" targets="Variable Bio.DocSQL.Query.suffix=Bio.DocSQL.Query-class.html#suffix"><a title="Bio.DocSQL.Query.suffix" class="py-name" href="#" onclick="return doclink('link-43', 'suffix', 'link-43');">suffix</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">str</tt><tt class="py-op">(</tt><tt id="link-44" 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-44', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-45', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"start"</tt><tt class="py-op">]</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-name">str</tt><tt class="py-op">(</tt><tt id="link-46" 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-46', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-47', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"end"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">seq_name</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-48" class="py-name"><a title="Bio.DocSQL.Query.suffix" class="py-name" href="#" onclick="return doclink('link-48', 'suffix', 'link-43');">suffix</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op"><></tt> <tt id="link-49" class="py-name"><a title="Bio.DocSQL.Query.suffix" class="py-name" href="#" onclick="return doclink('link-49', 'suffix', 'link-43');">suffix</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">seq_name</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s/%s-%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-50" 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-50', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-51', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"start"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-52" 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-52', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-53', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"end"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">seq_name</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ids_written</tt> <tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</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">"Duplicate record identifier: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">seq_name</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_ids_written</tt><tt class="py-op">.</tt><tt id="link-54" 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-54', 'append', 'link-54');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-55', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-56', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> <tt id="link-57" 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-57', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-58" 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-58', 'seq', 'link-26');">seq</a></tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'tostring', 'link-59');">tostring</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="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-comment">#The recommended placement for GS lines (per sequence annotation)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#is above the alignment (as a header block) or just below the</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#corresponding sequence.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#The recommended placement for GR lines (per sequence per column</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#annotation such as secondary structure) is just below the</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#corresponding sequence.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#We put both just below the corresponding sequence as this allows</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#us to write the file using a single pass through the records.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment">#AC = Accession</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-string">"accession"</tt> <tt class="py-keyword">in</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-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-61', 'annotations', 'link-32');">annotations</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-62', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-63', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GS %s AC %s\n"</tt> \ </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.clean()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean,Method Bio.SeqIO.Interfaces.SequenceWriter.clean()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#clean"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-64', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt id="link-65" 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-65', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-66', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-67" 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-67', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-68" 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-68', 'id', 'link-28');">id</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-69', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-70', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GS %s AC %s\n"</tt> \ </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-71', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt id="link-72" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-72', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-73" 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-73', 'id', 'link-28');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-comment">#DE = description</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-74" 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-74', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-75" 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-75', 'description', 'link-75');">description</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</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.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-76', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-77', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GS %s DE %s\n"</tt> \ </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-78', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-79', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-80" 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-80', 'description', 'link-75');">description</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment">#DE = database links</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">xref</tt> <tt class="py-keyword">in</tt> <tt id="link-81" 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-81', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-82" 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-82', 'dbxrefs', 'link-82');">dbxrefs</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</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.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-83', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-84', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GS %s DR %s\n"</tt> \ </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</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.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-85', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">xref</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-comment">#GS/GR = other per sequence annotation</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-86" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-86', 'key', 'link-86');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-87" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-87', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-88', 'annotations', 'link-32');">annotations</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-89" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-89', 'key', 'link-86');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-90', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-91', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-92" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-92', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GS %s %s %s\n"</tt> \ </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-93', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-94', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt><tt class="py-op">[</tt><tt id="link-95" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-95', 'key', 'link-86');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-96', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-97" 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-97', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-98', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt id="link-99" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-99', 'key', 'link-86');">key</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>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-100" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-100', 'key', 'link-86');">key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-101', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</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">str</tt><tt class="py-op">(</tt><tt id="link-102" 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-102', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-103', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt id="link-104" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-104', 'key', 'link-86');">key</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-name">len</tt><tt class="py-op">(</tt><tt id="link-105" 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-105', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-106" 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-106', 'seq', 'link-26');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-107', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-108', 'write', 'link-16');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=GR %s %s %s\n"</tt> \ </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">seq_name</tt><tt class="py-op">,</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-109', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-110', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt><tt class="py-op">[</tt><tt id="link-111" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-111', 'key', 'link-86');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.clean
