566 lines
115 KiB
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566 lines
115 KiB
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<h1 class="epydoc">Source Code for <a href="obitools.location-module.html">Package obitools.location</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.sequenceencoder=obitools.sequenceencoder-module.html"><a title="obitools.sequenceencoder" class="py-name" href="#" onclick="return doclink('link-1', 'sequenceencoder', 'link-1');">sequenceencoder</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Class obitools.sequenceencoder.Complement=obitools.sequenceencoder.Complement-class.html"><a title="obitools.sequenceencoder.Complement" class="py-name" href="#" onclick="return doclink('link-2', 'Complement', 'link-2');">Complement</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">import</tt> <tt id="link-3" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-3', 'obitools', 'link-0');">obitools</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">import</tt> <tt class="py-name">re</tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
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<a name="Location"></a><div id="Location-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="Location-toggle" onclick="return toggle('Location');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.location.Location-class.html">Location</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="Location-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Location-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
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<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"> Define a location on a sequence. </tt> </tt>
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<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"> """</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="Location.extractSequence"></a><div id="Location.extractSequence-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="Location.extractSequence-toggle" onclick="return toggle('Location.extractSequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.Location-class.html#extractSequence">extractSequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="Location.extractSequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Location.extractSequence-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"> Extract subsequence corresponding to a Location.</tt> </tt>
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<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> @param sequence: </tt> </tt>
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<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> @type sequence: C{BioSequence} or C{str}</tt> </tt>
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<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
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<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-4" 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
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-4', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</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="Class obitools.BioSequence=obitools.BioSequence-class.html"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-6', 'BioSequence', 'link-6');">BioSequence</a></tt><tt class="py-op">,</tt><tt class="py-name">str</tt><tt class="py-op">)</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-string">"sequence must be an instance of str or BioSequence"</tt> </tt>
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<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
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<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-7" class="py-name"><a title="obitools.ecopcr.sequence
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-7', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</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 id="link-8" 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-8', 'seq', 'link-8');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method obitools.location.ComplementLocation._extractSequence()=obitools.location.ComplementLocation-class.html#_extractSequence,Method obitools.location.CompositeLocation._extractSequence()=obitools.location.CompositeLocation-class.html#_extractSequence,Method obitools.location.PointLocation._extractSequence()=obitools.location.PointLocation-class.html#_extractSequence,Method obitools.location.SimpleLocation._extractSequence()=obitools.location.SimpleLocation-class.html#_extractSequence"><a title="obitools.location.ComplementLocation._extractSequence
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obitools.location.CompositeLocation._extractSequence
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obitools.location.PointLocation._extractSequence
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obitools.location.SimpleLocation._extractSequence" class="py-name" href="#" onclick="return doclink('link-9', '_extractSequence', 'link-9');">_extractSequence</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="obitools.ecopcr.sequence
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-10', 'sequence', 'link-4');">sequence</a></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">else</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-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="obitools.ecopcr.sequence
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-11', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-12', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Class obitools.AASequence=obitools.AASequence-class.html"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-13', 'AASequence', 'link-13');">AASequence</a></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">assert</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method obitools.location.ComplementLocation.needNucleic()=obitools.location.ComplementLocation-class.html#needNucleic,Method obitools.location.CompositeLocation.needNucleic()=obitools.location.CompositeLocation-class.html#needNucleic,Method obitools.location.Location.needNucleic()=obitools.location.Location-class.html#needNucleic,Method obitools.location.PointLocation.needNucleic()=obitools.location.PointLocation-class.html#needNucleic,Method obitools.location.SimpleLocation.needNucleic()=obitools.location.SimpleLocation-class.html#needNucleic,Method obitools.location.feature.Feature.needNucleic()=obitools.location.feature.Feature-class.html#needNucleic"><a title="obitools.location.ComplementLocation.needNucleic
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obitools.location.CompositeLocation.needNucleic
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obitools.location.Location.needNucleic
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obitools.location.PointLocation.needNucleic
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obitools.location.SimpleLocation.needNucleic
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obitools.location.feature.Feature.needNucleic" class="py-name" href="#" onclick="return doclink('link-14', 'needNucleic', 'link-14');">needNucleic</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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-string">"This location can be used only with Nucleic sequences"</tt> </tt>
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<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt id="link-15" class="py-name"><a title="obitools.BioSequence.seq
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obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-15', 'seq', 'link-8');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="obitools.location.ComplementLocation._extractSequence
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obitools.location.CompositeLocation._extractSequence
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obitools.location.PointLocation._extractSequence
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obitools.location.SimpleLocation._extractSequence" class="py-name" href="#" onclick="return doclink('link-16', '_extractSequence', 'link-9');">_extractSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="obitools.ecopcr.sequence
