376 lines
55 KiB
HTML
376 lines
55 KiB
HTML
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<a href="obitools-module.html">Package obitools</a> ::
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Module fasta
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<h1 class="epydoc">Source Code for <a href="obitools.fasta-module.html">Module obitools.fasta</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-docstring">"""</tt> </tt>
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<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">fasta module provides functions to read and write sequences in fasta format.</tt> </tt>
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<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
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<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
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<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
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<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 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-keyword">import</tt> <tt id="link-1" class="py-name" targets="Function obitools.bioSeqGenerator()=obitools-module.html#bioSeqGenerator"><a title="obitools.bioSeqGenerator" class="py-name" href="#" onclick="return doclink('link-1', 'bioSeqGenerator', 'link-1');">bioSeqGenerator</a></tt><tt class="py-op">,</tt><tt id="link-2" class="py-name" targets="Class obitools.BioSequence=obitools.BioSequence-class.html"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-2', 'BioSequence', 'link-2');">BioSequence</a></tt><tt class="py-op">,</tt><tt id="link-3" class="py-name" targets="Class obitools.AASequence=obitools.AASequence-class.html"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-3', 'AASequence', 'link-3');">AASequence</a></tt><tt class="py-op">,</tt><tt id="link-4" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-4', 'NucSequence', 'link-4');">NucSequence</a></tt> </tt>
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<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-5', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Package obitools.align=obitools.align-module.html"><a title="obitools.align" class="py-name" href="#" onclick="return doclink('link-6', 'align', 'link-6');">align</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Function obitools.align.alignmentReader()=obitools.align-module.html#alignmentReader"><a title="obitools.align.alignmentReader" class="py-name" href="#" onclick="return doclink('link-7', 'alignmentReader', 'link-7');">alignmentReader</a></tt> </tt>
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<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-8', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-9', 'utils', 'link-9');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" 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-10', 'universalOpen', 'link-10');">universalOpen</a></tt> </tt>
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<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</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-11" class="py-name" targets="Variable obitools.fasta._parseFastaTag=obitools.fasta-module.html#_parseFastaTag"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-11', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">=</tt><tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">'([a-zA-Z]\w*) *= *([^;]+);'</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>
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<a name="parseFastaDescription"></a><div id="parseFastaDescription-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="parseFastaDescription-toggle" onclick="return toggle('parseFastaDescription');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#parseFastaDescription">parseFastaDescription</a><tt class="py-op">(</tt><tt class="py-param">ds</tt><tt class="py-op">,</tt><tt class="py-param">tagparser</tt><tt class="py-op">=</tt><tt id="link-12" class="py-name"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-12', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="parseFastaDescription-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parseFastaDescription-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-name">info</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</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-number">0</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-number">1</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 class="py-op">)</tt> </tt>
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<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tagparser</tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">ds</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt id="link-13" 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-13', 'definition', 'link-13');">definition</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tagparser</tt><tt class="py-op">.</tt><tt class="py-name">sub</tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">,</tt><tt class="py-name">ds</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="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">info</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">try</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">info</tt><tt class="py-op">[</tt><tt class="py-name">k</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt class="py-name">info</tt><tt class="py-op">[</tt><tt class="py-name">k</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">except</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 class="py-keyword">pass</tt> </tt>
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<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
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<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-14" 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-14', 'definition', 'link-13');">definition</a></tt><tt class="py-op">,</tt><tt class="py-name">info</tt> </tt>
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</div><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt>
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<a name="_fastaJoinSeq"></a><div id="_fastaJoinSeq-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="_fastaJoinSeq-toggle" onclick="return toggle('_fastaJoinSeq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#_fastaJoinSeq">_fastaJoinSeq</a><tt class="py-op">(</tt><tt class="py-param">seqarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="_fastaJoinSeq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_fastaJoinSeq-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</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">seqarray</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
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</div><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
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<a name="_parseFasta"></a><div id="_parseFasta-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="_parseFasta-toggle" onclick="return toggle('_parseFasta');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#_parseFasta">_parseFasta</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">bioseqfactory</tt><tt class="py-op">,</tt><tt class="py-param">tagparser</tt><tt class="py-op">=</tt><tt id="link-15" class="py-name"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-15', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">,</tt><tt class="py-param">joinseq</tt><tt class="py-op">=</tt><tt id="link-16" class="py-name" targets="Function obitools.fasta._fastaJoinSeq()=obitools.fasta-module.html#_fastaJoinSeq"><a title="obitools.fasta._fastaJoinSeq" class="py-name" href="#" onclick="return doclink('link-16', '_fastaJoinSeq', 'link-16');">_fastaJoinSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="_parseFasta-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parseFasta-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> Parse a fasta record.</tt> </tt>
