<?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>Bio.PopGen.SimCoal.Cache</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">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PopGen-module.html">Package PopGen</a> ::
<a href="Bio.PopGen.SimCoal-module.html">Package SimCoal</a> ::
Module Cache
</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 private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.PopGen.SimCoal.Cache-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.PopGen.SimCoal.Cache-module.html">Module Bio.PopGen.SimCoal.Cache</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">This module allows to cache Simcoal2 results, and return on the fly</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">in case the calculation was done.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">logging</tt> <tt class="py-keyword">import</tt> <tt class="py-name">debug</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">sys</tt> <tt class="py-keyword">import</tt> <tt class="py-name">exit</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">tarfile</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">tempfile</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio.PopGen=Bio.PopGen-module.html"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-0', 'PopGen', 'link-0');">PopGen</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.PopGen.SimCoal=Bio.PopGen.SimCoal-module.html"><a title="Bio.PopGen.SimCoal" class="py-name" href="#" onclick="return doclink('link-1', 'SimCoal', 'link-1');">SimCoal</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.PopGen.FDist.Controller=Bio.PopGen.FDist.Controller-module.html,Module Bio.PopGen.SimCoal.Controller=Bio.PopGen.SimCoal.Controller-module.html"><a title="Bio.PopGen.FDist.Controller
Bio.PopGen.SimCoal.Controller" class="py-name" href="#" onclick="return doclink('link-2', 'Controller', 'link-2');">Controller</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.PopGen.SimCoal.Controller.SimCoalController=Bio.PopGen.SimCoal.Controller.SimCoalController-class.html"><a title="Bio.PopGen.SimCoal.Controller.SimCoalController" class="py-name" href="#" onclick="return doclink('link-3', 'SimCoalController', 'link-3');">SimCoalController</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-4', 'PopGen', 'link-0');">PopGen</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.EUtils.Config=Bio.EUtils.Config-module.html"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-5', 'Config', 'link-5');">Config</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> </tt>
<a name="SimCoalCache"></a><div id="SimCoalCache-def"><a name="L17"></a><tt class="py-lineno">17</tt> <a class="py-toggle" href="#" id="SimCoalCache-toggle" onclick="return toggle('SimCoalCache');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html">SimCoalCache</a><tt class="py-op">:</tt> </tt>
</div><div id="SimCoalCache-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SimCoalCache-expanded"><a name="SimCoalCache.__init__"></a><div id="SimCoalCache.__init__-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="SimCoalCache.__init__-toggle" onclick="return toggle('SimCoalCache.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Cache.SimCoalCache-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">simcoalDir</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="SimCoalCache.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalCache.__init__-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes the cache.</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> simcoalDir - where the binaries are</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> IMPORTANT: The cache only makes sense if the file nameunivically</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring"> identifies the model.</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring"> For now use use the model name as key,</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"> and it will probably stay like that.</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cacheDir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-6" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-6', 'Config', 'link-5');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">dataDir</tt><tt class="py-op">,</tt> <tt class="py-string">'SimCoal'</tt><tt class="py-op">,</tt> <tt class="py-string">'cache'</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 class="py-keyword">if</tt> <tt class="py-name">simcoalDir</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoalDir</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-7', 'Config', 'link-5');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">simcoalDir</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoalDir</tt> <tt class="py-op">=</tt> <tt class="py-name">simcoalDir</tt> </tt>
</div><a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> </tt>