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-17', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
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<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="obitools.ecopcr.sequence
|
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-18', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name"><a title="obitools
|
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-19', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-20', 'AASequence', 'link-13');">AASequence</a></tt><tt class="py-op">)</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">st</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-21', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-22', 'AASequence', 'link-13');">AASequence</a></tt> </tt>
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<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-keyword">else</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">st</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-23', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-24', 'NucSequence', 'link-24');">NucSequence</a></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 id="link-25" class="py-name"><a title="obitools.BioSequence.seq
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obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-25', 'seq', 'link-8');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">st</tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="obitools.ecopcr.sequence
|
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-26', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-27" 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
|
|
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-27', 'id', 'link-27');">id</a></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 id="link-28" class="py-name"><a title="obitools.BioSequence.seq
|
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obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-28', 'seq', 'link-8');">seq</a></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 id="link-29" class="py-name"><a title="obitools.ecopcr.sequence
|
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-29', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-30" 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-30', 'definition', 'link-30');">definition</a></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 class="py-op">**</tt><tt id="link-31" class="py-name"><a title="obitools.ecopcr.sequence
|
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-31', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-32" 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
|
|
obitools.cns.quality.QualitySequence.getTags" class="py-name" href="#" onclick="return doclink('link-32', 'getTags', 'link-32');">getTags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-33', 'seq', 'link-8');">seq</a></tt><tt class="py-op">[</tt><tt class="py-string">'location'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</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>
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<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">'length'</tt> <tt class="py-keyword">in</tt> <tt id="link-34" class="py-name"><a title="obitools.ecopcr.sequence
|
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obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-34', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="obitools.BioSequence.getTags
|
|
obitools.cns.quality.QualitySequence.getTags" class="py-name" href="#" onclick="return doclink('link-35', 'getTags', 'link-32');">getTags</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
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<a name="L40"></a><tt class="py-lineno"> 40</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-8');">seq</a></tt><tt class="py-op">[</tt><tt class="py-string">'length'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-37', 'seq', 'link-8');">seq</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> </tt>
|
|
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-38" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-38', 'seq', 'link-8');">seq</a></tt> </tt>
|
|
</div><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
|
|
<a name="Location.isDirect"></a><div id="Location.isDirect-def"><a name="L44"></a><tt class="py-lineno"> 44</tt> <a class="py-toggle" href="#" id="Location.isDirect-toggle" onclick="return toggle('Location.isDirect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.Location-class.html#isDirect">isDirect</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Location.isDirect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Location.isDirect-expanded"><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
|
|
<a name="Location.isSimple"></a><div id="Location.isSimple-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="Location.isSimple-toggle" onclick="return toggle('Location.isSimple');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.Location-class.html#isSimple">isSimple</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Location.isSimple-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Location.isSimple-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> Indicate if a location is composed of a single continuous </tt> </tt>
|
|
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> region or is composed by the junction of several locations</tt> </tt>
|
|
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> by the C{join} operator.</tt> </tt>
|
|
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> @return: C{True} if the location is composed of a single</tt> </tt>
|
|
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> continuous region.</tt> </tt>
|
|
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: bool</tt> </tt>
|
|
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
|
|
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
|
|
<a name="Location.isFullLength"></a><div id="Location.isFullLength-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="Location.isFullLength-toggle" onclick="return toggle('Location.isFullLength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.Location-class.html#isFullLength">isFullLength</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Location.isFullLength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Location.isFullLength-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
|
|
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> </tt>
|
|
<a name="Location.needNucleic"></a><div id="Location.needNucleic-def"><a name="L64"></a><tt class="py-lineno"> 64</tt> <a class="py-toggle" href="#" id="Location.needNucleic-toggle" onclick="return toggle('Location.needNucleic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.Location-class.html#needNucleic">needNucleic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="Location.needNucleic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Location.needNucleic-expanded"><a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> If a location contains a complement operator, it can be use</tt> </tt>
|
|
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> only on nucleic sequence.</tt> </tt>
|
|
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> @return: C{True} if location contains a complement operator</tt> </tt>
|
|
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: bool</tt> </tt>
|
|
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
|
|
</div></div><a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation"></a><div id="SimpleLocation-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="SimpleLocation-toggle" onclick="return toggle('SimpleLocation');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html">SimpleLocation</a><tt class="py-op">(</tt><tt class="py-base-class">Location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SimpleLocation-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> A simple location is describe a continuous region of </tt> </tt>
|
|
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> a sequence define by a C{begin} and a C{end} position.</tt> </tt>
