204 lines
27 KiB
HTML
204 lines
27 KiB
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<h1 class="epydoc">Source Code for <a href="obitools.alignment.ace-module.html">Module obitools.alignment.ace</a></h1>
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<pre class="py-src">
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<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.format=obitools.format-module.html"><a title="obitools.format" class="py-name" href="#" onclick="return doclink('link-1', 'format', 'link-1');">format</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Package obitools.format.genericparser=obitools.format.genericparser-module.html"><a title="obitools.format.genericparser" class="py-name" href="#" onclick="return doclink('link-2', 'genericparser', 'link-2');">genericparser</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class obitools.format.genericparser.GenericParser=obitools.format.genericparser.GenericParser-class.html"><a title="obitools.format.genericparser.GenericParser" class="py-name" href="#" onclick="return doclink('link-3', 'GenericParser', 'link-3');">GenericParser</a></tt> </tt>
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<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-5', 'utils', 'link-5');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Function obitools.utils.universalOpen()=obitools.utils-module.html#universalOpen"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-6', 'universalOpen', 'link-6');">universalOpen</a></tt> </tt>
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<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-7', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Module obitools.cns.fasta=obitools.cns.fasta-module.html,Module obitools.fasta=obitools.fasta-module.html,Module obitools.format.sequence.fasta=obitools.format.sequence.fasta-module.html"><a title="obitools.cns.fasta
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obitools.fasta
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obitools.format.sequence.fasta" class="py-name" href="#" onclick="return doclink('link-8', 'fasta', 'link-8');">fasta</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Function obitools.fasta.parseFastaDescription()=obitools.fasta-module.html#parseFastaDescription"><a title="obitools.fasta.parseFastaDescription" class="py-name" href="#" onclick="return doclink('link-9', 'parseFastaDescription', 'link-9');">parseFastaDescription</a></tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-10', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-11" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-11', 'NucSequence', 'link-11');">NucSequence</a></tt> </tt>
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<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt>
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<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">itertools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">imap</tt> </tt>
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<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
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<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
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<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
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<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable obitools.alignment.ace._contigIterator=obitools.alignment.ace-module.html#_contigIterator"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-12', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">=</tt><tt id="link-13" class="py-name"><a title="obitools.format.genericparser.GenericParser" class="py-name" href="#" onclick="return doclink('link-13', 'GenericParser', 'link-3');">GenericParser</a></tt><tt class="py-op">(</tt><tt class="py-string">'^CO '</tt><tt class="py-op">)</tt> </tt>
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<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
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<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt id="link-14" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-14', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method obitools.format.genericparser.GenericParser.addParseAction()=obitools.format.genericparser.GenericParser-class.html#addParseAction"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-15', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'AF'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nAF +(\S+) +([UC]) +(-?[0-9]+)'</tt><tt class="py-op">)</tt> </tt>
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<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt id="link-16" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-16', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-17', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'RD'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nRD +(\S+) +([0-9]+) +([0-9]+) +([0-9]+) *\n([A-Za-z\n*]+?)\n\n'</tt><tt class="py-op">)</tt> </tt>
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<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt id="link-18" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-18', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-19', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'DS'</tt><tt class="py-op">,</tt> <tt class="py-string">'\nDS +(.+)'</tt><tt class="py-op">)</tt> </tt>
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<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt id="link-20" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-20', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="obitools.format.genericparser.GenericParser.addParseAction" class="py-name" href="#" onclick="return doclink('link-21', 'addParseAction', 'link-15');">addParseAction</a></tt><tt class="py-op">(</tt><tt class="py-string">'CO'</tt><tt class="py-op">,</tt> <tt class="py-string">'^CO (\S+)'</tt><tt class="py-op">)</tt> </tt>
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<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
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<a name="contigIterator"></a><div id="contigIterator-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="contigIterator-toggle" onclick="return toggle('contigIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.alignment.ace-module.html#contigIterator">contigIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="contigIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="contigIterator-expanded"><a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-22', 'universalOpen', 'link-6');">universalOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
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<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt id="link-23" class="py-name"><a title="obitools.alignment.ace._contigIterator" class="py-name" href="#" onclick="return doclink('link-23', '_contigIterator', 'link-12');">_contigIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">contig</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
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<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rd</tt><tt class="py-op">,</tt><tt class="py-name">ds</tt><tt class="py-op">,</tt><tt class="py-name">af</tt> <tt class="py-keyword">in</tt> <tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'RD'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'DS'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'AF'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt id="link-24" class="py-name" targets="Variable obitools.BioSequence.id=obitools.BioSequence-class.html#id,Variable obitools.cns.quality.QualitySequence.id=obitools.cns.quality.QualitySequence-class.html#id,Variable obitools.obo.parser.OBOTerm.id=obitools.obo.parser.OBOTerm-class.html#id"><a title="obitools.BioSequence.id
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obitools.cns.quality.QualitySequence.id
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obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-24', 'id', 'link-24');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rd</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
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<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">shift</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">af</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
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<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">shift</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
