Files
obitools/doc/html/api/obitools.ecopcr.sequence-pysrc.html
2008-04-29 11:07:08 +00:00

166 lines
20 KiB
HTML

<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools.ecopcr.sequence</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="obitools-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Tree link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Index link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Help link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
</tr></table></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="obitools-module.html">Package&nbsp;obitools</a> ::
<a href="obitools.ecopcr-module.html">Package&nbsp;ecopcr</a> ::
Module&nbsp;sequence
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools.ecopcr.sequence-pysrc.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="obitools.ecopcr.sequence-module.html">Module obitools.ecopcr.sequence</a></h1>
<pre class="py-src">
<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
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-1', 'NucSequence', 'link-1');">NucSequence</a></tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-2', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Package obitools.ecopcr=obitools.ecopcr-module.html"><a title="obitools.ecopcr" class="py-name" href="#" onclick="return doclink('link-3', 'ecopcr', 'link-3');">ecopcr</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Class obitools.ecopcr.EcoPCRDBFile=obitools.ecopcr.EcoPCRDBFile-class.html"><a title="obitools.ecopcr.EcoPCRDBFile" class="py-name" href="#" onclick="return doclink('link-4', 'EcoPCRDBFile', 'link-4');">EcoPCRDBFile</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="obitools
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"><a title="obitools.ecopcr" class="py-name" href="#" onclick="return doclink('link-6', 'ecopcr', 'link-3');">ecopcr</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Module obitools.ecopcr.taxonomy=obitools.ecopcr.taxonomy-module.html"><a title="obitools.ecopcr.taxonomy" class="py-name" href="#" onclick="return doclink('link-7', 'taxonomy', 'link-7');">taxonomy</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name" targets="Class obitools.ecopcr.taxonomy.Taxonomy=obitools.ecopcr.taxonomy.Taxonomy-class.html"><a title="obitools.ecopcr.taxonomy.Taxonomy" class="py-name" href="#" onclick="return doclink('link-8', 'Taxonomy', 'link-8');">Taxonomy</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">glob</tt> <tt class="py-keyword">import</tt> <tt class="py-name">glob</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">struct</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Module obitools.gzip=obitools.gzip-module.html"><a title="obitools.gzip" class="py-name" href="#" onclick="return doclink('link-9', 'gzip', 'link-9');">gzip</a></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="ecoPCRDBSequenceIterator"></a><div id="ecoPCRDBSequenceIterator-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="ecoPCRDBSequenceIterator-toggle" onclick="return toggle('ecoPCRDBSequenceIterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html">ecoPCRDBSequenceIterator</a><tt class="py-op">(</tt><tt class="py-base-class">EcoPCRDBFile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ecoPCRDBSequenceIterator-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="ecoPCRDBSequenceIterator-expanded"><a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="ecoPCRDBSequenceIterator.__init__"></a><div id="ecoPCRDBSequenceIterator.__init__-def"><a name="L11"></a><tt class="py-lineno">11</tt> <a class="py-toggle" href="#" id="ecoPCRDBSequenceIterator.__init__-toggle" onclick="return toggle('ecoPCRDBSequenceIterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-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">path</tt><tt class="py-op">,</tt><tt class="py-param">taxonomy</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ecoPCRDBSequenceIterator.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ecoPCRDBSequenceIterator.__init__-expanded"><a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_path</tt> <tt class="py-op">=</tt> <tt class="py-name">path</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-10" class="py-name"><a title="obitools.ecopcr.taxonomy" class="py-name" href="#" onclick="return doclink('link-10', 'taxonomy', 'link-7');">taxonomy</a></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>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_taxonomy</tt><tt class="py-op">=</tt><tt id="link-11" class="py-name"><a title="obitools.ecopcr.taxonomy" class="py-name" href="#" onclick="return doclink('link-11', 'taxonomy', 'link-7');">taxonomy</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_taxonomy</tt><tt class="py-op">=</tt><tt id="link-12" class="py-name"><a title="obitools.ecopcr.taxonomy.Taxonomy" class="py-name" href="#" onclick="return doclink('link-12', 'Taxonomy', 'link-8');">Taxonomy</a></tt><tt class="py-op">(</tt><tt class="py-name">path</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seqfilesFiles</tt> <tt class="py-op">=</tt> <tt class="py-name">glob</tt><tt class="py-op">(</tt><tt class="py-string">'%s_???.sdx'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_path</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seqfilesFiles</tt><tt class="py-op">.</tt><tt class="py-name">sort</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> </tt>