|
|
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
|
|
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.__init__"></a><div id="SimpleLocation.__init__-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="SimpleLocation.__init__-toggle" onclick="return toggle('SimpleLocation.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">begin</tt><tt class="py-op">,</tt><tt class="py-param">end</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.__init__-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
|
|
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> Build a new C{SimpleLocation} instance. Valid</tt> </tt>
|
|
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> position are define on M{[1,N]} with N the length</tt> </tt>
|
|
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> of the sequence.</tt> </tt>
|
|
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> @param begin: start position of the location</tt> </tt>
|
|
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> @type begin: int</tt> </tt>
|
|
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> @param end: end position of the location</tt> </tt>
|
|
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> @type end: int</tt> </tt>
|
|
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">begin</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">end</tt> <tt class="py-op">></tt> <tt class="py-number">0</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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt> <tt class="py-op">=</tt> <tt class="py-name">begin</tt> </tt>
|
|
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt> <tt class="py-op">=</tt> <tt class="py-name">end</tt> </tt>
|
|
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation._extractSequence"></a><div id="SimpleLocation._extractSequence-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="SimpleLocation._extractSequence-toggle" onclick="return toggle('SimpleLocation._extractSequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#_extractSequence">_extractSequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation._extractSequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation._extractSequence-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
|
|
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-op">(</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-39', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">and</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt> <tt class="py-op"><=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-40', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
|
|
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-string">"Sequence length %d is too short"</tt> <tt class="py-op">%</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-41" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-41', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
|
|
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-42" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-42', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt><tt class="py-op">]</tt> </tt>
|
|
</div><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.isDirect"></a><div id="SimpleLocation.isDirect-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="SimpleLocation.isDirect-toggle" onclick="return toggle('SimpleLocation.isDirect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#isDirect">isDirect</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.isDirect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.isDirect-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.isSimple"></a><div id="SimpleLocation.isSimple-def"><a name="L107"></a><tt class="py-lineno">107</tt> <a class="py-toggle" href="#" id="SimpleLocation.isSimple-toggle" onclick="return toggle('SimpleLocation.isSimple');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#isSimple">isSimple</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.isSimple-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.isSimple-expanded"><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.isFullLength"></a><div id="SimpleLocation.isFullLength-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="SimpleLocation.isFullLength-toggle" onclick="return toggle('SimpleLocation.isFullLength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#isFullLength">isFullLength</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.isFullLength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.isFullLength-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">before</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">after</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.simplify"></a><div id="SimpleLocation.simplify-def"><a name="L113"></a><tt class="py-lineno">113</tt> <a class="py-toggle" href="#" id="SimpleLocation.simplify-toggle" onclick="return toggle('SimpleLocation.simplify');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#simplify">simplify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.simplify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.simplify-expanded"><a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-43" class="py-name" targets="Class obitools.location.PointLocation=obitools.location.PointLocation-class.html"><a title="obitools.location.PointLocation" class="py-name" href="#" onclick="return doclink('link-43', 'PointLocation', 'link-43');">PointLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
|
|
</div><a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.needNucleic"></a><div id="SimpleLocation.needNucleic-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="SimpleLocation.needNucleic-toggle" onclick="return toggle('SimpleLocation.needNucleic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#needNucleic">needNucleic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.needNucleic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.needNucleic-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
|
|
</div><a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
|
|
<a name="SimpleLocation.__str__"></a><div id="SimpleLocation.__str__-def"><a name="L122"></a><tt class="py-lineno">122</tt> <a class="py-toggle" href="#" id="SimpleLocation.__str__-toggle" onclick="return toggle('SimpleLocation.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.SimpleLocation-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="SimpleLocation.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SimpleLocation.__str__-expanded"><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">before</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-name">True</tt><tt class="py-op">:</tt><tt class="py-string">'<'</tt><tt class="py-op">,</tt><tt class="py-name">False</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">self</tt><tt class="py-op">.</tt><tt class="py-name">before</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">after</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-name">True</tt><tt class="py-op">:</tt><tt class="py-string">'>'</tt><tt class="py-op">,</tt><tt class="py-name">False</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">self</tt><tt class="py-op">.</tt><tt class="py-name">after</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s%d..%s%d"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">before</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_begin</tt><tt class="py-op">,</tt><tt class="py-name">after</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation"></a><div id="PointLocation-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="PointLocation-toggle" onclick="return toggle('PointLocation');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html">PointLocation</a><tt class="py-op">(</tt><tt class="py-base-class">Location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="PointLocation-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="PointLocation-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> A point location describes a location on a sequence</tt> </tt>
|
|
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> limited to a single position</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>
|
|
