<?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.Controller</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 Controller
</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.Controller-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.Controller-module.html">Module Bio.PopGen.SimCoal.Controller</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 control Simcoal2.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring"></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>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">tempfile</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">shutil</tt> <tt class="py-keyword">import</tt> <tt class="py-name">copyfile</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</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="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> </tt>
<a name="SimCoalController"></a><div id="SimCoalController-def"><a name="L14"></a><tt class="py-lineno">14</tt> <a class="py-toggle" href="#" id="SimCoalController-toggle" onclick="return toggle('SimCoalController');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Controller.SimCoalController-class.html">SimCoalController</a><tt class="py-op">:</tt> </tt>
</div><div id="SimCoalController-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="SimCoalController-expanded"><a name="SimCoalController.__init__"></a><div id="SimCoalController.__init__-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="SimCoalController.__init__-toggle" onclick="return toggle('SimCoalController.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Controller.SimCoalController-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">simcoal_dir</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimCoalController.__init__-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalController.__init__-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes the controller.</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> simcoal_dir is the directory where simcoal is.</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring"> The initializer checks for existance and executability of binaries.</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoal_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">simcoal_dir</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">os_name</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-0" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-0', 'name', 'link-0');">name</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</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">os_name</tt><tt class="py-op">==</tt><tt class="py-string">'nt'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">platform</tt><tt class="py-op">==</tt><tt class="py-string">'cygwin'</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">self</tt><tt class="py-op">.</tt><tt class="py-name">bin_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'simcoal2.exe'</tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-comment">#this is wrong (the exe name), most probably</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</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">bin_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'simcoal2'</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-comment">#This name is too specific</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dir_contents</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">simcoal_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</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">bin_name</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dir_contents</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</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">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoal_dir</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>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">bin_name</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">X_OK</tt><tt class="py-op">)</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">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"SimCoal not executable"</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"SimCoal not available"</tt> </tt>
</div><a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> </tt>
<a name="SimCoalController.run_simcoal"></a><div id="SimCoalController.run_simcoal-def"><a name="L38"></a><tt class="py-lineno">38</tt> <a class="py-toggle" href="#" id="SimCoalController.run_simcoal-toggle" onclick="return toggle('SimCoalController.run_simcoal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.SimCoal.Controller.SimCoalController-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">par_dir</tt> <tt class="py-op">=</tt> <tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SimCoalController.run_simcoal-collapsed" style="display:none;" pad="++" indent="++++++++"></div><div id="SimCoalController.run_simcoal-expanded"><a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-docstring">"""Executes SimCoal.</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-docstring"> """</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">par_dir</tt> <tt class="py-op">==</tt> <tt class="py-name">None</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">par_dir</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-1" 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-1', 'Config', 'link-1');">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="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-name">curr_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">par_dir</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">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">simcoal_dir</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">self</tt><tt class="py-op">.</tt><tt class="py-name">bin_name</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">par_file</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">num_sims</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt> <tt class="py-op">+</tt> <tt class="py-name">ploydi</tt> <tt class="py-op">+</tt> <tt class="py-string">' >/dev/null 2>&1'</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">os</tt><tt class="py-op">.</tt><tt class="py-name">chdir</tt><tt class="py-op">(</tt><tt class="py-name">curr_dir</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L48"></a><tt class="py-lineno">48</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 09:28:11 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>