Bio.SeqIO.Interfaces.SequenceWriter.clean" class="py-name" href="#" onclick="return doclink('link-112', 'clean', 'link-64');">clean</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-113" 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-113', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-114', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt id="link-115" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-115', 'key', 'link-86');">key</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>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment">#Should we print a warning?</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-comment">#It doesn't follow the PFAM standards, but should we record</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#this data anyway?</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
</div></div><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt>
<a name="StockholmIterator"></a><div id="StockholmIterator-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="StockholmIterator-toggle" onclick="return toggle('StockholmIterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html">StockholmIterator</a><tt class="py-op">(</tt><tt class="py-base-class">AlignmentIterator</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StockholmIterator-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-docstring">"""Loads a Stockholm file from PFAM into Alignment objects.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> The file may contain multiple concatenated alignments, which are loaded</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> and returned incrementally.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> This parser will detect if the Stockholm file follows the PFAM</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> conventions for sequence specific meta-data (lines starting #=GS</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> and #=GR) and populates the SeqRecord fields accordingly.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> Any annotation which does not follow the PFAM conventions is currently</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> ignored.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> If an accession is provided for an entry in the meta data, IT WILL NOT</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> be used as the record.id (it will be recorded in the record's</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> annotations). This is because some files have (sub) sequences from</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> different parts of the same accession (differentiated by different</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> start-end positions).</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> Wrap-around alignments are not supported - each sequences must be on</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> a single line. However, interlaced sequences should work.</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> For more information on the file format, please see:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> http://www.bioperl.org/wiki/Stockholm_multiple_alignment_format</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> For consistency with BioPerl and EMBOSS we call this the "stockholm"</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> format.</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment">#These dictionaries should be kept in sync with those</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#defined in the PfamStockholmWriter class.</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-116" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-116', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"SS"</tt> <tt class="py-op">:</tt> <tt class="py-string">"secondary_structure"</tt><tt class="py-op">,</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-string">"SA"</tt> <tt class="py-op">:</tt> <tt class="py-string">"surface_accessibility"</tt><tt class="py-op">,</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-string">"TM"</tt> <tt class="py-op">:</tt> <tt class="py-string">"transmembrane"</tt><tt class="py-op">,</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-string">"PP"</tt> <tt class="py-op">:</tt> <tt class="py-string">"posterior_probability"</tt><tt class="py-op">,</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-string">"LI"</tt> <tt class="py-op">:</tt> <tt class="py-string">"ligand_binding"</tt><tt class="py-op">,</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-string">"AS"</tt> <tt class="py-op">:</tt> <tt class="py-string">"active_site"</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">"IN"</tt> <tt class="py-op">:</tt> <tt class="py-string">"intron"</tt><tt class="py-op">}</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-comment">#Following dictionary deliberately does not cover AC, DE or DR</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-117" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-117', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"OS"</tt> <tt class="py-op">:</tt> <tt class="py-string">"organism"</tt><tt class="py-op">,</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-string">"OC"</tt> <tt class="py-op">:</tt> <tt class="py-string">"organism_classification"</tt><tt class="py-op">,</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-string">"LO"</tt> <tt class="py-op">:</tt> <tt class="py-string">"look"</tt><tt class="py-op">}</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="StockholmIterator.next"></a><div id="StockholmIterator.next-def"><a name="L176"></a><tt class="py-lineno">176</tt> <a class="py-toggle" href="#" id="StockholmIterator.next-toggle" onclick="return toggle('StockholmIterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next">next</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="StockholmIterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmIterator.next-expanded"><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt> <tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-118" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-118', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-119" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-119', 'readline', 'link-119');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-comment">#Empty file - just give up.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-120', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">'# STOCKHOLM 1.0'</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Did not find STOCKHOLM header"</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment">#import sys</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print >> sys.stderr, 'Warning file does not start with STOCKHOLM 1.0'</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-comment"># Note: If this file follows the PFAM conventions, there should be</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># a line containing the number of sequences, e.g. "#=GF SQ 67"</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># We do not check for this - perhaps we should, and verify that</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if present it agrees with our parsing.</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt id="link-121" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-121', 'ids', 'link-121');">ids</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">gs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</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">gr</tt> <tt class="py-op">=</tt> <tt class="py-op">{</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">gf</tt> <tt class="py-op">=</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 class="py-name">passed_end_alignment</tt> <tt class="py-op">=</tt> <tt id="link-122" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-122', 'False', 'link-122');">False</a></tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-123" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-123', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-124', 'readline', 'link-119');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> <tt class="py-comment">#end of file</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-125', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment">#remove trailing \n</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">'# STOCKHOLM 1.0'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">"//"</tt> <tt class="py-op">:</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-comment">#The "//" line indicates the end of the alignment.</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#There may still be more meta-data</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">passed_end_alignment</tt> <tt class="py-op">=</tt> <tt id="link-126" 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-126', 'True', 'link-126');">True</a></tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment">#blank line, ignore</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</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">"#"</tt> <tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-comment">#Sequence</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Format: "<seqname> <sequence>"</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-keyword">not</tt> <tt class="py-name">passed_end_alignment</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-127" 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-127', 'x', 'link-127');">x</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-128', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-129" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-129', 'x', 'link-127');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-130', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</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">parts</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="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment">#This might be someone attempting to store a zero length sequence?</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Could not split line into identifier "</tt> \ </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"and sequence:\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt id="link-131" 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-131', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt id="link-132" 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-132', 'seq', 'link-26');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parts</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-133" 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-133', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-134" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-134', 'ids', 'link-121');">ids</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-135', 'ids', 'link-121');">ids</a></tt><tt class="py-op">.