<a name="PointLocation.__init__"></a><div id="PointLocation.__init__-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="PointLocation.__init__-toggle" onclick="return toggle('PointLocation.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.__init__-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">position</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> </tt>
|
|
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pos</tt><tt class="py-op">=</tt><tt class="py-name">position</tt> </tt>
|
|
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation._extractSequence"></a><div id="PointLocation._extractSequence-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="PointLocation._extractSequence-toggle" onclick="return toggle('PointLocation._extractSequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#_extractSequence">_extractSequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation._extractSequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation._extractSequence-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
|
|
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_end</tt> <tt class="py-op"><=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-44" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-44', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
|
|
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">"Sequence length %d is too short"</tt> <tt class="py-op">%</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-45', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
|
|
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-46" class="py-name"><a title="obitools.ecopcr.sequence
|
|
obitools.format.sequence" class="py-name" href="#" onclick="return doclink('link-46', 'sequence', 'link-4');">sequence</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pos</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
|
|
</div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.isDirect"></a><div id="PointLocation.isDirect-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="PointLocation.isDirect-toggle" onclick="return toggle('PointLocation.isDirect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#isDirect">isDirect</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.isDirect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.isDirect-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.isSimple"></a><div id="PointLocation.isSimple-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="PointLocation.isSimple-toggle" onclick="return toggle('PointLocation.isSimple');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#isSimple">isSimple</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.isSimple-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.isSimple-expanded"><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.isFullLength"></a><div id="PointLocation.isFullLength-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="PointLocation.isFullLength-toggle" onclick="return toggle('PointLocation.isFullLength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#isFullLength">isFullLength</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.isFullLength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.isFullLength-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.simplify"></a><div id="PointLocation.simplify-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="PointLocation.simplify-toggle" onclick="return toggle('PointLocation.simplify');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#simplify">simplify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.simplify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.simplify-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
|
|
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.needNucleic"></a><div id="PointLocation.needNucleic-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="PointLocation.needNucleic-toggle" onclick="return toggle('PointLocation.needNucleic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#needNucleic">needNucleic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.needNucleic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.needNucleic-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
|
|
</div><a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
|
|
<a name="PointLocation.__str__"></a><div id="PointLocation.__str__-def"><a name="L159"></a><tt class="py-lineno">159</tt> <a class="py-toggle" href="#" id="PointLocation.__str__-toggle" onclick="return toggle('PointLocation.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.PointLocation-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="PointLocation.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="PointLocation.__str__-expanded"><a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_pos</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation"></a><div id="CompositeLocation-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="CompositeLocation-toggle" onclick="return toggle('CompositeLocation');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html">CompositeLocation</a><tt class="py-op">(</tt><tt class="py-base-class">Location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CompositeLocation-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
|
|
<a name="CompositeLocation.__init__"></a><div id="CompositeLocation.__init__-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="CompositeLocation.__init__-toggle" onclick="return toggle('CompositeLocation.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">locations</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">locations</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
|
|
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation._extractSequence"></a><div id="CompositeLocation._extractSequence-def"><a name="L169"></a><tt class="py-lineno">169</tt> <a class="py-toggle" href="#" id="CompositeLocation._extractSequence-toggle" onclick="return toggle('CompositeLocation._extractSequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#_extractSequence">_extractSequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation._extractSequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation._extractSequence-expanded"><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-47', 'seq', 'link-8');">seq</a></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-name">x</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="obitools.location.ComplementLocation._extractSequence
|
|
obitools.location.CompositeLocation._extractSequence
|
|
obitools.location.PointLocation._extractSequence
|
|
obitools.location.SimpleLocation._extractSequence" class="py-name" href="#" onclick="return doclink('link-48', '_extractSequence', 'link-9');">_extractSequence</a></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-4');">sequence</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">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-50" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-50', 'seq', 'link-8');">seq</a></tt> </tt>
|
|
</div><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.isDirect"></a><div id="CompositeLocation.isDirect-def"><a name="L174"></a><tt class="py-lineno">174</tt> <a class="py-toggle" href="#" id="CompositeLocation.isDirect-toggle" onclick="return toggle('CompositeLocation.isDirect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#isDirect">isDirect</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.isDirect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.isDirect-expanded"><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method obitools.location.ComplementLocation.isDirect()=obitools.location.ComplementLocation-class.html#isDirect,Method obitools.location.CompositeLocation.isDirect()=obitools.location.CompositeLocation-class.html#isDirect,Method obitools.location.Location.isDirect()=obitools.location.Location-class.html#isDirect,Method obitools.location.PointLocation.isDirect()=obitools.location.PointLocation-class.html#isDirect,Method obitools.location.SimpleLocation.isDirect()=obitools.location.SimpleLocation-class.html#isDirect,Method obitools.location.feature.Feature.isDirect()=obitools.location.feature.Feature-class.html#isDirect"><a title="obitools.location.ComplementLocation.isDirect
|
|
