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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignIO-module.html">Package AlignIO</a> ::
Module EmbossIO
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<h1 class="epydoc">Source Code for <a href="Bio.AlignIO.EmbossIO-module.html">Module Bio.AlignIO.EmbossIO</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 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">#</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</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="L8"></a><tt class="py-lineno"> 8</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="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="EmbossWriter"></a><div id="EmbossWriter-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="EmbossWriter-toggle" onclick="return toggle('EmbossWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossWriter-class.html">EmbossWriter</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="EmbossWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="EmbossWriter-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-docstring">"""Emboss alignment writer</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> Writes a simplfied version of the EMBOSS pairs/simple file format.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> A lot of the information their tools record in their headers is not</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> available and is ommitted.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> </tt>
<a name="EmbossWriter.write_header"></a><div id="EmbossWriter.write_header-def"><a name="L18"></a><tt class="py-lineno"> 18</tt> <a class="py-toggle" href="#" id="EmbossWriter.write_header-toggle" onclick="return toggle('EmbossWriter.write_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossWriter-class.html#write_header">write_header</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="EmbossWriter.write_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EmbossWriter.write_header-expanded"><a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt id="link-7" 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-7', 'handle', 'link-7');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-7');">handle</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-9', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"########################################\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt id="link-11" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-11', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# Program: Biopython\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt id="link-13" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-13', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-14" 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-14', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# Report_file: %s\n"</tt> <tt class="py-op">%</tt> <tt id="link-15" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'name', 'link-16');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</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="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <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-7');">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-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"########################################\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="EmbossWriter.write_footer"></a><div id="EmbossWriter.write_footer-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="EmbossWriter.write_footer-toggle" onclick="return toggle('EmbossWriter.write_footer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossWriter-class.html#write_footer">write_footer</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="EmbossWriter.write_footer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EmbossWriter.write_footer-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-19', 'handle', 'link-7');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-20', 'handle', 'link-7');">handle</a></tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt id="link-21" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-21', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-22" 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-22', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#---------------------------------------\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <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-7');">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-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#---------------------------------------\n"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="EmbossWriter.write_alignment"></a><div id="EmbossWriter.write_alignment-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="EmbossWriter.write_alignment-toggle" onclick="return toggle('EmbossWriter.write_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossWriter-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="EmbossWriter.write_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EmbossWriter.write_alignment-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write (another) single alignment to an open file."""</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 id="link-25" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-25', 'handle', 'link-7');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-26', 'handle', 'link-7');">handle</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-27" 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-27', 'alignment', 'link-27');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'get_all_seqs', 'link-28');">get_all_seqs</a></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 id="link-29" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-29', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=======================================\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-31', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-32" 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-32', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-33', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-34" 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-34', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# Aligned_sequences: %i\n"</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 class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-35" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-35', 'i', 'link-35');">i</a></tt><tt class="py-op">,</tt> <tt id="link-36" 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-36', 'record', 'link-36');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt class="py-name">records</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-37', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-38" 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-38', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# %i: %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-35');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-40" 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-40', 'record', 'link-36');">record</a></tt><tt class="py-op">.</tt><tt id="link-41" 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-41', 'id', 'link-41');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt id="link-42" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-42', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-43" 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-43', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-44" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-44', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-45" 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-45', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"# Length: %i\n"</tt> <tt class="py-op">%</tt> <tt id="link-46" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-46', 'alignment', 'link-27');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-47" 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-47', 'get_alignment_length', 'link-47');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-48', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-49" 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-49', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt id="link-50" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-50', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-51" 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-51', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"#=======================================\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-52', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-53" 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-53', 'write', 'link-10');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-comment">#...</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-54" 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-54', 'False', 'link-54');">False</a></tt> </tt>