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<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> @attention: internal purpuse function</tt> </tt>
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<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: a sequence object containing all lines corresponding</tt> </tt>
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<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> to one fasta sequence</tt> </tt>
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<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: C{list} or C{tuple} of C{str}</tt> </tt>
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<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> @param bioseqfactory: a callable object return a BioSequence</tt> </tt>
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<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> instance.</tt> </tt>
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<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> @type bioseqfactory: a callable object</tt> </tt>
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<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> @param tagparser: a compiled regular expression usable</tt> </tt>
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<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> to identify key, value couples from </tt> </tt>
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<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> title line.</tt> </tt>
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<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> @type tagparser: regex instance</tt> </tt>
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<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> @return: a C{BioSequence} instance </tt> </tt>
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<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">title</tt> <tt class="py-op">=</tt> <tt id="link-17" 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-17', 'seq', 'link-17');">seq</a></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">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">split</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>
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<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'id', 'link-18');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">title</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
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<a name="L52"></a><tt class="py-lineno"> 52</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">title</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
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<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt id="link-19" 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-19', 'definition', 'link-13');">definition</a></tt><tt class="py-op">,</tt><tt class="py-name">info</tt><tt class="py-op">=</tt><tt id="link-20" 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-20', 'parseFastaDescription', 'link-20');">parseFastaDescription</a></tt><tt class="py-op">(</tt><tt class="py-name">title</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-name">tagparser</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
|
|
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt id="link-21" 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-21', 'definition', 'link-13');">definition</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
|
|
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
|
|
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-22', 'seq', 'link-17');">seq</a></tt><tt class="py-op">=</tt><tt class="py-name">joinseq</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-23', 'seq', 'link-17');">seq</a></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>
|
|
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bioseqfactory</tt><tt class="py-op">(</tt><tt id="link-24" 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-24', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt> <tt id="link-25" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-25', 'seq', 'link-17');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-26" 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-26', 'definition', 'link-13');">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>
|
|
</div><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> </tt>
|
|
<a name="fastaIterator"></a><div id="fastaIterator-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="fastaIterator-toggle" onclick="return toggle('fastaIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#fastaIterator">fastaIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt><tt class="py-param">bioseqfactory</tt><tt class="py-op">=</tt><tt id="link-27" class="py-name"><a title="obitools.bioSeqGenerator" class="py-name" href="#" onclick="return doclink('link-27', 'bioSeqGenerator', 'link-1');">bioSeqGenerator</a></tt><tt class="py-op">,</tt><tt class="py-param">tagparser</tt><tt class="py-op">=</tt><tt id="link-28" class="py-name"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-28', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">,</tt><tt class="py-param">joinseq</tt><tt class="py-op">=</tt><tt id="link-29" class="py-name"><a title="obitools.fasta._fastaJoinSeq" class="py-name" href="#" onclick="return doclink('link-29', '_fastaJoinSeq', 'link-16');">_fastaJoinSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="fastaIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fastaIterator-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> iterate through a fasta file sequence by sequence.</tt> </tt>
|
|
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> Returned sequences by this iterator will be BioSequence</tt> </tt>
|
|
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> instances</tt> </tt>
|
|
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
|
|
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> @param file: a line iterator containing fasta data or a filename</tt> </tt>
|
|
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> @type file: an iterable object or str</tt> </tt>
|
|
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> @param bioseqfactory: a callable object return a BioSequence</tt> </tt>
|
|
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> instance.</tt> </tt>
|
|
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> @type bioseqfactory: a callable object</tt> </tt>
|
|
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
|
|
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> @param tagparser: a compiled regular expression usable</tt> </tt>
|
|
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> to identify key, value couples from </tt> </tt>
|
|
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> title line.</tt> </tt>
|
|
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> @type tagparser: regex instance</tt> </tt>
|
|