obitools.location.CompositeLocation.isDirect
|
|
obitools.location.Location.isDirect
|
|
obitools.location.PointLocation.isDirect
|
|
obitools.location.SimpleLocation.isDirect
|
|
obitools.location.feature.Feature.isDirect" class="py-name" href="#" onclick="return doclink('link-51', 'isDirect', 'link-51');">isDirect</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
|
|
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.isSimple"></a><div id="CompositeLocation.isSimple-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="CompositeLocation.isSimple-toggle" onclick="return toggle('CompositeLocation.isSimple');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#isSimple">isSimple</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.isSimple-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.isSimple-expanded"><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
|
|
</div><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.simplify"></a><div id="CompositeLocation.simplify-def"><a name="L181"></a><tt class="py-lineno">181</tt> <a class="py-toggle" href="#" id="CompositeLocation.simplify-toggle" onclick="return toggle('CompositeLocation.simplify');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#simplify">simplify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.simplify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.simplify-expanded"><a name="L182"></a><tt class="py-lineno">182</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</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="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> </tt>
|
|
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt id="link-52" class="py-name" targets="Class obitools.location.CompositeLocation=obitools.location.CompositeLocation-class.html"><a title="obitools.location.CompositeLocation" class="py-name" href="#" onclick="return doclink('link-52', 'CompositeLocation', 'link-52');">CompositeLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method obitools.location.ComplementLocation.simplify()=obitools.location.ComplementLocation-class.html#simplify,Method obitools.location.CompositeLocation.simplify()=obitools.location.CompositeLocation-class.html#simplify,Method obitools.location.PointLocation.simplify()=obitools.location.PointLocation-class.html#simplify,Method obitools.location.SimpleLocation.simplify()=obitools.location.SimpleLocation-class.html#simplify,Method obitools.location.feature.Feature.simplify()=obitools.location.feature.Feature-class.html#simplify"><a title="obitools.location.ComplementLocation.simplify
|
|
obitools.location.CompositeLocation.simplify
|
|
obitools.location.PointLocation.simplify
|
|
obitools.location.SimpleLocation.simplify
|
|
obitools.location.feature.Feature.simplify" class="py-name" href="#" onclick="return doclink('link-53', 'simplify', 'link-53');">simplify</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt>
|
|
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">and</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">,</tt> <tt id="link-54" class="py-name" targets="Class obitools.location.ComplementLocation=obitools.location.ComplementLocation-class.html"><a title="obitools.location.ComplementLocation" class="py-name" href="#" onclick="return doclink('link-54', 'ComplementLocation', 'link-54');">ComplementLocation</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="obitools.location.ComplementLocation" class="py-name" href="#" onclick="return doclink('link-55', 'ComplementLocation', 'link-54');">ComplementLocation</a></tt><tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="obitools.location.CompositeLocation" class="py-name" href="#" onclick="return doclink('link-56', 'CompositeLocation', 'link-52');">CompositeLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="obitools.location.ComplementLocation.simplify
|
|
obitools.location.CompositeLocation.simplify
|
|
obitools.location.PointLocation.simplify
|
|
obitools.location.SimpleLocation.simplify
|
|
obitools.location.feature.Feature.simplify" class="py-name" href="#" onclick="return doclink('link-57', 'simplify', 'link-53');">simplify</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L191"></a><tt class="py-lineno">191</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">rep</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
|
|
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rep</tt> </tt>
|
|
</div><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.isFullLength"></a><div id="CompositeLocation.isFullLength-def"><a name="L195"></a><tt class="py-lineno">195</tt> <a class="py-toggle" href="#" id="CompositeLocation.isFullLength-toggle" onclick="return toggle('CompositeLocation.isFullLength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#isFullLength">isFullLength</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.isFullLength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.isFullLength-expanded"><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">and</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name" targets="Method obitools.location.ComplementLocation.isFullLength()=obitools.location.ComplementLocation-class.html#isFullLength,Method obitools.location.CompositeLocation.isFullLength()=obitools.location.CompositeLocation-class.html#isFullLength,Method obitools.location.Location.isFullLength()=obitools.location.Location-class.html#isFullLength,Method obitools.location.PointLocation.isFullLength()=obitools.location.PointLocation-class.html#isFullLength,Method obitools.location.SimpleLocation.isFullLength()=obitools.location.SimpleLocation-class.html#isFullLength,Method obitools.location.feature.Feature.isFullLength()=obitools.location.feature.Feature-class.html#isFullLength"><a title="obitools.location.ComplementLocation.isFullLength
|
|
obitools.location.CompositeLocation.isFullLength
|
|
obitools.location.Location.isFullLength
|
|
obitools.location.PointLocation.isFullLength
|
|
obitools.location.SimpleLocation.isFullLength
|
|
obitools.location.feature.Feature.isFullLength" class="py-name" href="#" onclick="return doclink('link-58', 'isFullLength', 'link-58');">isFullLength</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.needNucleic"></a><div id="CompositeLocation.needNucleic-def"><a name="L198"></a><tt class="py-lineno">198</tt> <a class="py-toggle" href="#" id="CompositeLocation.needNucleic-toggle" onclick="return toggle('CompositeLocation.needNucleic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#needNucleic">needNucleic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.needNucleic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.needNucleic-expanded"><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-op">:</tt> <tt class="py-name">x</tt> <tt class="py-keyword">or</tt> <tt class="py-name">y</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="obitools.location.ComplementLocation.needNucleic
|
|
obitools.location.CompositeLocation.needNucleic
|
|
obitools.location.Location.needNucleic
|
|
obitools.location.PointLocation.needNucleic
|
|
obitools.location.SimpleLocation.needNucleic
|
|
obitools.location.feature.Feature.needNucleic" class="py-name" href="#" onclick="return doclink('link-59', 'needNucleic', 'link-14');">needNucleic</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">z</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
|
|
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">False</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
|
|
<a name="CompositeLocation.__str__"></a><div id="CompositeLocation.__str__-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="CompositeLocation.__str__-toggle" onclick="return toggle('CompositeLocation.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.CompositeLocation-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="CompositeLocation.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CompositeLocation.__str__-expanded"><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"join(%s)"</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-name">str</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L205"></a><tt class="py-lineno">205</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_locs</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
|
|