</tt><tt id="link-136" 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-136', 'append', 'link-54');">append</a></tt><tt class="py-op">(</tt><tt id="link-137" 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-137', 'id', 'link-28');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt id="link-138" 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-138', 'setdefault', 'link-138');">setdefault</a></tt><tt class="py-op">(</tt><tt id="link-139" 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-139', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-140" 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-140', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt id="link-141" 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-141', 'seq', 'link-26');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"."</tt><tt class="py-op">,</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</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">line</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">5</tt> <tt class="py-op">:</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment">#Comment line or meta-data</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"#=GF "</tt> <tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment">#Generic per-File annotation, free text</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">#Format: #=GF <feature> <free text></tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-142" 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-142', 'feature', 'link-142');">feature</a></tt><tt class="py-op">,</tt> <tt id="link-143" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-143', 'text', 'link-143');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-144', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-145', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-comment">#Each feature key could be used more than once,</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#so store the entries as a list of strings.</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-146" 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-146', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gf</tt> <tt class="py-op">:</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">gf</tt><tt class="py-op">[</tt><tt id="link-147" 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-147', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-148" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-148', 'text', 'link-143');">text</a></tt><tt class="py-op">]</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">gf</tt><tt class="py-op">[</tt><tt id="link-149" 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-149', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-150" 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-150', 'append', 'link-54');">append</a></tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-151', 'text', 'link-143');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'#=GC '</tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-comment">#Generic per-Column annotation, exactly 1 char per column</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Format: "#=GC <feature> <exactly 1 char per column>"</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'#=GS '</tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment">#Generic per-Sequence annotation, free text</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Format: "#=GS <seqname> <feature> <free text>"</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-152" 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-152', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt id="link-153" 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-153', 'feature', 'link-142');">feature</a></tt><tt class="py-op">,</tt> <tt id="link-154" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-154', 'text', 'link-143');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-155', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-156', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-comment">#if id not in ids :</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># ids.append(id)</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-157" 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-157', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gs</tt> <tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">gs</tt><tt class="py-op">[</tt><tt id="link-158" 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-158', 'id', 'link-28');">id</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="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-159" 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-159', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gs</tt><tt class="py-op">[</tt><tt id="link-160" 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-160', 'id', 'link-28');">id</a></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-name">gs</tt><tt class="py-op">[</tt><tt id="link-161" 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-161', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-162" 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-162', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-163" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-163', 'text', 'link-143');">text</a></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">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">gs</tt><tt class="py-op">[</tt><tt id="link-164" 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-164', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-165" 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-165', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-166" 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-166', 'append', 'link-54');">append</a></tt><tt class="py-op">(</tt><tt id="link-167" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-167', 'text', 'link-143');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"#=GR "</tt> <tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-comment">#Generic per-Sequence AND per-Column markup</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Format: "#=GR <seqname> <feature> <exactly 1 char per column>"</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-168" 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-168', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt id="link-169" 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-169', 'feature', 'link-142');">feature</a></tt><tt class="py-op">,</tt> <tt id="link-170" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-170', 'text', 'link-143');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-171', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-172', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment">#if id not in ids :</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># ids.append(id)</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-173" 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-173', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gr</tt> <tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">gr</tt><tt class="py-op">[</tt><tt id="link-174" 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-174', 'id', 'link-28');">id</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="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-175" 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-175', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gr</tt><tt class="py-op">[</tt><tt id="link-176" 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-176', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">gr</tt><tt class="py-op">[</tt><tt id="link-177" 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-177', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-178" 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-178', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-name">gr</tt><tt class="py-op">[</tt><tt id="link-179" 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-179', 'id', 'link-28');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><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-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt id="link-181" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-181', 'text', 'link-143');">text</a></tt><tt class="py-op">.</tt><tt id="link-182" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-182', 'strip', 'link-120');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># append to any previous entry</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Should we check the length matches the alignment length?</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># For iterlaced sequences the GR data can be split over</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># multiple lines</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Next line... </tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-183" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-183', 'ids', 'link-121');">ids</a></tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-comment">#assert len(gs) <= len(ids)</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#assert len(gr) <= len(ids)</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-184', 'ids', 'link-121');">ids</a></tt> <tt class="py-op">=</tt> <tt id="link-185" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-185', 'ids', 'link-121');">ids</a></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-186" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequences()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequences"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequences" class="py-name" href="#" onclick="return doclink('link-186', 'sequences', 'link-186');">sequences</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seqs</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_annotation</tt> <tt class="py-op">=</tt> <tt class="py-name">gs</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_col_annotation</tt> <tt class="py-op">=</tt> <tt class="py-name">gr</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-187" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-187', 'ids', 'link-121');">ids</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">seqs</tt> <tt class="py-op">:</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="L285"></a><tt class="py-lineno">285</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">records_per_alignment</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> \ </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_per_alignment</tt> <tt class="py-op"><></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-188', 'ids', 'link-121');">ids</a></tt><tt class="py-op">)</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Found %i records in this alignment, told to expect %i"</tt> \ </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-189" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-189', 'ids', 'link-121');">ids</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">records_per_alignment</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt id="link-190" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-190', 'alignment', 'link-9');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-191" class="py-name"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-191', 'Alignment', 'link-3');">Alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-192" 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-192', 'alphabet', 'link-192');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Introduce an annotated alignment class?