</div></div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="EmbossIterator"></a><div id="EmbossIterator-def"><a name="L52"></a><tt class="py-lineno"> 52</tt> <a class="py-toggle" href="#" id="EmbossIterator-toggle" onclick="return toggle('EmbossIterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossIterator-class.html">EmbossIterator</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="EmbossIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="EmbossIterator-expanded"><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-docstring">"""Emboss alignment iterator</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> For reading the (pairwise) alignments from EMBOSS tools in what they</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> call the "pairs" and "simple" formats.</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="EmbossIterator.next"></a><div id="EmbossIterator.next-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="EmbossIterator.next-toggle" onclick="return toggle('EmbossIterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.EmbossIO.EmbossIterator-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="EmbossIterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EmbossIterator.next-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <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-7');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-56', 'handle', 'link-7');">handle</a></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment">#Header we saved from when we were parsing</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the previous alignment.</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">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="L67"></a><tt class="py-lineno"> 67</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="L68"></a><tt class="py-lineno"> 68</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="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-57" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-57', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-58" 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-58', 'readline', 'link-58');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</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="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</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>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-59', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-60" 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-60', 'readline', 'link-58');">readline</a></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-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">length_of_seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">number_of_seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-61" 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-61', 'ids', 'link-61');">ids</a></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 class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">while</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="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-comment">#Read in the rest of this alignment header,</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">#try and discover the number of records expected</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">#and their length</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-op">.</tt><tt id="link-62" 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-62', 'split', 'link-62');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt id="link-63" 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-63', 'key', 'link-63');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-65" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-65', 'key', 'link-63');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"aligned_sequences"</tt> <tt class="py-op">:</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-name">number_of_seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-66" 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-66', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</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-67" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-67', 'ids', 'link-61');">ids</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment"># Should now expect the record identifiers...</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">for</tt> <tt id="link-68" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-68', 'i', 'link-35');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">number_of_seqs</tt><tt class="py-op">)</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">line</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-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-70" 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-70', 'readline', 'link-58');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">parts</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-op">.</tt><tt id="link-71" 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-71', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-72', 'split', 'link-62');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-73" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-73', 'i', 'link-35');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt id="link-75" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-75', 'ids', 'link-61');">ids</a></tt><tt class="py-op">.</tt><tt id="link-76" 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-76', 'append', 'link-76');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-77" 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-77', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-78', 'ids', 'link-61');">ids</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">number_of_seqs</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-79" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-79', 'key', 'link-63');">key</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"length"</tt> <tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">length_of_seqs</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">parts</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-80" 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-80', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-comment">#And read in another line...</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-81', 'handle', 'link-7');">handle</a></tt><tt class="py-op">.</tt><tt id="link-82" 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-82', 'readline', 'link-58');">readline</a></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-keyword">if</tt> <tt class="py-name">number_of_seqs</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">SyntaxError</tt><tt class="py-op">(</tt><tt class="py-string">"Number of sequences missing!"</tt><tt class="py-op">)</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">length_of_seqs</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">SyntaxError</tt><tt class="py-op">(</tt><tt class="py-string">"Length of sequences missing!"