<a name="SimCoalCache.run_simcoal"></a><div id="SimCoalCache.run_simcoal-def"><a name="L35"></a><tt class="py-lineno">35</tt> <a class="py-toggle" href="#" id="SimCoalCache.run_simcoal-toggle" onclick="return toggle('SimCoalCache.run_simcoal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#run_simcoal">run_simcoal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">par_file</tt><tt class="py-op">,</tt> <tt class="py-param">num_sims</tt><tt class="py-op">,</tt> <tt class="py-param">ploydi</tt> <tt class="py-op">=</tt> <tt class="py-string">'1'</tt><tt class="py-op">,</tt> <tt class="py-param">parDir</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="SimCoalCache.run_simcoal-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalCache.run_simcoal-expanded"><a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parDir</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-name">parDir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-8" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-8', 'Config', 'link-5');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">dataDir</tt><tt class="py-op">,</tt> <tt class="py-string">'SimCoal'</tt><tt class="py-op">,</tt> <tt class="py-string">'runs'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">par_file_root</tt> <tt class="py-op">=</tt> <tt class="py-name">par_file</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">tar_name</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</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">self</tt><tt class="py-op">.</tt><tt class="py-name">cacheDir</tt><tt class="py-op">,</tt> <tt class="py-name">ploydi</tt><tt class="py-op">,</tt> <tt class="py-name">par_file_root</tt> <tt class="py-op">+</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-string">'.tar.bz2'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">access</tt><tt class="py-op">(</tt><tt class="py-name">tar_name</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">R_OK</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">tf</tt> <tt class="py-op">=</tt> <tt class="py-name">tarfile</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-9', 'open', 'link-9');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">tar_name</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">tar_num_sims</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">tf</tt><tt class="py-op">.</tt><tt class="py-name">getmembers</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">3</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">tar_num_sims</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tar_num_sims</tt> <tt class="py-op">>=</tt> <tt class="py-name">num_sims</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt class="py-name">extractall</tt><tt class="py-op">(</tt><tt class="py-name">parDir</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-10', 'close', 'link-10');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-11', 'close', 'link-10');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">NameError</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> <tt class="py-comment">#not opened in the first place, OK.</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-name">scc</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.PopGen.SimCoal.Controller.SimCoalController" class="py-name" href="#" onclick="return doclink('link-12', 'SimCoalController', 'link-3');">SimCoalController</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoalDir</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-name">scc</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.PopGen.SimCoal.Cache.SimCoalCache.run_simcoal()=Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#run_simcoal,Method Bio.PopGen.SimCoal.Controller.SimCoalController.run_simcoal()=Bio.PopGen.SimCoal.Controller.SimCoalController-class.html#run_simcoal"><a title="Bio.PopGen.SimCoal.Cache.SimCoalCache.run_simcoal
Bio.PopGen.SimCoal.Controller.SimCoalController.run_simcoal" class="py-name" href="#" onclick="return doclink('link-13', 'run_simcoal', 'link-13');">run_simcoal</a></tt><tt class="py-op">(</tt><tt class="py-name">par_file</tt><tt class="py-op">,</tt> <tt class="py-name">num_sims</tt><tt class="py-op">,</tt> <tt class="py-name">ploydi</tt><tt class="py-op">,</tt> <tt class="py-name">parDir</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> <tt class="py-name">tf</tt> <tt class="py-op">=</tt> <tt class="py-name">tarfile</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-14', 'open', 'link-9');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">tar_name</tt><tt class="py-op">,</tt> <tt class="py-string">'w:bz2'</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-15', 'add', 'link-15');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</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">parDir</tt><tt class="py-op">,</tt> <tt class="py-name">par_file_root</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">par_file_root</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-16', 'close', 'link-10');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> </tt>
<a name="SimCoalCache.listSimulations"></a><div id="SimCoalCache.listSimulations-def"><a name="L61"></a><tt class="py-lineno">61</tt> <a class="py-toggle" href="#" id="SimCoalCache.listSimulations-toggle" onclick="return toggle('SimCoalCache.listSimulations');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#listSimulations">listSimulations</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ploidy</tt> <tt class="py-op">=</tt> <tt class="py-string">'1'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimCoalCache.listSimulations-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalCache.listSimulations-expanded"><a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"><tt class="py-docstring"> Lists available simulations.</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt id="link-17" class="py-name" targets="Variable Bio.expressions.hmmpfam.files=Bio.expressions.hmmpfam-module.html#files"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-17', 'files', 'link-17');">files</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cacheDir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">ploidy</tt><tt class="py-op">)</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</tt> <tt class="py-line"> <tt class="py-name">sims</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt id="link-18" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-18', 'files', 'link-17');">files</a></tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">endswith</tt><tt class="py-op">(</tt><tt class="py-string">'.tar.bz2'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> <tt class="py-name">sims</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-19', 'append', 'link-19');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">8</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sims</tt> </tt>