</div></div><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation"></a><div id="ComplementLocation-def"><a name="L207"></a><tt class="py-lineno">207</tt> <a class="py-toggle" href="#" id="ComplementLocation-toggle" onclick="return toggle('ComplementLocation');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html">ComplementLocation</a><tt class="py-op">(</tt><tt class="py-base-class">Location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ComplementLocation-expanded"><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-docstring">"""</tt> </tt>
|
|
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
|
|
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.__init__"></a><div id="ComplementLocation.__init__-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="ComplementLocation.__init__-toggle" onclick="return toggle('ComplementLocation.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.__init__-expanded"><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt> <tt class="py-op">=</tt> <tt id="link-60" class="py-name" targets="Package obitools.location=obitools.location-module.html"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-60', 'location', 'link-60');">location</a></tt> </tt>
|
|
</div><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation._extractSequence"></a><div id="ComplementLocation._extractSequence-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="ComplementLocation._extractSequence-toggle" onclick="return toggle('ComplementLocation._extractSequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#_extractSequence">_extractSequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation._extractSequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation._extractSequence-expanded"><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt id="link-61" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-61', 'seq', 'link-8');">seq</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="obitools.location.ComplementLocation._extractSequence
|
|
obitools.location.CompositeLocation._extractSequence
|
|
obitools.location.PointLocation._extractSequence
|
|
obitools.location.SimpleLocation._extractSequence" class="py-name" href="#" onclick="return doclink('link-62', '_extractSequence', 'link-9');">_extractSequence</a></tt><tt class="py-op">(</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-4');">sequence</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt id="link-64" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-64', 'seq', 'link-8');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="obitools.sequenceencoder.Complement" class="py-name" href="#" onclick="return doclink('link-65', 'Complement', 'link-2');">Complement</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name" targets="Static Method obitools.sequenceencoder.Complement.encode()=obitools.sequenceencoder.Complement-class.html#encode,Static Method obitools.sequenceencoder.SequenceEncoder.encode()=obitools.sequenceencoder.SequenceEncoder-class.html#encode"><a title="obitools.sequenceencoder.Complement.encode
|
|
obitools.sequenceencoder.SequenceEncoder.encode" class="py-name" href="#" onclick="return doclink('link-66', 'encode', 'link-66');">encode</a></tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-67', 'seq', 'link-8');">seq</a></tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-68" class="py-name"><a title="obitools.BioSequence.seq
|
|
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-68', 'seq', 'link-8');">seq</a></tt> </tt>
|
|
</div><a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.isDirect"></a><div id="ComplementLocation.isDirect-def"><a name="L219"></a><tt class="py-lineno">219</tt> <a class="py-toggle" href="#" id="ComplementLocation.isDirect-toggle" onclick="return toggle('ComplementLocation.isDirect');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#isDirect">isDirect</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.isDirect-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.isDirect-expanded"><a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">False</tt> </tt>
|
|
</div><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.isSimple"></a><div id="ComplementLocation.isSimple-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="ComplementLocation.isSimple-toggle" onclick="return toggle('ComplementLocation.isSimple');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#isSimple">isSimple</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.isSimple-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.isSimple-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method obitools.location.ComplementLocation.isSimple()=obitools.location.ComplementLocation-class.html#isSimple,Method obitools.location.CompositeLocation.isSimple()=obitools.location.CompositeLocation-class.html#isSimple,Method obitools.location.Location.isSimple()=obitools.location.Location-class.html#isSimple,Method obitools.location.PointLocation.isSimple()=obitools.location.PointLocation-class.html#isSimple,Method obitools.location.SimpleLocation.isSimple()=obitools.location.SimpleLocation-class.html#isSimple,Method obitools.location.feature.Feature.isSimple()=obitools.location.feature.Feature-class.html#isSimple"><a title="obitools.location.ComplementLocation.isSimple
|
|
obitools.location.CompositeLocation.isSimple
|
|
obitools.location.Location.isSimple
|
|
obitools.location.PointLocation.isSimple
|
|
obitools.location.SimpleLocation.isSimple
|
|
obitools.location.feature.Feature.isSimple" class="py-name" href="#" onclick="return doclink('link-69', 'isSimple', 'link-69');">isSimple</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.isFullLength"></a><div id="ComplementLocation.isFullLength-def"><a name="L225"></a><tt class="py-lineno">225</tt> <a class="py-toggle" href="#" id="ComplementLocation.isFullLength-toggle" onclick="return toggle('ComplementLocation.isFullLength');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#isFullLength">isFullLength</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.isFullLength-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.isFullLength-expanded"><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="obitools.location.ComplementLocation.isFullLength
|
|
obitools.location.CompositeLocation.isFullLength
|
|
obitools.location.Location.isFullLength
|
|
obitools.location.PointLocation.isFullLength
|
|
obitools.location.SimpleLocation.isFullLength
|
|
obitools.location.feature.Feature.isFullLength" class="py-name" href="#" onclick="return doclink('link-70', 'isFullLength', 'link-58');">isFullLength</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.simplify"></a><div id="ComplementLocation.simplify-def"><a name="L228"></a><tt class="py-lineno">228</tt> <a class="py-toggle" href="#" id="ComplementLocation.simplify-toggle" onclick="return toggle('ComplementLocation.simplify');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#simplify">simplify</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.simplify-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.simplify-expanded"><a name="L229"></a><tt class="py-lineno">229</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">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">,</tt> <tt id="link-71" class="py-name"><a title="obitools.location.ComplementLocation" class="py-name" href="#" onclick="return doclink('link-71', 'ComplementLocation', 'link-54');">ComplementLocation</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="obitools.location.ComplementLocation.simplify
|
|
obitools.location.CompositeLocation.simplify
|
|
obitools.location.PointLocation.simplify
|
|
obitools.location.SimpleLocation.simplify
|
|
obitools.location.feature.Feature.simplify" class="py-name" href="#" onclick="return doclink('link-72', 'simplify', 'link-53');">simplify</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
|
|
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.needNucleic"></a><div id="ComplementLocation.needNucleic-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="ComplementLocation.needNucleic-toggle" onclick="return toggle('ComplementLocation.needNucleic');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#needNucleic">needNucleic</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.needNucleic-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.needNucleic-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">True</tt> </tt>