</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#For now, store the annotation a new private property:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-193" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-193', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt class="py-name">_annotations</tt> <tt class="py-op">=</tt> <tt class="py-name">gr</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">alignment_length</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-194', 'values', 'link-194');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-195" 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-195', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">in</tt> <tt id="link-196" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-196', 'ids', 'link-121');">ids</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt id="link-197" 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-197', 'seq', 'link-26');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-198" 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-198', 'id', 'link-28');">id</a></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">alignment_length</tt> <tt class="py-op"><></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-199" 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-199', 'seq', 'link-26');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</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">"Sequences have different lengths, or repeated identifier"</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt id="link-200" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-200', 'name', 'link-30');">name</a></tt><tt class="py-op">,</tt> <tt id="link-201" 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-201', 'start', 'link-201');">start</a></tt><tt class="py-op">,</tt> <tt id="link-202" 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-202', 'end', 'link-202');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name" targets="Method Bio.AlignIO.StockholmIO.StockholmIterator._identifier_split()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_identifier_split,Method Bio.SeqIO.StockholmIO.StockholmIterator._identifier_split()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#_identifier_split"><a title="Bio.AlignIO.StockholmIO.StockholmIterator._identifier_split
Bio.SeqIO.StockholmIO.StockholmIterator._identifier_split" class="py-name" href="#" onclick="return doclink('link-203', '_identifier_split', 'link-203');">_identifier_split</a></tt><tt class="py-op">(</tt><tt id="link-204" 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-204', 'id', 'link-28');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt id="link-205" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-205', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-206" class="py-name" targets="Method Bio.Align.Generic.Alignment.add_sequence()=Bio.Align.Generic.Alignment-class.html#add_sequence,Method Bio.Nexus.Nexus.Nexus.add_sequence()=Bio.Nexus.Nexus.Nexus-class.html#add_sequence,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-206', 'add_sequence', 'link-206');">add_sequence</a></tt><tt class="py-op">(</tt><tt id="link-207" 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-207', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt id="link-208" 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-208', 'seq', 'link-26');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-209" 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-209', 'start', 'link-201');">start</a></tt><tt class="py-op">=</tt><tt id="link-210" 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-210', 'start', 'link-201');">start</a></tt><tt class="py-op">,</tt> <tt id="link-211" 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-211', 'end', 'link-202');">end</a></tt><tt class="py-op">=</tt><tt id="link-212" 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-212', 'end', 'link-202');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt id="link-213" 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-213', 'record', 'link-20');">record</a></tt> <tt class="py-op">=</tt> <tt id="link-214" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-214', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-215', 'get_all_seqs', 'link-10');">get_all_seqs</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-number">1</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-keyword">assert</tt> <tt id="link-216" 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-216', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-217" 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-217', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt id="link-218" 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-218', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">or</tt> <tt id="link-219" 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-219', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-220" 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-220', 'description', 'link-75');">description</a></tt> <tt class="py-op">==</tt> <tt id="link-221" 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-221', 'id', 'link-28');">id</a></tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt id="link-222" 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-222', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-223" 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-223', 'id', 'link-28');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-224" 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-224', 'id', 'link-28');">id</a></tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt id="link-225" 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-225', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-226" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-226', 'name', 'link-30');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-227" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-227', 'name', 'link-30');">name</a></tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt id="link-228" 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-228', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-229" 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-229', 'description', 'link-75');">description</a></tt> <tt class="py-op">=</tt> <tt id="link-230" 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-230', 'id', 'link-28');">id</a></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-comment">#will be overridden by _populate_meta_data if an explicit</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">#accession is provided:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-231" 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-231', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-232', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-233" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-233', 'name', 'link-30');">name</a></tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name" targets="Method Bio.AlignIO.StockholmIO.StockholmIterator._populate_meta_data()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_populate_meta_data,Method Bio.SeqIO.StockholmIO.StockholmIterator._populate_meta_data()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#_populate_meta_data"><a title="Bio.AlignIO.StockholmIO.StockholmIterator._populate_meta_data
Bio.SeqIO.StockholmIO.StockholmIterator._populate_meta_data" class="py-name" href="#" onclick="return doclink('link-234', '_populate_meta_data', 'link-234');">_populate_meta_data</a></tt><tt class="py-op">(</tt><tt id="link-235" 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-235', 'id', 'link-28');">id</a></tt><tt class="py-op">,</tt> <tt id="link-236" 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-236', 'record', 'link-20');">record</a></tt><tt class="py-op">)</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-237" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-237', 'alignment', 'link-9');">alignment</a></tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> </tt>
<a name="StockholmIterator._identifier_split"></a><div id="StockholmIterator._identifier_split-def"><a name="L322"></a><tt class="py-lineno">322</tt> <a class="py-toggle" href="#" id="StockholmIterator._identifier_split-toggle" onclick="return toggle('StockholmIterator._identifier_split');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_identifier_split">_identifier_split</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmIterator._identifier_split-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmIterator._identifier_split-expanded"><a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns (name,start,end) string tuple from an identier."""</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-238" class="py-name" targets="Variable Bio.expressions.blocks.identifier=Bio.expressions.blocks-module.html#identifier"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-238', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">.</tt><tt id="link-239" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-239', 'find', 'link-239');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">)</tt><tt class="py-op"><></tt><tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-name">start_end</tt> <tt class="py-op">=</tt> <tt id="link-240" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-240', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-241', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">start_end</tt><tt class="py-op">.</tt><tt id="link-242" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-242', 'count', 'link-11');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt id="link-243" 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-243', 'start', 'link-201');">start</a></tt><tt class="py-op">,</tt> <tt id="link-244" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-244', 'end', 'link-202');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-245" 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-245', 'map', 'link-245');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">,</tt> <tt class="py-name">start_end</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-246', 'split', 'link-130');">split</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="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt id="link-247" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-247', 'name', 'link-30');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-248" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-248', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-249', 'split', 'link-130');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">"/"</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-keyword">return</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-30');">name</a></tt><tt class="py-op">,</tt> <tt id="link-251" 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-251', 'start', 'link-201');">start</a></tt><tt class="py-op">,</tt> <tt id="link-252" 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-252', 'end', 'link-202');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt id="link-253" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-253', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div><a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