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> @return: an iterator on C{BioSequence} instance</tt> </tt>
|
|
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaNucIterator}</tt> </tt>
|
|
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaAAIterator}</tt> </tt>
|
|
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
|
|
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> </tt>
|
|
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-30', 'universalOpen', 'link-10');">universalOpen</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt><tt class="py-string">'ru'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt id="link-31" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-31', 'seq', 'link-17');">seq</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ligne</tt> <tt class="py-keyword">in</tt> <tt class="py-name">file</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ligne</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-keyword">and</tt> <tt id="link-32" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-32', 'seq', 'link-17');">seq</a></tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-33" class="py-name" targets="Function obitools.fasta._parseFasta()=obitools.fasta-module.html#_parseFasta"><a title="obitools.fasta._parseFasta" class="py-name" href="#" onclick="return doclink('link-33', '_parseFasta', 'link-33');">_parseFasta</a></tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-34', 'seq', 'link-17');">seq</a></tt><tt class="py-op">,</tt><tt class="py-name">bioseqfactory</tt><tt class="py-op">,</tt><tt class="py-name">tagparser</tt><tt class="py-op">,</tt><tt class="py-name">joinseq</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt id="link-35" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-35', 'seq', 'link-17');">seq</a></tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-36', 'seq', 'link-17');">seq</a></tt><tt class="py-op">.</tt><tt id="link-37" 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
|
|
obitools.table.Table.append
|
|
obitools.table.TableRow.append
|
|
obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ligne</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
|
|
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-38" class="py-name"><a title="obitools.fasta._parseFasta" class="py-name" href="#" onclick="return doclink('link-38', '_parseFasta', 'link-33');">_parseFasta</a></tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-39', 'seq', 'link-17');">seq</a></tt><tt class="py-op">,</tt><tt class="py-name">bioseqfactory</tt><tt class="py-op">,</tt><tt class="py-name">tagparser</tt><tt class="py-op">,</tt><tt class="py-name">joinseq</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
|
|
<a name="fastaNucIterator"></a><div id="fastaNucIterator-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="fastaNucIterator-toggle" onclick="return toggle('fastaNucIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#fastaNucIterator">fastaNucIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt><tt class="py-param">tagparser</tt><tt class="py-op">=</tt><tt id="link-40" class="py-name"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-40', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="fastaNucIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fastaNucIterator-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> iterate through a fasta file sequence by sequence.</tt> </tt>
|
|
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> Returned sequences by this iterator will be NucSequence</tt> </tt>
|
|
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> instances</tt> </tt>
|
|
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> @param file: a line iterator containint fasta data</tt> </tt>
|
|
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> @type file: an iterable object</tt> </tt>
|
|
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
|
|
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> @param tagparser: a compiled regular expression usable</tt> </tt>
|
|
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> to identify key, value couples from </tt> </tt>
|
|
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> title line.</tt> </tt>
|
|
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> @type tagparser: regex instance</tt> </tt>
|
|
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> @return: an iterator on C{NucBioSequence} instance</tt> </tt>
|
|
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaIterator}</tt> </tt>
|
|
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaAAIterator}</tt> </tt>
|
|
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-41" class="py-name" targets="Function obitools.fasta.fastaIterator()=obitools.fasta-module.html#fastaIterator"><a title="obitools.fasta.fastaIterator" class="py-name" href="#" onclick="return doclink('link-41', 'fastaIterator', 'link-41');">fastaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt id="link-42" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-42', 'NucSequence', 'link-4');">NucSequence</a></tt><tt class="py-op">,</tt><tt class="py-name">tagparser</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> </tt>
|
|
<a name="fastaAAIterator"></a><div id="fastaAAIterator-def"><a name="L116"></a><tt class="py-lineno">116</tt> <a class="py-toggle" href="#" id="fastaAAIterator-toggle" onclick="return toggle('fastaAAIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#fastaAAIterator">fastaAAIterator</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt><tt class="py-param">tagparser</tt><tt class="py-op">=</tt><tt id="link-43" class="py-name"><a title="obitools.fasta._parseFastaTag" class="py-name" href="#" onclick="return doclink('link-43', '_parseFastaTag', 'link-11');">_parseFastaTag</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="fastaAAIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fastaAAIterator-expanded"><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> iterate through a fasta file sequence by sequence.</tt> </tt>
|
|
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> Returned sequences by this iterator will be AASequence</tt> </tt>
|
|
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> instances</tt> </tt>
|
|
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> @param file: a line iterator containing fasta data</tt> </tt>
|
|
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> @type file: an iterable object</tt> </tt>
|
|
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> @param tagparser: a compiled regular expression usable</tt> </tt>
|
|
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> to identify key, value couples from </tt> </tt>
|
|
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> title line.</tt> </tt>
|
|
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> @type tagparser: regex instance</tt> </tt>
|
|
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> @return: an iterator on C{AABioSequence} instance</tt> </tt>
|
|
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
|
|
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaIterator}</tt> </tt>
|
|
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> @see: L{fastaNucIterator}</tt> </tt>
|
|
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-44" class="py-name"><a title="obitools.fasta.fastaIterator" class="py-name" href="#" onclick="return doclink('link-44', 'fastaIterator', 'link-41');">fastaIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt id="link-45" class="py-name"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-45', 'AASequence', 'link-3');">AASequence</a></tt><tt class="py-op">,</tt><tt class="py-name">tagparser</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
