<?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.FDist.Controller.FDistController</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.FDist-module.html">Package FDist</a> :: <a href="Bio.PopGen.FDist.Controller-module.html">Module Controller</a> :: Class FDistController </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.FDist.Controller.FDistController-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FDistController</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController">source code</a></span></p> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.PopGen.FDist.Async.FDistAsync-class.html">Async.FDistAsync</a></li> </ul> </dd></dl> <hr /> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">fdist_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">ext</span>=<span class="summary-sig-default">None</span>)</span><br /> Initializes the controller.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#_get_path" class="summary-sig-name" onclick="show_private();">_get_path</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">app</span>)</span><br /> Returns the path to an fdist application.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._get_path">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#_get_temp_file" class="summary-sig-name" onclick="show_private();">_get_temp_file</a>(<span class="summary-sig-arg">self</span>)</span><br /> Gets a temporary file name.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._get_temp_file">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_datacal" class="summary-sig-name">run_datacal</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">data_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span><br /> Executes datacal.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_datacal">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#_generate_intfile" class="summary-sig-name" onclick="show_private();">_generate_intfile</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">data_dir</span>)</span><br /> Generates an INTFILE.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._generate_intfile">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_fdist" class="summary-sig-name">run_fdist</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">npops</span>, <span class="summary-sig-arg">nsamples</span>, <span class="summary-sig-arg">fst</span>, <span class="summary-sig-arg">sample_size</span>, <span class="summary-sig-arg">mut</span>=<span class="summary-sig-default">0</span>, <span class="summary-sig-arg">num_sims</span>=<span class="summary-sig-default">20000</span>, <span class="summary-sig-arg">data_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span><br /> Executes fdist.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_fdist">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_fdist_force_fst" class="summary-sig-name">run_fdist_force_fst</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">npops</span>, <span class="summary-sig-arg">nsamples</span>, <span class="summary-sig-arg">fst</span>, <span class="summary-sig-arg">sample_size</span>, <span class="summary-sig-arg">mut</span>=<span class="summary-sig-default">0</span>, <span class="summary-sig-arg">num_sims</span>=<span class="summary-sig-default">20000</span>, <span class="summary-sig-arg">data_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">try_runs</span>=<span class="summary-sig-default">5000</span>, <span class="summary-sig-arg">limit</span>=<span class="summary-sig-default">0.001</span>)</span><br /> Exectues fdist trying to force Fst.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_fdist_force_fst">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_cplot" class="summary-sig-name">run_cplot</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">ci</span>=<span class="summary-sig-default">0.95</span>, <span class="summary-sig-arg">data_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span><br /> Executes cplot.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_cplot">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_pv" class="summary-sig-name">run_pv</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">out_file</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">probs.dat</code><code class="variable-quote">'</code></span>, <span class="summary-sig-arg">data_dir</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span><br /> Executes pv.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_pv">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== METHOD DETAILS ==================== --> <a name="section-MethodDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Method Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-MethodDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="__init__"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>, <span class="sig-arg">fdist_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>, <span class="sig-arg">ext</span>=<span class="sig-default">None</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.__init__">source code</a></span> </td> </tr></table> <pre class="literalblock"> Initializes the controller. fdist_dir is the directory where fdist2 is. ext is the extension of binaries (.exe on windows, none on Unix) </pre> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_get_path"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_get_path</span>(<span class="sig-arg">self</span>, <span class="sig-arg">app</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._get_path">source code</a></span> </td> </tr></table> <p>Returns the path to an fdist application.</p> <p>Includes Path where fdist can be found plus executable extension.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_get_temp_file"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_get_temp_file</span>(<span class="sig-arg">self</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._get_temp_file">source code</a></span> </td> </tr></table> <p>Gets a temporary file name.</p> <p>Returns a temporary file name, if executing inside jython tries to replace unexisting tempfile.mkstemp().</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="run_datacal"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">run_datacal</span>(<span class="sig-arg">self</span>, <span class="sig-arg">data_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_datacal">source code</a></span> </td> </tr></table> <p>Executes datacal.</p> <p>data_dir - Where the data is found.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_generate_intfile"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_generate_intfile</span>(<span class="sig-arg">self</span>, <span class="sig-arg">data_dir</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController._generate_intfile">source code</a></span> </td> </tr></table> <p>Generates an INTFILE.</p> <p>Parameter: data_dir - data directory</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="run_fdist"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">run_fdist</span>(<span class="sig-arg">self</span>, <span class="sig-arg">npops</span>, <span class="sig-arg">nsamples</span>, <span class="sig-arg">fst</span>, <span class="sig-arg">sample_size</span>, <span class="sig-arg">mut</span>=<span class="sig-default">0</span>, <span class="sig-arg">num_sims</span>=<span class="sig-default">20000</span>, <span class="sig-arg">data_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_fdist">source code</a></span> </td> </tr></table> <p>Executes fdist.</p> <p>Parameters: npops - Number of populations nsamples - Number of populations sampled fst - expected Fst sample_size - Sample size per population mut - 1=Stepwise, 0=Infinite allele num_sims - number of simulations data_dir - Where the data is found</p> <p>Returns: fst - Average Fst</p> <p>Important Note: This can take quite a while to run!</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="run_fdist_force_fst"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">run_fdist_force_fst</span>(<span class="sig-arg">self</span>, <span class="sig-arg">npops</span>, <span class="sig-arg">nsamples</span>, <span class="sig-arg">fst</span>, <span class="sig-arg">sample_size</span>, <span class="sig-arg">mut</span>=<span class="sig-default">0</span>, <span class="sig-arg">num_sims</span>=<span class="sig-default">20000</span>, <span class="sig-arg">data_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>, <span class="sig-arg">try_runs</span>=<span class="sig-default">5000</span>, <span class="sig-arg">limit</span>=<span class="sig-default">0.001</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_fdist_force_fst">source code</a></span> </td> </tr></table> <pre class="literalblock"> Exectues fdist trying to force Fst. Parameters: try_runs - Number of simulations on the part trying to get Fst correct limit - Interval limit Other parameters can be seen on run_fdist. </pre> <dl class="fields"> </dl> </td></tr></table> </div> <a name="run_cplot"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">run_cplot</span>(<span class="sig-arg">self</span>, <span class="sig-arg">ci</span>=<span class="sig-default">0.95</span>, <span class="sig-arg">data_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_cplot">source code</a></span> </td> </tr></table> <p>Executes cplot.</p> <p>ci - Confidence interval. data_dir - Where the data is found.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="run_pv"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">run_pv</span>(<span class="sig-arg">self</span>, <span class="sig-arg">out_file</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">probs.dat</code><code class="variable-quote">'</code></span>, <span class="sig-arg">data_dir</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">.</code><code class="variable-quote">'</code></span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.PopGen.FDist.Controller-pysrc.html#FDistController.run_pv">source code</a></span> </td> </tr></table> <p>Executes pv.</p> <p>out_file - Name of output file. data_dir - Where the data is found.</p> <dl class="fields"> </dl> </td></tr></table> </div> <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 09:26:37 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. 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