|
|
</div><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> </tt>
|
|
<a name="ComplementLocation.__str__"></a><div id="ComplementLocation.__str__-def"><a name="L237"></a><tt class="py-lineno">237</tt> <a class="py-toggle" href="#" id="ComplementLocation.__str__-toggle" onclick="return toggle('ComplementLocation.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location.ComplementLocation-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="ComplementLocation.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ComplementLocation.__str__-expanded"><a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"complement(%s)"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_loc</tt> </tt>
|
|
</div></div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
|
|
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> </tt>
|
|
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
|
|
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Internal functions used for location parsing</tt> </tt>
|
|
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
|
|
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
|
|
<a name="__sublocationIterator"></a><div id="__sublocationIterator-def"><a name="L245"></a><tt class="py-lineno">245</tt> <a class="py-toggle" href="#" id="__sublocationIterator-toggle" onclick="return toggle('__sublocationIterator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location-module.html#__sublocationIterator">__sublocationIterator</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="__sublocationIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__sublocationIterator-expanded"><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">sl</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
|
|
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">text</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">plevel</tt><tt class="py-op">>=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-string">'('</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
|
|
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">.</tt><tt id="link-73" 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-73', 'append', 'link-73');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">')'</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">plevel</tt><tt class="py-op">-=</tt><tt class="py-number">1</tt> </tt>
|
|
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">.</tt><tt id="link-74" 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-74', 'append', 'link-73');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">c</tt><tt class="py-op">==</tt><tt class="py-string">','</tt> <tt class="py-keyword">and</tt> <tt class="py-name">plevel</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">sl</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">sl</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">.</tt><tt id="link-75" 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-75', 'append', 'link-73');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">sl</tt> <tt class="py-keyword">and</tt> <tt class="py-name">plevel</tt><tt class="py-op">==</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">sl</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> </tt>
|
|
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> </tt>
|
|
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> </tt>
|
|
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
|
|
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Internal functions used for location parsing</tt> </tt>
|
|
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
|
|
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
|
|
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt id="link-76" class="py-name" targets="Variable obitools.location.__simplelocparser=obitools.location-module.html#__simplelocparser"><a title="obitools.location.__simplelocparser" class="py-name" href="#" onclick="return doclink('link-76', '__simplelocparser', 'link-76');">__simplelocparser</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">'(?P<before><?)(?P<from>[0-9]+)(\.\.(?P<after>>?)(?P<to>[0-9]+))?'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
|
|
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
|
|
<a name="__locationParser"></a><div id="__locationParser-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="__locationParser-toggle" onclick="return toggle('__locationParser');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location-module.html#__locationParser">__locationParser</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="__locationParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__locationParser-expanded"><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-name">text</tt><tt class="py-op">=</tt><tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">strip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'join('</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">text</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-string">')'</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-77" class="py-name"><a title="obitools.location.CompositeLocation" class="py-name" href="#" onclick="return doclink('link-77', 'CompositeLocation', 'link-52');">CompositeLocation</a></tt><tt class="py-op">(</tt><tt id="link-78" class="py-name" targets="Function obitools.location.__locationParser()=obitools.location-module.html#__locationParser"><a title="obitools.location.__locationParser" class="py-name" href="#" onclick="return doclink('link-78', '__locationParser', 'link-78');">__locationParser</a></tt><tt class="py-op">(</tt><tt class="py-name">sl</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sl</tt> <tt class="py-keyword">in</tt> <tt id="link-79" class="py-name" targets="Function obitools.location.__sublocationIterator()=obitools.location-module.html#__sublocationIterator"><a title="obitools.location.__sublocationIterator" class="py-name" href="#" onclick="return doclink('link-79', '__sublocationIterator', 'link-79');">__sublocationIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-number">11</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'complement('</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">text</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-string">')'</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">subl</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="obitools.location.__locationParser" class="py-name" href="#" onclick="return doclink('link-80', '__locationParser', 'link-78');">__locationParser</a></tt><tt class="py-op">(</tt><tt class="py-name">sl</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">sl</tt> <tt class="py-keyword">in</tt> <tt id="link-81" class="py-name"><a title="obitools.location.__sublocationIterator" class="py-name" href="#" onclick="return doclink('link-81', '__sublocationIterator', 'link-79');">__sublocationIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">[</tt><tt class="py-number">11</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>
|
|
<a name="L282"></a><tt class="py-lineno">282</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">subl</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="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">subl</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="obitools.location.CompositeLocation" class="py-name" href="#" onclick="return doclink('link-82', 'CompositeLocation', 'link-52');">CompositeLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">subl</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">subl</tt> <tt class="py-op">=</tt> <tt class="py-name">subl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
|
|
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-83" class="py-name"><a title="obitools.location.ComplementLocation" class="py-name" href="#" onclick="return doclink('link-83', 'ComplementLocation', 'link-54');">ComplementLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">subl</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
|
|