<a name="StockholmIterator._get_meta_data"></a><div id="StockholmIterator._get_meta_data-def"><a name="L332"></a><tt class="py-lineno">332</tt> <a class="py-toggle" href="#" id="StockholmIterator._get_meta_data-toggle" onclick="return toggle('StockholmIterator._get_meta_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_get_meta_data">_get_meta_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">,</tt> <tt class="py-param">meta_dict</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmIterator._get_meta_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmIterator._get_meta_data-expanded"><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-docstring">"""Takes an itentifier and returns dict of all meta-data matching it.</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-docstring"> For example, given "Q9PN73_CAMJE/149-220" will return all matches to</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-docstring"> this or "Q9PN73_CAMJE" which the identifier without its /start-end</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-docstring"> suffix.</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"> In the example below, the suffix is required to match the AC, but must</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"> be removed to match the OS and OC meta-data.</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 class="py-docstring"> # STOCKHOLM 1.0</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-docstring"> #=GS Q9PN73_CAMJE/149-220 AC Q9PN73</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-docstring"> Q9PN73_CAMJE/149-220 NKA...</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"> ...</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> #=GS Q9PN73_CAMJE OS Campylobacter jejuni</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"> #=GS Q9PN73_CAMJE OC Bacteria </tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-docstring"> This function will return an empty dictionary if no data is found."""</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt id="link-254" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-254', 'name', 'link-30');">name</a></tt><tt class="py-op">,</tt> <tt id="link-255" 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-255', 'start', 'link-201');">start</a></tt><tt class="py-op">,</tt> <tt id="link-256" 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-256', 'end', 'link-202');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator._identifier_split
Bio.SeqIO.StockholmIO.StockholmIterator._identifier_split" class="py-name" href="#" onclick="return doclink('link-257', '_identifier_split', 'link-203');">_identifier_split</a></tt><tt class="py-op">(</tt><tt id="link-258" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-258', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-259" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-259', 'name', 'link-30');">name</a></tt><tt class="py-op">==</tt><tt id="link-260" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-260', 'identifier', 'link-238');">identifier</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">identifier_keys</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-261" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-261', 'identifier', 'link-238');">identifier</a></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">else</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">identifier_keys</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-262" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-262', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">,</tt> <tt id="link-263" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-263', 'name', 'link-30');">name</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-name">answer</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">identifier_key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">identifier_keys</tt> <tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-264" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.feature_key()=Bio.GenBank._FeatureConsumer-class.html#feature_key,Method Bio.GenBank._RecordConsumer.feature_key()=Bio.GenBank._RecordConsumer-class.html#feature_key,Variable Bio.expressions.genbank.feature_key=Bio.expressions.genbank-module.html#feature_key"><a title="Bio.GenBank._FeatureConsumer.feature_key
Bio.GenBank._RecordConsumer.feature_key
Bio.expressions.genbank.feature_key" class="py-name" href="#" onclick="return doclink('link-264', 'feature_key', 'link-264');">feature_key</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">meta_dict</tt><tt class="py-op">[</tt><tt class="py-name">identifier_key</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-name">answer</tt><tt class="py-op">[</tt><tt id="link-265" class="py-name"><a title="Bio.GenBank._FeatureConsumer.feature_key
Bio.GenBank._RecordConsumer.feature_key
Bio.expressions.genbank.feature_key" class="py-name" href="#" onclick="return doclink('link-265', 'feature_key', 'link-264');">feature_key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">meta_dict</tt><tt class="py-op">[</tt><tt class="py-name">identifier_key</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-266" class="py-name"><a title="Bio.GenBank._FeatureConsumer.feature_key
Bio.GenBank._RecordConsumer.feature_key
Bio.expressions.genbank.feature_key" class="py-name" href="#" onclick="return doclink('link-266', 'feature_key', 'link-264');">feature_key</a></tt><tt class="py-op">]</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt> <tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">answer</tt> </tt>
</div><a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
<a name="StockholmIterator._populate_meta_data"></a><div id="StockholmIterator._populate_meta_data-def"><a name="L365"></a><tt class="py-lineno">365</tt> <a class="py-toggle" href="#" id="StockholmIterator._populate_meta_data-toggle" onclick="return toggle('StockholmIterator._populate_meta_data');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_populate_meta_data">_populate_meta_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">identifier</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="StockholmIterator._populate_meta_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StockholmIterator._populate_meta_data-expanded"><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-docstring">"""Adds meta-date to a SecRecord's annotations dictionary.</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-docstring"> This function applies the PFAM conventions."""</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">seq_data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name" targets="Method Bio.AlignIO.StockholmIO.StockholmIterator._get_meta_data()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#_get_meta_data,Method Bio.SeqIO.StockholmIO.StockholmIterator._get_meta_data()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#_get_meta_data"><a title="Bio.AlignIO.StockholmIO.StockholmIterator._get_meta_data
Bio.SeqIO.StockholmIO.StockholmIterator._get_meta_data" class="py-name" href="#" onclick="return doclink('link-267', '_get_meta_data', 'link-267');">_get_meta_data</a></tt><tt class="py-op">(</tt><tt id="link-268" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-268', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_annotation</tt><tt class="py-op">)</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-269" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-269', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_data</tt> <tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-comment">#Note this dictionary contains lists!</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-270" 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-270', 'feature', 'link-142');">feature</a></tt><tt class="py-op">==</tt><tt class="py-string">"AC"</tt> <tt class="py-op">:</tt> <tt class="py-comment">#ACcession number</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seq_data</tt><tt class="py-op">[</tt><tt id="link-271" 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-271', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt id="link-272" 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-272', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-273" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-273', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">seq_data</tt><tt class="py-op">[</tt><tt id="link-274" 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-274', 'feature', 'link-142');">feature</a></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="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-275" class="py-name"><a title="Bio.Std.feature
Bio.expressions.embl.embl65.feature
