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<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
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<!-- ==================== 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>
<pre class="base-tree">
object --+
|
<strong class="uidshort">FDistController</strong>
</pre>
<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>
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<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<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>
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<span class="summary-type"> </span>
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<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 class="summary-sig-arg">version</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">crit_freq</span>=<span class="summary-sig-default">0.99</span>,
<span class="summary-sig-arg">p</span>=<span class="summary-sig-default">0.5</span>,
<span class="summary-sig-arg">beta</span>=<span class="summary-sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</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>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<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>
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<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">50000</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">is_dominant</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">theta</span>=<span class="summary-sig-default">0.06</span>,
<span class="summary-sig-arg">beta</span>=<span class="summary-sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</code></span>,
<span class="summary-sig-arg">max_freq</span>=<span class="summary-sig-default">0.99</span>)</span><br />
Executes (d)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>
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<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">50000</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 class="summary-sig-arg">is_dominant</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">theta</span>=<span class="summary-sig-default">0.06</span>,
<span class="summary-sig-arg">beta</span>=<span class="summary-sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</code></span>,
<span class="summary-sig-arg">max_freq</span>=<span class="summary-sig-default">0.99</span>)</span><br />
Executes 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 class="summary-sig-arg">version</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">smooth</span>=<span class="summary-sig-default">0.04</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 class="summary-sig-arg">version</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">smooth</span>=<span class="summary-sig-default">0.04</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>
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</td>
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<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__sizeof__</code>,
<code>__str__</code>,
<code>__subclasshook__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
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<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
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<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>
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<a name="__init__"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<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">
<dt>Overrides:
object.__init__
</dt>
</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 class="sig-arg">version</span>=<span class="sig-default">1</span>,
<span class="sig-arg">crit_freq</span>=<span class="sig-default">0.99</span>,
<span class="sig-arg">p</span>=<span class="sig-default">0.5</span>,
<span class="sig-arg">beta</span>=<span class="sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</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">50000</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">is_dominant</span>=<span class="sig-default">False</span>,
<span class="sig-arg">theta</span>=<span class="sig-default">0.06</span>,
<span class="sig-arg">beta</span>=<span class="sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</code></span>,
<span class="sig-arg">max_freq</span>=<span class="sig-default">0.99</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>
<pre class="literalblock">
Executes (d)fdist.
Parameters:
npops - Number of populations
nsamples - Number of populations sampled
fst - expected Fst
sample_size - Sample size per population
For dfdist: if zero a sample size file has to be provided
mut - 1=Stepwise, 0=Infinite allele
num_sims - number of simulations
data_dir - Where the data is found
is_dominant - If true executes dfdist
theta - Theta (=2Nmu)
beta - Parameters for the beta prior
max_freq - Maximum allowed frequency of the commonest allele
Returns:
fst - Average Fst
Important Note: This can take quite a while to run!
</pre>
<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">50000</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 class="sig-arg">is_dominant</span>=<span class="sig-default">False</span>,
<span class="sig-arg">theta</span>=<span class="sig-default">0.06</span>,
<span class="sig-arg">beta</span>=<span class="sig-default"><code class="variable-group">(</code>0.25<code class="variable-op">, </code>0.25<code class="variable-group">)</code></span>,
<span class="sig-arg">max_freq</span>=<span class="sig-default">0.99</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">
Executes 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 class="sig-arg">version</span>=<span class="sig-default">1</span>,
<span class="sig-arg">smooth</span>=<span class="sig-default">0.04</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 class="sig-arg">version</span>=<span class="sig-default">1</span>,
<span class="sig-arg">smooth</span>=<span class="sig-default">0.04</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>
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