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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SeqIO-module.html">Package SeqIO</a> ::
Module AceIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.AceIO-module.html">Module Bio.SeqIO.AceIO</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-docstring">"""Bio.SeqIO support for the "ace" file format.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">You are expected to use this module via the Bio.SeqIO functions.</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring">See also the Bio.Sequencing.Ace module which offers more than just accessing</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">the contig consensus sequences in an ACE file as SeqRecord objects."""</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html,Package Bio.builders.SeqRecord=Bio.builders.SeqRecord-module.html,Package Bio.writers.SeqRecord=Bio.writers.SeqRecord-module.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-7', 'Alphabet', 'link-7');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Variable Bio.Alphabet.generic_nucleotide=Bio.Alphabet-module.html#generic_nucleotide"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-8', 'generic_nucleotide', 'link-8');">generic_nucleotide</a></tt><tt class="py-op">,</tt> <tt id="link-9" class="py-name" targets="Class Bio.Alphabet.Gapped=Bio.Alphabet.Gapped-class.html"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-9', 'Gapped', 'link-9');">Gapped</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Package Bio.Sequencing=Bio.Sequencing-module.html"><a title="Bio.Sequencing" class="py-name" href="#" onclick="return doclink('link-11', 'Sequencing', 'link-11');">Sequencing</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Module Bio.Sequencing.Ace=Bio.Sequencing.Ace-module.html"><a title="Bio.Sequencing.Ace" class="py-name" href="#" onclick="return doclink('link-12', 'Ace', 'link-12');">Ace</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function!</tt> </tt>
<a name="AceIterator"></a><div id="AceIterator-def"><a name="L19"></a><tt class="py-lineno">19</tt> <a class="py-toggle" href="#" id="AceIterator-toggle" onclick="return toggle('AceIterator');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.AceIO-module.html#AceIterator">AceIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="AceIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="AceIterator-expanded"><a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns SeqRecord objects from an ACE file.</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> This uses the Bio.Sequencing.Ace module to do the hard work. Note that</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> by iterating over the file in a single pass, we are forced to ignore any</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> WA, CT, RT or WR footer tags."""</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ace_contig</tt> <tt class="py-keyword">in</tt> <tt id="link-13" class="py-name"><a title="Bio.Sequencing.Ace" class="py-name" href="#" onclick="return doclink('link-13', 'Ace', 'link-12');">Ace</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Class Bio.Blast.NCBIStandalone.Iterator=Bio.Blast.NCBIStandalone.Iterator-class.html,Class Bio.CDD.Iterator=Bio.CDD.Iterator-class.html,Class Bio.Compass.Iterator=Bio.Compass.Iterator-class.html,Class Bio.ECell.Iterator=Bio.ECell.Iterator-class.html,Class Bio.Enzyme.Iterator=Bio.Enzyme.Iterator-class.html,Class Bio.Fasta.Iterator=Bio.Fasta.Iterator-class.html,Class Bio.GenBank.Iterator=Bio.GenBank.Iterator-class.html,Class Bio.Gobase.Iterator=Bio.Gobase.Iterator-class.html,Class Bio.IntelliGenetics.Iterator=Bio.IntelliGenetics.Iterator-class.html,Class Bio.LocusLink.Iterator=Bio.LocusLink.Iterator-class.html,Class Bio.Medline.Iterator=Bio.Medline.Iterator-class.html,Class Bio.MetaTool.Iterator=Bio.MetaTool.Iterator-class.html,Class Bio.NBRF.Iterator=Bio.NBRF.Iterator-class.html,Class Bio.Prosite.Iterator=Bio.Prosite.Iterator-class.html,Class Bio.Prosite.Prodoc.Iterator=Bio.Prosite.Prodoc.Iterator-class.html,Class Bio.Rebase.Iterator=Bio.Rebase.Iterator-class.html,Class Bio.SCOP.Cla.Iterator=Bio.SCOP.Cla.Iterator-class.html,Class Bio.SCOP.Des.Iterator=Bio.SCOP.Des.Iterator-class.html,Class Bio.SCOP.Dom.Iterator=Bio.SCOP.Dom.Iterator-class.html,Class Bio.SCOP.Hie.Iterator=Bio.SCOP.Hie.Iterator-class.html,Class Bio.SCOP.Raf.Iterator=Bio.SCOP.Raf.Iterator-class.html,Class Bio.Saf.Iterator=Bio.Saf.Iterator-class.html,Class Bio.Sequencing.Ace.Iterator=Bio.Sequencing.Ace.Iterator-class.html,Class Bio.Sequencing.Phd.Iterator=Bio.Sequencing.Phd.Iterator-class.html,Class Bio.SwissProt.SProt.Iterator=Bio.SwissProt.SProt.Iterator-class.html,Class Bio.UniGene.Iterator=Bio.UniGene.Iterator-class.html,Module Martel.Iterator=Martel.Iterator-module.html,Class Martel.Iterator.Iterator=Martel.Iterator.Iterator-class.html"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-14', 'Iterator', 'link-14');">Iterator</a></tt><tt class="py-op">(</tt><tt id="link-15" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-15', 'handle', 'link-15');">handle</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name"><a title="Bio.Sequencing.Ace" class="py-name" href="#" onclick="return doclink('link-16', 'Ace', 'link-12');">Ace</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Class Bio.CDD.RecordParser=Bio.CDD.RecordParser-class.html,Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.ECell.RecordParser=Bio.ECell.RecordParser-class.html,Class Bio.Enzyme.RecordParser=Bio.Enzyme.RecordParser-class.html,Class Bio.Fasta.RecordParser=Bio.Fasta.