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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PopGen-module.html">Package PopGen</a> ::
Package SimCoal
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<h1 class="epydoc">Source Code for <a href="Bio.PopGen.SimCoal-module.html">Package Bio.PopGen.SimCoal</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. 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 class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></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">SimCoal2 execution module and support functions.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </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">os</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">sys</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-comment">#This is a workaround to work with the test system</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#In any case the problem is with the test system</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">for</tt> <tt id="link-0" class="py-name" targets="Variable Bio.PopGen.SimCoal.instance=Bio.PopGen.SimCoal-module.html#instance"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-0', 'instance', 'link-0');">instance</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">:</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt id="link-1" class="py-name" targets="Variable Bio.PopGen.SimCoal.test_path=Bio.PopGen.SimCoal-module.html#test_path"><a title="Bio.PopGen.SimCoal.test_path" class="py-name" href="#" onclick="return doclink('link-1', 'test_path', 'link-1');">test_path</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-2" class="py-name"><a title="Bio.PopGen.SimCoal.instance" class="py-name" href="#" onclick="return doclink('link-2', 'instance', 'link-0');">instance</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Bio'</tt><tt class="py-op">,</tt> <tt class="py-string">'PopGen'</tt><tt class="py-op">,</tt> <tt class="py-string">'SimCoal'</tt><tt class="py-op">,</tt> <tt class="py-string">'data'</tt><tt class="py-op">)</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</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 id="link-3" class="py-name"><a title="Bio.PopGen.SimCoal.test_path" class="py-name" href="#" onclick="return doclink('link-3', 'test_path', 'link-1');">test_path</a></tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">F_OK</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt id="link-4" class="py-name" targets="Variable Bio.PopGen.SimCoal.builtin_tpl_dir=Bio.PopGen.SimCoal-module.html#builtin_tpl_dir"><a title="Bio.PopGen.SimCoal.builtin_tpl_dir" class="py-name" href="#" onclick="return doclink('link-4', 'builtin_tpl_dir', 'link-4');">builtin_tpl_dir</a></tt> <tt class="py-op">=</tt> <tt id="link-5" class="py-name"><a title="Bio.PopGen.SimCoal.test_path" class="py-name" href="#" onclick="return doclink('link-5', 'test_path', 'link-1');">test_path</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> </tt><script type="text/javascript">
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