</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-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="L112"></a><tt class="py-lineno">112</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">number_of_seqs</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">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="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">number_of_seqs</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="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">""</tt> <tt class="py-keyword">for</tt> <tt id="link-83" 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-83', 'id', 'link-41');">id</a></tt> <tt class="py-keyword">in</tt> <tt id="link-84" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-84', 'ids', 'link-61');">ids</a></tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-85" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-85', 'index', 'link-85');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment">#Parse the seqs</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</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">21</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">id_start</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">21</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-87', 'split', 'link-62');">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="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">seq_end</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">21</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-88" 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-88', 'strip', 'link-64');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-89', 'split', 'link-62');">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="L124"></a><tt class="py-lineno">124</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">id_start</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seq_end</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="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment">#identifier, seq start position, seq, seq end position</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#(an aligned seq is broken up into multiple lines)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-90" 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-90', 'id', 'link-41');">id</a></tt><tt class="py-op">,</tt> <tt id="link-91" 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-91', 'start', 'link-91');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-name">id_start</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt id="link-92" 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-92', 'seq', 'link-92');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-93" 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-93', 'end', 'link-93');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">seq_end</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-comment">#The identifier is truncated...</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt id="link-94" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-94', 'index', 'link-85');">index</a></tt> <tt class="py-keyword">and</tt> <tt id="link-95" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-95', 'index', 'link-85');">index</a></tt> <tt class="py-op"><</tt> <tt class="py-name">number_of_seqs</tt><tt class="py-op">,</tt> \ </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-string">"Expected index %i in range [0,%i)"</tt> \ </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-96" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-96', 'index', 'link-85');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">number_of_seqs</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-97" 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-97', 'id', 'link-41');">id</a></tt><tt class="py-op">==</tt><tt id="link-98" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-98', 'ids', 'link-61');">ids</a></tt><tt class="py-op">[</tt><tt id="link-99" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-99', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt> <tt class="py-keyword">or</tt> <tt id="link-100" 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-100', 'id', 'link-41');">id</a></tt> <tt class="py-op">==</tt> <tt id="link-101" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-101', 'ids', 'link-61');">ids</a></tt><tt class="py-op">[</tt><tt id="link-102" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-102', 'index', 'link-85');">index</a></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-103" 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-103', 'id', 'link-41');">id</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-comment">#Check the start...</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-104" 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-104', 'start', 'link-91');">start</a></tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-105" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-105', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"-"</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>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-string">"Found %i chars so far for %s, file says start %i:\n%s"</tt> \ </tt>
<a name="L139"></a><tt class="py-lineno">139</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 class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-106" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-106', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-107" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-107', 'id', 'link-41');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-108" 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-108', 'start', 'link-91');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-109" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-109', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-110" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-110', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt id="link-111" 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-111', 'seq', 'link-92');">seq</a></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment">#Check the end ...</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-112" 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-112', 'end', 'link-93');">end</a></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">seqs</tt><tt class="py-op">[</tt><tt id="link-113" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-113', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"-"</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>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-string">"Found %i chars so far for %s, file says end %i:\n%s"</tt> \ </tt>
<a name="L146"></a><tt class="py-lineno">146</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 class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-114" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-114', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-115" 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-115', 'id', 'link-41');">id</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-116" 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-116', 'end', 'link-93');">end</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-117" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-117', 'index', 'link-85');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt id="link-118" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-118', 'index', 'link-85');">index</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-119" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-119', 'index', 'link-85');">index</a></tt> <tt class="py-op">>=</tt> <tt class="py-name">number_of_seqs</tt> <tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-120', 'index', 'link-85');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-comment">#just a start value, this is just alignment annotation (?)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#print "Skipping: " + line.rstrip()</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-121" 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-121', 'strip', 'link-64');">strip</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>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-comment">#Just a spacer?