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.Gobase.RecordParser=Bio.Gobase.RecordParser-class.html,Class Bio.IntelliGenetics.RecordParser=Bio.IntelliGenetics.RecordParser-class.html,Class Bio.LocusLink.RecordParser=Bio.LocusLink.RecordParser-class.html,Class Bio.Medline.RecordParser=Bio.Medline.RecordParser-class.html,Class Bio.MetaTool.RecordParser=Bio.MetaTool.RecordParser-class.html,Class Bio.NBRF.RecordParser=Bio.NBRF.RecordParser-class.html,Class Bio.PopGen.FDist.RecordParser=Bio.PopGen.FDist.RecordParser-class.html,Class Bio.PopGen.GenePop.RecordParser=Bio.PopGen.GenePop.RecordParser-class.html,Class Bio.Prosite.Prodoc.RecordParser=Bio.Prosite.Prodoc.RecordParser-class.html,Class Bio.Prosite.RecordParser=Bio.Prosite.RecordParser-class.html,Class Bio.Rebase.RecordParser=Bio.Rebase.RecordParser-class.html,Class Bio.Saf.RecordParser=Bio.Saf.RecordParser-class.html,Class Bio.Sequencing.Ace.RecordParser=Bio.Sequencing.Ace.RecordParser-class.html,Class Bio.Sequencing.Phd.RecordParser=Bio.Sequencing.Phd.RecordParser-class.html,Class Bio.SwissProt.SProt.RecordParser=Bio.SwissProt.SProt.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html,Class Martel.Parser.RecordParser=Martel.Parser.RecordParser-class.html"><a title="Bio.CDD.RecordParser
Bio.Compass.RecordParser
Bio.ECell.RecordParser
Bio.Enzyme.RecordParser
Bio.Fasta.RecordParser
Bio.GenBank.RecordParser
Bio.Gobase.RecordParser
Bio.IntelliGenetics.RecordParser
Bio.LocusLink.RecordParser
Bio.Medline.RecordParser
Bio.MetaTool.RecordParser
Bio.NBRF.RecordParser
Bio.PopGen.FDist.RecordParser
Bio.PopGen.GenePop.RecordParser
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.RecordParser
Bio.Rebase.RecordParser
Bio.Saf.RecordParser
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Phd.RecordParser
Bio.SwissProt.SProt.RecordParser
Bio.UniGene.RecordParser
Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-17', 'RecordParser', 'link-17');">RecordParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-comment">#Convert the ACE contig record into a SeqRecord...</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">consensus_seq_str</tt> <tt class="py-op">=</tt> <tt class="py-name">ace_contig</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-18', 'sequence', 'link-18');">sequence</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"*"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">consensus_seq_str</tt> <tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-comment">#For consistency with most other file formats, map</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#any * gaps into 0 gaps.</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-string">"-"</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">consensus_seq_str</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">consensus_seq</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-19', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">consensus_seq_str</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>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-20', 'Gapped', 'link-9');">Gapped</a></tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-21', 'generic_nucleotide', 'link-8');">generic_nucleotide</a></tt><tt class="py-op">,</tt> <tt class="py-name">gap_char</tt><tt class="py-op">=</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">consensus_seq</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-22', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">consensus_seq_str</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-23', 'generic_nucleotide', 'link-8');">generic_nucleotide</a></tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Consensus base quality (BQ lines). Note that any gaps</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#(* character) in the consensus does not get a quality entry.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#This really needs Biopython support for per-letter-annotation.</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-comment">#TODO? - Base segments (BS lines) which indicates which read</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#phrap has chosen to be the consensus at a particular position.</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Perhaps as SeqFeature objects?</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Supporting reads (RD lines, plus perhaps QA and DS lines)</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Perhaps as SeqFeature objects?</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">seq_record</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-24', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">consensus_seq</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt id="link-25" 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-25', 'id', 'link-25');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ace_contig</tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'name', 'link-26');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-27', 'name', 'link-26');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">ace_contig</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-28', 'name', 'link-26');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">seq_record</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-comment">#All done</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt><script type="text/javascript">
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