<a name="ecoPCRDBSequenceIterator.__ecoSequenceIterator"></a><div id="ecoPCRDBSequenceIterator.__ecoSequenceIterator-def"><a name="L22"></a><tt class="py-lineno">22</tt> <a class="py-toggle" href="#" id="ecoPCRDBSequenceIterator.__ecoSequenceIterator-toggle" onclick="return toggle('ecoPCRDBSequenceIterator.__ecoSequenceIterator');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html#__ecoSequenceIterator">__ecoSequenceIterator</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ecoPCRDBSequenceIterator.__ecoSequenceIterator-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ecoPCRDBSequenceIterator.__ecoSequenceIterator-expanded"><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method obitools.ecopcr.EcoPCRDBFile._ecoRecordIterator()=obitools.ecopcr.EcoPCRDBFile-class.html#_ecoRecordIterator"><a title="obitools.ecopcr.EcoPCRDBFile._ecoRecordIterator" class="py-name" href="#" onclick="return doclink('link-13', '_ecoRecordIterator', 'link-13');">_ecoRecordIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">lrecord</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> <tt class="py-name">lnames</tt> <tt class="py-op">=</tt> <tt class="py-name">lrecord</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">*</tt><tt class="py-number">4</tt><tt class="py-op">+</tt><tt class="py-number">20</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">taxid</tt><tt class="py-op">,</tt><tt class="py-name">seqid</tt><tt class="py-op">,</tt><tt class="py-name">deflength</tt><tt class="py-op">,</tt><tt class="py-name">seqlength</tt><tt class="py-op">,</tt><tt class="py-name">cptseqlength</tt><tt class="py-op">,</tt><tt class="py-name">string</tt><tt class="py-op">)</tt><tt class="py-op">=</tt><tt class="py-name">struct</tt><tt class="py-op">.</tt><tt class="py-name">unpack</tt><tt class="py-op">(</tt><tt class="py-string">'&gt; I 20s I I I %ds'</tt> <tt class="py-op">%</tt> <tt class="py-name">lnames</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">de</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">deflength</tt><tt class="py-op">]</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt id="link-14" 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
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-14', 'seq', 'link-14');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name"><a title="obitools.gzip" class="py-name" href="#" onclick="return doclink('link-15', 'gzip', 'link-9');">gzip</a></tt><tt class="py-op">.</tt><tt class="py-name">zlib</tt><tt class="py-op">.</tt><tt class="py-name">decompress</tt><tt class="py-op">(</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-name">deflength</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt id="link-16" class="py-name" targets="Module obitools.utils.bioseq=obitools.utils.bioseq-module.html"><a title="obitools.utils.bioseq" class="py-name" href="#" onclick="return doclink('link-16', 'bioseq', 'link-16');">bioseq</a></tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-17', 'NucSequence', 'link-1');">NucSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">seqid</tt><tt class="py-op">,</tt><tt id="link-18" class="py-name"><a title="obitools.BioSequence.seq
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-18', 'seq', 'link-14');">seq</a></tt><tt class="py-op">,</tt><tt class="py-name">de</tt><tt class="py-op">,</tt><tt class="py-name">taxidx</tt><tt class="py-op">=</tt><tt class="py-name">taxid</tt><tt class="py-op">,</tt><tt class="py-name">taxid</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_taxonomy</tt><tt class="py-op">.</tt><tt class="py-name">_taxonomy</tt><tt class="py-op">[</tt><tt class="py-name">taxid</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-19" class="py-name"><a title="obitools.utils.bioseq" class="py-name" href="#" onclick="return doclink('link-19', 'bioseq', 'link-16');">bioseq</a></tt> </tt>
</div><a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="ecoPCRDBSequenceIterator.__iter__"></a><div id="ecoPCRDBSequenceIterator.__iter__-def"><a name="L32"></a><tt class="py-lineno">32</tt> <a class="py-toggle" href="#" id="ecoPCRDBSequenceIterator.__iter__-toggle" onclick="return toggle('ecoPCRDBSequenceIterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html#__iter__">__iter__</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="ecoPCRDBSequenceIterator.__iter__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="ecoPCRDBSequenceIterator.__iter__-expanded"><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seqfile</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seqfilesFiles</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-20" class="py-name"><a title="obitools.BioSequence.seq
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-20', 'seq', 'link-14');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__ecoSequenceIterator()=obitools.ecopcr.sequence.ecoPCRDBSequenceIterator-class.html#__ecoSequenceIterator"><a title="obitools.ecopcr.sequence.ecoPCRDBSequenceIterator.__ecoSequenceIterator" class="py-name" href="#" onclick="return doclink('link-21', '__ecoSequenceIterator', 'link-21');">__ecoSequenceIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">seqfile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-22" class="py-name"><a title="obitools.BioSequence.seq
obitools.WrappedBioSequence.seq" class="py-name" href="#" onclick="return doclink('link-22', 'seq', 'link-14');">seq</a></tt> </tt>
</div></div><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="obitools-module.html">Home</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Tree link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Index link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Help link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Project homepage -->
<th class="navbar" align="right" width="100%">
<table border="0" cellpadding="0" cellspacing="0">
<tr><th class="navbar" align="center"
><a class="navbar" target="_top" href="http://www.grenoble.prabi.fr/trac/OBITools">OBITools</a></th>
</tr></table></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
<a href="epydoc-log.html">Generated by Epydoc
3.0beta1 on Tue Apr 29 13:03:55 2008</a>
</td>
<td align="right" class="footer">
<a href="http://epydoc.sourceforge.net">http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie()
// -->
</script>
</body>
</html>