</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">line</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-122" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-122', 'False', 'link-54');">False</a></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-name">line</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-7');">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-58');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</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-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"#---------------------------------------"</tt> \ </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</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>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-comment">#End of alignment</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_header</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-125" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-125', 'index', 'link-85');">index</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="L171"></a><tt class="py-lineno">171</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="L172"></a><tt class="py-lineno">172</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-126" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-126', 'ids', 'link-61');">ids</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</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="L174"></a><tt class="py-lineno">174</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-127" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-127', 'ids', 'link-61');">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="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-128" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-128', 'alignment', 'link-27');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-129" 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-129', '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-130" 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-130', 'alphabet', 'link-130');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <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-41');">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-92');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt id="link-133" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-133', 'ids', 'link-61');">ids</a></tt><tt class="py-op">,</tt> <tt class="py-name">seqs</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-134" 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-134', 'seq', 'link-92');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op"><></tt> <tt class="py-name">length_of_seqs</tt> <tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">SyntaxError</tt><tt class="py-op">(</tt><tt class="py-string">"Error parsing alignment - sequences of different length?"</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt id="link-135" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-135', 'alignment', 'link-27');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-136" 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-136', 'add_sequence', 'link-136');">add_sequence</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-41');">id</a></tt><tt class="py-op">,</tt> <tt id="link-138" 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-138', 'seq', 'link-92');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-139" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-139', 'alignment', 'link-27');">alignment</a></tt> </tt>
</div></div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="L183"></a><tt class="py-lineno">183</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="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Running a quick self-test"</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment">#http://emboss.sourceforge.net/docs/themes/alnformats/align.simple</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">simple_example</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-string">"""########################################</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-string"># Program: alignret</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-string"># Rundate: Wed Jan 16 17:16:13 2002</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-string"># Report_file: stdout</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-string">########################################</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 4</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-string"># 1: IXI_234</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-string"># 2: IXI_235</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-string"># 3: IXI_236</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-string"># 4: IXI_237</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-string"># Length: 131</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-string"># Identity: 95/131 (72.5%)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-string"># Similarity: 127/131 (96.9%)</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-string"># Gaps: 25/131 (19.1%)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-string"># Score: 100.0</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-string">IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-string">IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-string">IXI_236 1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT 48</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-string">IXI_237 1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT 45</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-string"> |||||:|||||||||::::::: |||||:||||:::::|||||:|||||</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-string">IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-string">IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-string">IXI_236 49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G 96</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-string">IXI_237 46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G 93</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-string"> ||:||||||||||||||||||||:::::::::::||||||||||||| |</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-string">IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-string">IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-string">IXI_236 97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE 127</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-string">IXI_237 94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE 124</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-string"> |||:||||:|||||:|||||||::|||||||</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-string">#---------------------------------------</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-string">#---------------------------------------</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-comment">#http://emboss.sourceforge.net/docs/themes/alnformats/align.pair</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">pair_example</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-string">"""########################################</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-string"># Program: water</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-string"># Rundate: Wed Jan 16 17:23:19 2002</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-string"># Report_file: stdout</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-string">########################################</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-string"># 1: IXI_234</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-string"># 2: IXI_235</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-string"># Length: 131</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-string"># Identity: 112/131 (85.5%)</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-string"># Similarity: 112/131 (85.5%)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-string"># Gaps: 19/131 (14.5%)</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-string"># Score: 591.5</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-string">IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-string"> ||||||||||||||| ||||||||||||||||||||||||||</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-string">IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-string">IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-string"> |||||||||||||||||||||||| ||||||||||||||||</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-string">IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-string">IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-string"> |||||||||||||||||||||||||||||||</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-string">IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"><tt class="py-string">#---------------------------------------</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"><tt class="py-string">#--------------------------------------- </tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">pair_example2</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-string">"""########################################</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"><tt