Bio.expressions.genbank.feature" class="py-name" href="#" onclick="return doclink('link-275', 'feature', 'link-142');">feature</a></tt><tt class="py-op">==</tt><tt class="py-string">"DE"</tt> <tt class="py-op">:</tt> <tt class="py-comment">#DEscription</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt id="link-276" 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-276', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-277" 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-277', 'description', 'link-75');">description</a></tt> <tt class="py-op">=</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">seq_data</tt><tt class="py-op">[</tt><tt id="link-278" 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-278', 'feature', 'link-142');">feature</a></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-keyword">elif</tt> <tt id="link-279" 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-279', 'feature', 'link-142');">feature</a></tt><tt class="py-op">==</tt><tt class="py-string">"DR"</tt> <tt class="py-op">:</tt> <tt class="py-comment">#Database Reference</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-comment">#Should we try and parse the strings?</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-280" 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-280', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.dbxrefs" class="py-name" href="#" onclick="return doclink('link-281', 'dbxrefs', 'link-82');">dbxrefs</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seq_data</tt><tt class="py-op">[</tt><tt id="link-282" 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-282', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-283" 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-283', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-284', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt id="link-285" 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-285', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-286" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-286', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gs_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gs_mapping" class="py-name" href="#" onclick="return doclink('link-287', 'pfam_gs_mapping', 'link-8');">pfam_gs_mapping</a></tt><tt class="py-op">[</tt><tt id="link-288" 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-288', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">", "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">seq_data</tt><tt class="py-op">[</tt><tt id="link-289" 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-289', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-comment">#Ignore it?</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-290" 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-290', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-291', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"GS:"</tt> <tt class="py-op">+</tt> <tt id="link-292" 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-292', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">", "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">seq_data</tt><tt class="py-op">[</tt><tt id="link-293" 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-293', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">seq_col_data</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator._get_meta_data
Bio.SeqIO.StockholmIO.StockholmIterator._get_meta_data" class="py-name" href="#" onclick="return doclink('link-294', '_get_meta_data', 'link-267');">_get_meta_data</a></tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Bio.expressions.blocks.identifier" class="py-name" href="#" onclick="return doclink('link-295', 'identifier', 'link-238');">identifier</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">seq_col_annotation</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-296" 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-296', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">seq_col_data</tt> <tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-comment">#Note this dictionary contains strings!</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-297" 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-297', 'feature', 'link-142');">feature</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-298', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt id="link-299" 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-299', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-300', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-301" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.AlignIO.StockholmIO.StockholmWriter.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmIterator.pfam_gr_mapping
Bio.SeqIO.StockholmIO.StockholmWriter.pfam_gr_mapping" class="py-name" href="#" onclick="return doclink('link-301', 'pfam_gr_mapping', 'link-7');">pfam_gr_mapping</a></tt><tt class="py-op">[</tt><tt id="link-302" 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-302', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_col_data</tt><tt class="py-op">[</tt><tt id="link-303" 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-303', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-comment">#Ignore it?</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-304" 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-304', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-305" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-305', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"GR:"</tt> <tt class="py-op">+</tt> <tt id="link-306" 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-306', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_col_data</tt><tt class="py-op">[</tt><tt id="link-307" 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-307', 'feature', 'link-142');">feature</a></tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> </tt>
<a name="L396"></a><tt class="py-lineno">396</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="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Testing..."</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">cStringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-comment"># This example with its slightly odd (partial) annotation is from here:</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I don't know what the "GR_O31699/88-139_IN ..." line is meant to be.</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sth_example</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-string">"""# STOCKHOLM 1.0</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-string">#=GF ID CBS</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-string">#=GF AC PF00571</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-string">#=GF DE CBS domain</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-string">#=GF AU Bateman A</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-string">#=GF CC CBS domains are small intracellular modules mostly found </tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-string">#=GF CC in 2 or four copies within a protein. </tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-string">#=GF SQ 67</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"><tt class="py-string">#=GS O31698/18-71 AC O31698</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-string">#=GS O83071/192-246 AC O83071</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-string">#=GS O83071/259-312 AC O83071</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-string">#=GS O31698/88-139 AC O31698</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-string">#=GS O31698/88-139 OS Bacillus subtilis</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-string">O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-string">#=GR O83071/192-246 SA 999887756453524252..55152525....36463774777</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-string">O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-string">#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-string">O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-string">#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-string">O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-string">#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-string">#=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-string">O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"><tt class="py-string">#=GR O31699/88-139 AS ________________*__________________________</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-string">#=GR_O31699/88-139_IN ____________1______________2__________0____</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-string">//</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-comment"># Interlaced example from BioPerl documentation. Also note the blank line.</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># http://www.bioperl.org/wiki/Stockholm_multiple_alignment_format</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">sth_example2</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-string">"""# STOCKHOLM 1.0</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-string">#=GC SS_cons .................<<<<<<<<...<<<<<<<........>>>>>>>..</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-string">AP001509.1 UUAAUCGAGCUCAACACUCUUCGUAUAUCCUC-UCAAUAUGG-GAUGAGGGU</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-string">#=GR AP001509.1 SS -----------------<<<<<<<<---..<<-<<-------->>->>..--</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-string">AE007476.1 AAAAUUGAAUAUCGUUUUACUUGUUUAU-GUCGUGAAU-UGG-CACGA-CGU</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-string">#=GR AE007476.1 SS -----------------<<<<<<<<-----<<.<<-------->>.>>----</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-string">#=GC SS_cons ......<<<<<<<.......>>>>>>>..>>>>>>>>...............</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-string">AP001509.1 CUCUAC-AGGUA-CCGUAAA-UACCUAGCUACGAAAAGAAUGCAGUUAAUGU</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-string">#=GR AP001509.1 SS -------<<<<<--------->>>>>--->>>>>>>>---------------</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-string">AE007476.1 UUCUACAAGGUG-CCGG-AA-CACCUAACAAUAAGUAAGUCAGCAGUGAGAU</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-string">#=GR AE007476.1 SS ------.<<<<<--------->>>>>.-->>>>>>>>---------------</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-string">//"""</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"StockholmIterator(stockholm alignment file)"</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-308" class="py-name" targets="Class Bio.AlignIO.StockholmIO.StockholmIterator=Bio.AlignIO.StockholmIO.StockholmIterator-class.html,Class Bio.SeqIO.StockholmIO.StockholmIterator=Bio.SeqIO.StockholmIO.StockholmIterator-class.html"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-308', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt id="link-309" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-309', 'count', 'link-11');">count</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-310" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-310', 'alignment', 'link-9');">alignment</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt> <tt class="py-op">:</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-311" 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-311', 'record', 'link-20');">record</a></tt> <tt class="py-keyword">in</tt> <tt id="link-312" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-312', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-313" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-313', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt id="link-314" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-314', 'count', 'link-11');">count</a></tt><tt class="py-op">=</tt><tt id="link-315" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-315', 'count', 'link-11');">count</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-316" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-316', 'count', 'link-11');">count</a></tt> <tt class="py-op">==</tt> <tt class="py-number">5</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-comment">#Check the last record...