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<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">>></tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt><tt class="py-string">"Sequence %s in contig %s has a negative paddng value %d : skipped"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="obitools.BioSequence.id
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obitools.cns.quality.QualitySequence.id
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obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-25', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'CO'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">shift</tt><tt class="py-op">)</tt> </tt>
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<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-comment">#continue</tt> </tt>
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<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
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<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt id="link-26" class="py-name" targets="Variable obitools.BioSequence.definition=obitools.BioSequence-class.html#definition,Variable obitools.WrappedBioSequence.definition=obitools.WrappedBioSequence-class.html#definition,Variable obitools.cns.quality.QualitySequence.definition=obitools.cns.quality.QualitySequence-class.html#definition,Variable obitools.obo.parser.OBOTerm.definition=obitools.obo.parser.OBOTerm-class.html#definition"><a title="obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
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obitools.cns.quality.QualitySequence.definition
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obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-26', 'definition', 'link-26');">definition</a></tt><tt class="py-op">,</tt><tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="obitools.fasta.parseFastaDescription" class="py-name" href="#" onclick="return doclink('link-27', 'parseFastaDescription', 'link-9');">parseFastaDescription</a></tt><tt class="py-op">(</tt><tt class="py-name">ds</tt><tt class="py-op">)</tt> </tt>
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<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">shift</tt> </tt>
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<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt id="link-28" class="py-name" targets="Variable obitools.BioSequence.seq=obitools.BioSequence-class.html#seq,Variable obitools.WrappedBioSequence.seq=obitools.WrappedBioSequence-class.html#seq"><a title="obitools.BioSequence.seq
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obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-28', 'seq', 'link-28');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rd</tt><tt class="py-op">[</tt><tt class="py-number">4</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">'\n'</tt><tt class="py-op">,</tt><tt class="py-string">''</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-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">contig</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
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obitools.table.Table.append
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obitools.table.TableRow.append
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obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-29', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-30', 'NucSequence', 'link-11');">NucSequence</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="obitools.BioSequence.id
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obitools.cns.quality.QualitySequence.id
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obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-31', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt id="link-32" class="py-name"><a title="obitools.BioSequence.seq
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obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-32', 'seq', 'link-28');">seq</a></tt><tt class="py-op">,</tt><tt id="link-33" class="py-name"><a title="obitools.BioSequence.definition
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obitools.WrappedBioSequence.definition
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obitools.cns.quality.QualitySequence.definition
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obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-33', 'definition', 'link-26');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> </tt>
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<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">maxlen</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">)</tt> </tt>
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<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-name">minshift</tt><tt class="py-op">=</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">)</tt> </tt>
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<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
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<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt>
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<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">s</tt> <tt class="py-keyword">in</tt> <tt class="py-name">contig</tt><tt class="py-op">:</tt> </tt>
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<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method obitools.BioSequence.getTags()=obitools.BioSequence-class.html#getTags,Method obitools.cns.quality.QualitySequence.getTags()=obitools.cns.quality.QualitySequence-class.html#getTags"><a title="obitools.BioSequence.getTags
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obitools.cns.quality.QualitySequence.getTags" class="py-name" href="#" onclick="return doclink('link-34', 'getTags', 'link-34');">getTags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
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<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">-=</tt><tt class="py-name">minshift</tt><tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
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<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-name">head</tt> <tt class="py-op">=</tt> <tt class="py-string">'-'</tt> <tt class="py-op">*</tt> <tt class="py-op">(</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> </tt>
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<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">tail</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">maxlen</tt> <tt class="py-op">+</tt> <tt class="py-name">minshift</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'shift'</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
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|
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-string">'tail'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">tail</tt> </tt>
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|
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">newseq</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-35', 'NucSequence', 'link-11');">NucSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="obitools.BioSequence.id
|
|
obitools.cns.quality.QualitySequence.id
|
|
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-36', 'id', 'link-24');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">head</tt> <tt class="py-op">+</tt> <tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-37', 'seq', 'link-28');">seq</a></tt><tt class="py-op">+</tt> <tt class="py-string">'-'</tt> <tt class="py-op">*</tt> <tt class="py-name">tail</tt><tt class="py-op">,</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="obitools.BioSequence.definition
|
|
obitools.WrappedBioSequence.definition
|
|
obitools.cns.quality.QualitySequence.definition
|
|
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-38', 'definition', 'link-26');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
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|
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="obitools.align.Alignement.append
|
|
obitools.table.Table.append
|
|
obitools.table.TableRow.append
|
|
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-39', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">newseq</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> </tt>
|
|
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">entry</tt><tt class="py-op">[</tt><tt class="py-string">'CO'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">rep</tt> </tt>
|
|
</div><a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> </tt><script type="text/javascript">
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