</div><a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> </tt>
<a name="SimCoalCache.getSimulation"></a><div id="SimCoalCache.getSimulation-def"><a name="L72"></a><tt class="py-lineno">72</tt> <a class="py-toggle" href="#" id="SimCoalCache.getSimulation-toggle" onclick="return toggle('SimCoalCache.getSimulation');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#getSimulation">getSimulation</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sim_name</tt><tt class="py-op">,</tt> <tt class="py-param">ploidy</tt> <tt class="py-op">=</tt> <tt class="py-string">'1'</tt><tt class="py-op">,</tt> <tt class="py-param">parDir</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="SimCoalCache.getSimulation-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalCache.getSimulation-expanded"><a name="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"><tt class="py-docstring"> Makes available a cached simulation.</tt> </tt>
<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"> @param sim_name simulation name.</tt> </tt>
<a name="L77"></a><tt class="py-lineno">77</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L78"></a><tt class="py-lineno">78</tt> <tt class="py-line"><tt class="py-docstring"> This mainly means untaring a file.</tt> </tt>
<a name="L79"></a><tt class="py-lineno">79</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L80"></a><tt class="py-lineno">80</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">parDir</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L81"></a><tt class="py-lineno">81</tt> <tt class="py-line"> <tt class="py-name">parDir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-20" class="py-name"><a title="Bio.EUtils.Config" class="py-name" href="#" onclick="return doclink('link-20', 'Config', 'link-5');">Config</a></tt><tt class="py-op">.</tt><tt class="py-name">dataDir</tt><tt class="py-op">,</tt> <tt class="py-string">'SimCoal'</tt><tt class="py-op">,</tt> <tt class="py-string">'runs'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno">82</tt> <tt class="py-line"> <tt class="py-name">tar_name</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</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">self</tt><tt class="py-op">.</tt><tt class="py-name">cacheDir</tt><tt class="py-op">,</tt> <tt class="py-name">ploidy</tt><tt class="py-op">,</tt> <tt class="py-name">sim_name</tt> <tt class="py-op">+</tt> </tt>
<a name="L83"></a><tt class="py-lineno">83</tt> <tt class="py-line"> <tt class="py-string">'.tar.bz2'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno">84</tt> <tt class="py-line"> <tt class="py-name">tf</tt> <tt class="py-op">=</tt> <tt class="py-name">tarfile</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-21', 'open', 'link-9');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">tar_name</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno">85</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt class="py-name">extractall</tt><tt class="py-op">(</tt><tt class="py-name">parDir</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno">86</tt> <tt class="py-line"> <tt class="py-name">tf</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-22', 'close', 'link-10');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L87"></a><tt class="py-lineno">87</tt> <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno">88</tt> <tt class="py-line"> </tt>
<a name="L89"></a><tt class="py-lineno">89</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno">90</tt> <tt class="py-line"> <tt class="py-name">cache</tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name" targets="Module Bio.PopGen.SimCoal.Cache=Bio.PopGen.SimCoal.Cache-module.html"><a title="Bio.PopGen.SimCoal.Cache" class="py-name" href="#" onclick="return doclink('link-23', 'Cache', 'link-23');">Cache</a></tt><tt class="py-op">(</tt><tt class="py-string">'/home/work/werk/consolidator/sc_cache'</tt><tt class="py-op">,</tt> </tt>
<a name="L91"></a><tt class="py-lineno">91</tt> <tt class="py-line"> <tt class="py-string">'/home/work/software/simcoal'</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno">92</tt> <tt class="py-line"> <tt class="py-name">cache</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.PopGen.SimCoal.Cache.SimCoalCache.run_simcoal
Bio.PopGen.SimCoal.Controller.SimCoalController.run_simcoal" class="py-name" href="#" onclick="return doclink('link-24', 'run_simcoal', 'link-13');">run_simcoal</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">,</tt> <tt class="py-string">'island_snp-50_0.0025_10_0.083_100_60.par'</tt><tt class="py-op">,</tt> <tt class="py-number">102</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno">93</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">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:42 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" 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>