|
|
<a name="formatFasta"></a><div id="formatFasta-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="formatFasta-toggle" onclick="return toggle('formatFasta');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.fasta-module.html#formatFasta">formatFasta</a><tt class="py-op">(</tt><tt class="py-param">data</tt><tt class="py-op">,</tt><tt class="py-param">gbmode</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="formatFasta-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="formatFasta-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> Convert a seqence or a set of sequences in a</tt> </tt>
|
|
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> string following the fasta format</tt> </tt>
|
|
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> @param data: sequence or a set of sequences</tt> </tt>
|
|
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> @type data: BioSequence instance or an iterable object </tt> </tt>
|
|
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> on BioSequence instances</tt> </tt>
|
|
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> @param gbmode: if set to C{True} identifier part of the title</tt> </tt>
|
|
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> line follows recommendation from nbci to allow</tt> </tt>
|
|
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> sequence indexing with the blast formatdb command.</tt> </tt>
|
|
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> @type gbmode: bool</tt> </tt>
|
|
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> @return: a fasta formated string</tt> </tt>
|
|
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: str</tt> </tt>
|
|
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-46', 'BioSequence', 'link-2');">BioSequence</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">data</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L156"></a><tt class="py-lineno">156</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>
|
|
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name" targets="Module obitools.ecopcr.sequence=obitools.ecopcr.sequence-module.html,Package obitools.format.sequence=obitools.format.sequence-module.html"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-47', 'sequence', 'link-47');">sequence</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-48" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-48', 'seq', 'link-17');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-49" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-49', 'sequence', 'link-47');">sequence</a></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">if</tt> <tt id="link-50" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-50', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-51" 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-51', 'definition', 'link-13');">definition</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt id="link-52" 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-52', 'definition', 'link-13');">definition</a></tt><tt class="py-op">=</tt><tt class="py-string">''</tt> </tt>
|
|
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt id="link-53" 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-53', 'definition', 'link-13');">definition</a></tt><tt class="py-op">=</tt><tt id="link-54" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-54', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-55" 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-55', 'definition', 'link-13');">definition</a></tt> </tt>
|
|
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">frgseq</tt> <tt class="py-op">=</tt> <tt class="py-string">'\n'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-56" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-56', 'seq', 'link-17');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">:</tt><tt class="py-name">x</tt><tt class="py-op">+</tt><tt class="py-number">60</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">xrange</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-57', 'seq', 'link-17');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">60</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">=</tt><tt class="py-string">'; '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'%s=%s'</tt> <tt class="py-op">%</tt> <tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt id="link-58" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-58', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Variable obitools.sequenceencoder.Complement._info=obitools.sequenceencoder.Complement-class.html#_info"><a title="obitools.sequenceencoder.Complement._info" class="py-name" href="#" onclick="return doclink('link-59', '_info', 'link-59');">_info</a></tt><tt class="py-op">.</tt><tt class="py-name">items</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">info</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">info</tt><tt class="py-op">=</tt><tt class="py-name">info</tt><tt class="py-op">+</tt><tt class="py-string">';'</tt> </tt>
|
|
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-60" 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-60', 'id', 'link-18');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-61', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-62" 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-62', 'id', 'link-18');">id</a></tt> </tt>
|
|
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">gbmode</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'gi'</tt> <tt class="py-keyword">in</tt> <tt id="link-63" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-63', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-64" 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-64', 'id', 'link-18');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"gi|%s|%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-65', 'sequence', 'link-47');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-string">'gi'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt id="link-66" 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-66', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-67" 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-67', 'id', 'link-18');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"lcl|%s|"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-68" 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-68', 'id', 'link-18');">id</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">title</tt><tt class="py-op">=</tt><tt class="py-string">'>%s %s %s'</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-69" 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-69', 'id', 'link-18');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">info</tt><tt class="py-op">,</tt><tt id="link-70" 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-70', 'definition', 'link-13');">definition</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-71" 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-71', 'append', 'link-37');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%s\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">title</tt><tt class="py-op">,</tt><tt class="py-name">frgseq</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 class="py-keyword">return</tt> <tt class="py-string">'\n'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">rep</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt><script type="text/javascript">
|
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