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name"><a title="obitools.location.__simplelocparser" class="py-name" href="#" onclick="return doclink('link-84', '__simplelocparser', 'link-76');">__simplelocparser</a></tt><tt class="py-op">.</tt><tt class="py-name">match</tt><tt class="py-op">(</tt><tt class="py-name">text</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">data</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">"Misformated location : %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">text</tt> </tt>
|
|
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt class="py-name">groupdict</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'to'</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
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<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-name">sl</tt> <tt class="py-op">=</tt> <tt id="link-85" class="py-name"><a title="obitools.location.PointLocation" class="py-name" href="#" onclick="return doclink('link-85', 'PointLocation', 'link-43');">PointLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'from'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
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<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-name">sl</tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name" targets="Class obitools.location.SimpleLocation=obitools.location.SimpleLocation-class.html"><a title="obitools.location.SimpleLocation" class="py-name" href="#" onclick="return doclink('link-86', 'SimpleLocation', 'link-86');">SimpleLocation</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'from'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'to'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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|
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">.</tt><tt class="py-name">before</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'before'</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'<'</tt> </tt>
|
|
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-name">sl</tt><tt class="py-op">.</tt><tt class="py-name">after</tt><tt class="py-op">=</tt><tt class="py-name">data</tt><tt class="py-op">[</tt><tt class="py-string">'after'</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'>'</tt> </tt>
|
|
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sl</tt> </tt>
|
|
</div><a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> </tt>
|
|
<a name="locationGenerator"></a><div id="locationGenerator-def"><a name="L299"></a><tt class="py-lineno">299</tt> <a class="py-toggle" href="#" id="locationGenerator-toggle" onclick="return toggle('locationGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location-module.html#locationGenerator">locationGenerator</a><tt class="py-op">(</tt><tt class="py-param">locstring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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|
</div><div id="locationGenerator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="locationGenerator-expanded"><a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> Parse a location string as present in genbank or embl file.</tt> </tt>
|
|
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
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|
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> @param locstring: string description of the location in embl/gb format</tt> </tt>
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|
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> @type locstring: str</tt> </tt>
|
|
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> @return: a Location instance</tt> </tt>
|
|
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: C{Location} subclass instance</tt> </tt>
|
|
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-87" class="py-name"><a title="obitools.location.__locationParser" class="py-name" href="#" onclick="return doclink('link-87', '__locationParser', 'link-78');">__locationParser</a></tt><tt class="py-op">(</tt><tt class="py-name">locstring</tt><tt class="py-op">)</tt> </tt>
|
|
</div><a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> </tt>
|
|
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
|
|
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt id="link-88" class="py-name" targets="Variable obitools.location._matchExternalRef=obitools.location-module.html#_matchExternalRef"><a title="obitools.location._matchExternalRef" class="py-name" href="#" onclick="return doclink('link-88', '_matchExternalRef', 'link-88');">_matchExternalRef</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-Z0-9_|]+(\.[0-9]+)?(?=:)'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> </tt>
|
|
<a name="extractExternalRefs"></a><div id="extractExternalRefs-def"><a name="L314"></a><tt class="py-lineno">314</tt> <a class="py-toggle" href="#" id="extractExternalRefs-toggle" onclick="return toggle('extractExternalRefs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.location-module.html#extractExternalRefs">extractExternalRefs</a><tt class="py-op">(</tt><tt class="py-param">locstring</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
|
|
</div><div id="extractExternalRefs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="extractExternalRefs-expanded"><a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
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|
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-docstring"> When a location describe external references (ex: D28156.1:1..>1292)</tt> </tt>
|
|
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-docstring"> separate the external reference part of the location and the location</tt> </tt>
|
|
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-docstring"> by itself.</tt> </tt>
|
|
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"><tt class="py-docstring"> @param locstring: text representation of the location.</tt> </tt>
|
|
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-docstring"> @type locstring: str</tt> </tt>
|
|
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-docstring"> @return: a tuple with a set of string describing accession number</tt> </tt>
|
|
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"> of the referred sequences and a C{Location} instance.</tt> </tt>
|
|
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
|
|
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: tuple(set,Location)</tt> </tt>
|
|
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
|
|
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">set</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">.</tt><tt class="py-name">group</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 id="link-89" class="py-name"><a title="obitools.location._matchExternalRef" class="py-name" href="#" onclick="return doclink('link-89', '_matchExternalRef', 'link-88');">_matchExternalRef</a></tt><tt class="py-op">.</tt><tt class="py-name">finditer</tt><tt class="py-op">(</tt><tt class="py-name">locstring</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">clean</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">':|'</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">re</tt><tt class="py-op">.</tt><tt class="py-name">escape</tt><tt class="py-op">(</tt><tt class="py-name">x</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">m</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">':'</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">cloc</tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name" targets="Function obitools.location.locationGenerator()=obitools.location-module.html#locationGenerator"><a title="obitools.location.locationGenerator" class="py-name" href="#" onclick="return doclink('link-90', 'locationGenerator', 'link-90');">locationGenerator</a></tt><tt class="py-op">(</tt><tt class="py-name">clean</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">locstring</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
|
|
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> </tt>
|
|
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-name">cloc</tt> </tt>
|
|
</div><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt><script type="text/javascript">
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