class="py-string"># Program: needle</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"><tt class="py-string"># Rundate: Sun 27 Apr 2007 17:20:35</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-string"># Commandline: needle</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-string"># [-asequence] Spo0F.faa</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-string"># [-bsequence] paired_r.faa</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-string"># -sformat2 pearson</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-string"># Align_format: srspair</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-string"># Report_file: ref_rec .needle</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-string">########################################</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-string"># 1: ref_rec</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-string"># 2: gi|94968718|receiver</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-string"># Length: 124</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-string"># Identity: 32/124 (25.8%)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-string"># Similarity: 64/124 (51.6%)</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-string"># Gaps: 17/124 (13.7%)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-string"># Score: 112.0</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-string"># </tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-string">ref_rec 1 KILIVDD----QYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDL 46</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-string"> :|:.|| :.|.|::|.: :.|.....:|.:|.||:.:..:..|.:</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-string">gi|94968718|r 1 -VLLADDHALVRRGFRLMLED--DPEIEIVAEAGDGAQAVKLAGELHPRV 47</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-string">ref_rec 47 VLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALT 96</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-string"> |::|..:|||.|::..|:::....:|.|:::|.:.|...::.:.|.||..</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-string">gi|94968718|r 48 VVMDCAMPGMSGMDATKQIRTQWPDIAVLMLTMHSEDTWVRLALEAGANG 97</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-string">ref_rec 97 HFAK-PFDIDEIRDAV-------- 111</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-string"> :..| ..|:|.|: || </tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-string">gi|94968718|r 98 YILKSAIDLDLIQ-AVRRVANGET 120</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-string"># 1: ref_rec</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"><tt class="py-string"># 2: gi|94968761|receiver</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-string"># Length: 119</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-string"># Identity: 34/119 (28.6%)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-string"># Similarity: 58/119 (48.7%)</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-string"># Gaps: 9/119 ( 7.6%)</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-string"># Score: 154.0</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-string"># </tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-string">ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLLD 50</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-string"> ||||||:......|:..|...|::.....|.::||:|...:..||:|.|</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-string">gi|94968761|r 1 -ILIVDDEANTLASLSRAFRLAGHEATVCDNAVRALEIAKSKPFDLILSD 49</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-string">ref_rec 51 MKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFAK 100</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-string"> :.:||.||:.:|:.:|.......|::|:....::|..::..||||....|</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-string">gi|94968761|r 50 VVMPGRDGLTLLEDLKTAGVQAPVVMMSGQAHIEMAVKATRLGALDFLEK 99</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-string">ref_rec 101 PFDIDEIRDAV-------- 111</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-string"> |...|::...| </tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-string">gi|94968761|r 100 PLSTDKLLLTVENALKLKR 118</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-string"># 1: ref_rec</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-string"># 2: gi|94967506|receiver</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-string"># Length: 120</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-string"># Identity: 29/120 (24.2%)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-string"># Similarity: 53/120 (44.2%)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-string"># Gaps: 9/120 ( 7.5%)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-string"># Score: 121.0</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-string"># </tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-string">ref_rec 1 -KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTKERPDLVLL 49</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-string"> .|::|||..|..:.:..||.:.|:..........|.:.:.....||.::</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-string">gi|94967506|r 1 LHIVVVDDDPGTCVYIESVFAELGHTCKSFVRPEAAEEYILTHPVDLAIV 50</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-string">ref_rec 50 DMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA 99</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-string"> |:.:....|:|:|:|.:|....:..:|:|....|:|...|...||:.:..</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-string">gi|94967506|r 51 DVYLGSTTGVEVLRRCRVHRPKLYAVIITGQISLEMAARSIAEGAVDYIQ 100</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-string">ref_rec 100 KPFDIDEIRDAV-------- 111</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-string"> ||.|||.:.:.. </tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-string">gi|94967506|r 101 KPIDIDALLNIAERALEHKE 120</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-string"># 1: ref_rec</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-string"># 2: gi|94970045|receiver</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-string"># Length: 118</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-string"># Identity: 30/118 (25.4%)</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-string"># Similarity: 64/118 (54.2%)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-string"># Gaps: 9/118 ( 7.6%)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-string"># Score: 126.0</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-string"># </tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-string">ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIVTK--ERPDLVL 48</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-string"> :|:|:|:..:|....:.....||:...|.:|.:||.:.:| ||.|:::</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-string">gi|94970045|r 1 -VLLVEDEEALRAAAGDFLETRGYKIMTARDGTEALSMASKFAERIDVLI 49</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-string">ref_rec 49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF 98</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-string"> .|:.:||:.|..:.:.:..|....:|:.|:.|.: :.:..:.|:.:.:.|</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-string">gi|94970045|r 50 TDLVMPGISGRVLAQELVKIHPETKVMYMSGYDD-ETVMVNGEIDSSSAF 98</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"><tt class="py-string">ref_rec 99 -AKPFDID----EIRDAV 111</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"><tt class="py-string"> .|||.:| :||:.:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt class="py-string">gi|94970045|r 99 LRKPFRMDALSAKIREVL 116</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-string"># Aligned_sequences: 2</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-string"># 1: ref_rec</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-string"># 2: gi|94970041|receiver</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-string"># Matrix: EBLOSUM62</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"><tt class="py-string"># Gap_penalty: 10.0</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-string"># Extend_penalty: 0.5</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-string"># Length: 125</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"><tt class="py-string"># Identity: 35/125 (28.0%)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"><tt class="py-string"># Similarity: 70/125 (56.0%)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"><tt class="py-string"># Gaps: 18/125 (14.4%)</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"><tt class="py-string"># Score: 156.5</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"><tt class="py-string"># </tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-string">#</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-string">#=======================================</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-string">ref_rec 1 KILIVDDQYGIRILLNEVFNKEGYQTFQAANGLQALDIV--TKERPDLVL 48</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-string"> .:|:|:|:.