</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-317" 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-317', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-318" 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-318', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O31699/88-139'</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-319" 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-319', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-320" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-320', 'name', 'link-30');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O31699'</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-321" 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-321', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-322" 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-322', 'description', 'link-75');">description</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O31699/88-139'</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-323" 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-323', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-324" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-324', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">4</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-comment">#weight</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-325" 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-325', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-326" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-326', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'O31699'</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-327" 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-327', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-328" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-328', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"start"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">88</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-329" 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-329', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-330" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-330', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"end"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">139</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-331" 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-331', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-332" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-332', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"active_site"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'________________*__________________________'</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt id="link-333" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-333', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt id="link-334" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-334', 'count', 'link-11');">count</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-335" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-335', 'alignment', 'link-9');">alignment</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterator</tt> <tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-336" 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-336', 'record', 'link-20');">record</a></tt> <tt class="py-keyword">in</tt> <tt id="link-337" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-337', 'alignment', 'link-9');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-338" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-338', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt id="link-339" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-339', 'count', 'link-11');">count</a></tt><tt class="py-op">=</tt><tt id="link-340" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-340', 'count', 'link-11');">count</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-341" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-341', 'count', 'link-11');">count</a></tt><tt class="py-op">==</tt><tt class="py-number">1</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-comment">#Check the last record...</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-342" 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-342', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-343" 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-343', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O83071/192-246'</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-344" 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-344', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-345" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-345', 'name', 'link-30');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O83071'</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-346" 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-346', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-347" 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-347', 'description', 'link-75');">description</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'O83071/192-246'</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-348" 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-348', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-349" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-349', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">4</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-comment">#weight</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-350" 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-350', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-351', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"accession"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'O83071'</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-352" 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-352', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-353" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-353', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"start"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">192</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-354" 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-354', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-355" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-355', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"end"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-number">246</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-356" 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-356', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-357" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-357', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"surface_accessibility"</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">"999887756453524252..55152525....36463774777"</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-358" 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-358', 'id', 'link-28');">id</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-359" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-359', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-360" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-360', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-string">'O83071/192-246'</tt><tt class="py-op">,</tt> <tt class="py-string">'O83071/259-312'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698/18-71'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698/88-139'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31699/88-139'</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-361" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-361', 'name', 'link-30');">name</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-362" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-362', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-363" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-363', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-string">'O83071'</tt><tt class="py-op">,</tt> <tt class="py-string">'O83071'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31699'</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-364" 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-364', 'description', 'link-75');">description</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-365" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-365', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-366" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-366', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-op">[</tt><tt class="py-string">'O83071/192-246'</tt><tt class="py-op">,</tt> <tt class="py-string">'O83071/259-312'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698/18-71'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31698/88-139'</tt><tt class="py-op">,</tt> <tt class="py-string">'O31699/88-139'</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"StockholmIterator(interlaced stockholm alignment file)"</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-name">iterator</tt> <tt class="py-op">=</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt id="link-367" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-367', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-368" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-368', 'next', 'link-368');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-369" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-369', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt id="link-370" 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-370', 'record', 'link-20');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-371" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-371', 'next', 'link-368');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-372" 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-372', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-373" 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-373', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"AP001509.1"</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-374" 