|:|.|:..:.:::||...:|.:|.:||:|| :.::.|::|</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-string">gi|94970041|r 1 TVLLVEDEEGVRKLVRGILSRQGYHVLEATSGEEALEIVRESTQKIDMLL 50</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-string">ref_rec 49 LDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHF 98</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-string"> .|:.:.||.|.|:.:|:::...:::||.|:.|.:..:::. |.||..</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-string">gi|94970041|r 51 SDVVLVGMSGRELSERLRIQMPSLKVIYMSGYTDDAIVRH----GVLTES 96</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-string">ref_rec 99 A----KPFDIDEIRDAV-------- 111</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-string"> | |||..|.:...| </tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-string">gi|94970041|r 97 AEFLQKPFTSDSLLRKVRAVLQKRQ 121</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-string"></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 class="py-string">#---------------------------------------</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-string">#---------------------------------------</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-name">alignments</tt> <tt class="py-op">=</tt> <tt id="link-140" 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-140', 'list', 'link-140');">list</a></tt><tt class="py-op">(</tt><tt id="link-141" class="py-name" targets="Class Bio.AlignIO.EmbossIO.EmbossIterator=Bio.AlignIO.EmbossIO.EmbossIterator-class.html"><a title="Bio.AlignIO.EmbossIO.EmbossIterator" class="py-name" href="#" onclick="return doclink('link-141', 'EmbossIterator', 'link-141');">EmbossIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">pair_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alignments</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-142', 'get_all_seqs', 'link-28');">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">2</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-143" 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-143', 'id', 'link-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-144', 'get_all_seqs', 'link-28');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"IXI_234"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_235"</tt><tt class="py-op">]</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">alignments</tt> <tt class="py-op">=</tt> <tt id="link-145" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-145', 'list', 'link-140');">list</a></tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="Bio.AlignIO.EmbossIO.EmbossIterator" class="py-name" href="#" onclick="return doclink('link-146', 'EmbossIterator', 'link-141');">EmbossIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">simple_example</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</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">alignments</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-147', 'get_all_seqs', 'link-28');">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">4</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-148" 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-148', 'id', 'link-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-149', 'get_all_seqs', 'link-28');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"IXI_234"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_235"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_236"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_237"</tt><tt class="py-op">]</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">alignments</tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-150', 'list', 'link-140');">list</a></tt><tt class="py-op">(</tt><tt id="link-151" class="py-name"><a title="Bio.AlignIO.EmbossIO.EmbossIterator" class="py-name" href="#" onclick="return doclink('link-151', 'EmbossIterator', 'link-141');">EmbossIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">pair_example</tt> <tt class="py-op">+</tt> <tt class="py-name">simple_example</tt><tt class="py-op">)</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 class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alignments</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-152', 'get_all_seqs', 'link-28');">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">2</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-153', 'get_all_seqs', 'link-28');">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">4</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-154" 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-154', 'id', 'link-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-155', 'get_all_seqs', 'link-28');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"IXI_234"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_235"</tt><tt class="py-op">]</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-156" 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-156', 'id', 'link-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-157', 'get_all_seqs', 'link-28');">get_all_seqs</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> \ </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"IXI_234"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_235"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_236"</tt><tt class="py-op">,</tt> <tt class="py-string">"IXI_237"</tt><tt class="py-op">]</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-comment">#for a in EmbossIterator(StringIO(pair_example2)) :</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># print "Next:"</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for r in a.get_all_seqs() :</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># print r.seq.tostring()[:20] + "...", r.id</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-name">alignments</tt> <tt class="py-op">=</tt> <tt id="link-158" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-158', 'list', 'link-140');">list</a></tt><tt class="py-op">(</tt><tt id="link-159" class="py-name"><a title="Bio.AlignIO.EmbossIO.EmbossIterator" class="py-name" href="#" onclick="return doclink('link-159', 'EmbossIterator', 'link-141');">EmbossIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">pair_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</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">alignments</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">5</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-160" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-160', 'get_all_seqs', 'link-28');">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">2</tt> </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-name">r</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-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-162', 'get_all_seqs', 'link-28');">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-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"ref_rec"</tt><tt class="py-op">,</tt> <tt class="py-string">"gi|94968718|receiver"</tt><tt class="py-op">]</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">[</tt><tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-163" 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-163', 'id', 'link-41');">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">alignments</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-164', 'get_all_seqs', 'link-28');">get_all_seqs</a></tt><tt class="py-op">(</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 class="py-op">==</tt> <tt class="py-op">[</tt><tt class="py-string">"ref_rec"</tt><tt class="py-op">,</tt> <tt class="py-string">"gi|94970041|receiver"</tt><tt class="py-op">]</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> </tt><script type="text/javascript">
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