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-374', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-375" 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-375', 'seq', 'link-26');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">104</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"secondary_structure"</tt> <tt class="py-keyword">in</tt> <tt id="link-376" 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-376', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-377" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-377', 'annotations', 'link-32');">annotations</a></tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-378" 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-378', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-379', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"secondary_structure"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">104</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt id="link-380" 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-380', 'record', 'link-20');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-381" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-381', 'next', 'link-368');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-382" 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-382', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-383" 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-383', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"AE007476.1"</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-384" 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-384', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-385" 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-385', 'seq', 'link-26');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">104</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-string">"secondary_structure"</tt> <tt class="py-keyword">in</tt> <tt id="link-386" 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-386', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-387" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-387', 'annotations', 'link-32');">annotations</a></tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-388" 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-388', 'record', 'link-20');">record</a></tt><tt class="py-op">.</tt><tt id="link-389" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-389', 'annotations', 'link-32');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">"secondary_structure"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">104</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt id="link-390" 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-390', 'record', 'link-20');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-391" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-391', 'next', 'link-368');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">StopIteration</tt> <tt class="py-op">:</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt id="link-392" 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-392', 'record', 'link-20');">record</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-393" 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-393', 'record', 'link-20');">record</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"StockholmIterator(concatenated stockholm alignment files)"</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-394" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-394', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-395" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-395', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-396" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-396', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-397" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-397', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-398" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-398', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-399" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-399', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-400" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-400', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-401" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-401', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example2</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-402" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-402', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-403" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-403', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example2</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"--------"</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Checking write/read"</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt id="link-404" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-404', 'handle', 'link-15');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-name">list1</tt> <tt class="py-op">=</tt> <tt id="link-405" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-405', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-406" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-406', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">sth_example2</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> <tt class="py-op">+</tt> <tt class="py-name">sth_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt id="link-407" class="py-name" targets="Class Bio.AlignIO.StockholmIO.StockholmWriter=Bio.AlignIO.StockholmIO.StockholmWriter-class.html,Class Bio.SeqIO.StockholmIO.StockholmWriter=Bio.SeqIO.StockholmIO.StockholmWriter-class.html"><a title="Bio.AlignIO.StockholmIO.StockholmWriter
Bio.SeqIO.StockholmIO.StockholmWriter" class="py-name" href="#" onclick="return doclink('link-407', 'StockholmWriter', 'link-407');">StockholmWriter</a></tt><tt class="py-op">(</tt><tt id="link-408" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-408', 'handle', 'link-15');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-409" class="py-name" targets="Method Bio.AlignIO.Interfaces.AlignmentWriter.write_file()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#write_file,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_file,Method Bio.SeqIO.ClustalIO.ClustalWriter.write_file()=Bio.SeqIO.ClustalIO.ClustalWriter-class.html#write_file,Method Bio.SeqIO.Interfaces.SequenceWriter.write_file()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#write_file,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_file()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_file,Method Bio.SeqIO.PhylipIO.PhylipWriter.write_file()=Bio.SeqIO.PhylipIO.PhylipWriter-class.html#write_file,Method Bio.SeqIO.StockholmIO.StockholmWriter.write_file()=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#write_file"><a title="Bio.AlignIO.Interfaces.AlignmentWriter.write_file
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_file
Bio.SeqIO.ClustalIO.ClustalWriter.write_file
Bio.SeqIO.Interfaces.SequenceWriter.write_file
Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_file
Bio.SeqIO.PhylipIO.PhylipWriter.write_file
Bio.SeqIO.StockholmIO.StockholmWriter.write_file" class="py-name" href="#" onclick="return doclink('link-409', 'write_file', 'link-409');">write_file</a></tt><tt class="py-op">(</tt><tt class="py-name">list1</tt><tt class="py-op">)</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt id="link-410" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-410', 'handle', 'link-15');">handle</a></tt><tt class="py-op">.</tt><tt id="link-411" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-411', 'seek', 'link-411');">seek</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">list2</tt> <tt class="py-op">=</tt> <tt id="link-412" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-412', 'list', 'link-394');">list</a></tt><tt class="py-op">(</tt><tt id="link-413" class="py-name"><a title="Bio.AlignIO.StockholmIO.StockholmIterator
Bio.SeqIO.StockholmIO.StockholmIterator" class="py-name" href="#" onclick="return doclink('link-413', 'StockholmIterator', 'link-308');">StockholmIterator</a></tt><tt class="py-op">(</tt><tt id="link-414" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-414', 'handle', 'link-15');">handle</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">list1</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">list2</tt><tt class="py-op">)</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a1</tt><tt class="py-op">,</tt><tt class="py-name">a2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">list1</tt><tt class="py-op">,</tt> <tt class="py-name">list2</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a1</tt><tt class="py-op">.</tt><tt id="link-415" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-415', 'get_all_seqs', 'link-10');">get_all_seqs</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-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a2</tt><tt class="py-op">.</tt><tt id="link-416" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-416', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">r1</tt><tt class="py-op">,</tt> <tt class="py-name">r2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">a1</tt><tt class="py-op">.</tt><tt id="link-417" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-417', 'get_all_seqs', 'link-10');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">a2</tt><tt class="py-op">.</tt><tt id="link-418" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-418', 'get_all_seqs', 'link-10');">get_all_seqs</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="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-419" 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-419', 'id', 'link-28');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-420" 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-420', 'id', 'link-28');">id</a></tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">r1</tt><tt class="py-op">.</tt><tt id="link-421" 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-421', 'seq', 'link-26');">seq</a></tt><tt class="py-op">.</tt><tt id="link-422" class="py-name"><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-422', 'tostring', 'link-59');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">r2</tt><tt class="py-op">.</tt><tt id="link-423" 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-423', 'seq', 'link-26');">seq</a></tt><tt class="py-op">.</tt><tt id="link-424" class="py-name"><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-424', 'tostring', 'link-59');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> </tt><script type="text/javascript">
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