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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.Async-module.html">Module Async</a> ::
Class SplitFDist
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SplitFDist</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist">source code</a></span></p>
<p>Splits a FDist run.</p>
<p>The idea is to split a certain number of simulations in smaller
numbers (e.g. 30.000 sims split in 30 packets of 1.000). This allows to
run simulations in parallel, thus taking advantage of multi-core
CPUs.</p>
<p>Each SplitFDist object can only be used to run a single FDist
simulation.</p>
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<td><span class="summary-sig"><a href="Bio.PopGen.FDist.Async.SplitFDist-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">report_fun</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">num_thr</span>=<span class="summary-sig-default">2</span>,
<span class="summary-sig-arg">split_size</span>=<span class="summary-sig-default">1000</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 />
Constructor.</td>
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<span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.PopGen.FDist.Async.SplitFDist-class.html#monitor" class="summary-sig-name">monitor</a>(<span class="summary-sig-arg">self</span>)</span><br />
Monitors and reports (using report_fun) execution.</td>
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<span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.monitor">source code</a></span>
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<td><span class="summary-sig"><a name="acquire"></a><span class="summary-sig-name">acquire</span>(<span class="summary-sig-arg">self</span>)</span><br />
Allows the external acquisition of the lock.</td>
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<td><span class="summary-sig"><a name="release"></a><span class="summary-sig-name">release</span>(<span class="summary-sig-arg">self</span>)</span><br />
Allows the external release of the lock.</td>
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<td><span class="summary-sig"><a href="Bio.PopGen.FDist.Async.SplitFDist-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 />
Runs FDist.</td>
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<span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.run_fdist">source code</a></span>
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">report_fun</span>=<span class="sig-default">None</span>,
<span class="sig-arg">num_thr</span>=<span class="sig-default">2</span>,
<span class="sig-arg">split_size</span>=<span class="sig-default">1000</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>
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><span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.__init__">source code</a></span>
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<pre class="literalblock">
Constructor.
Parameters:
report_fun - Function that is called when a single packet is
run, it should have a single parameter: Fst.
num_thr - Number of desired threads, typically the number
of cores.
split_size - Size that a full simulation will be split in.
ext - Binary extension name (e.g. nothing on Unix, '.exe' on
Windows).
</pre>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">monitor</span>(<span class="sig-arg">self</span>)</span>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.monitor">source code</a></span>
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<p>Monitors and reports (using report_fun) execution.</p>
<p>Every time a partial simulation ends, calls report_fun. IMPORTANT:
monitor calls can be concurrent with other events, ie, a tasks might end
while report_fun is being called. This means that report_fun should be
consider that other events might be happening while it is running (it can
call acquire/release if necessary).</p>
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<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>
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><span class="codelink"><a href="Bio.PopGen.FDist.Async-pysrc.html#SplitFDist.run_fdist">source code</a></span>
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<p>Runs FDist.</p>
<p>Parameters can be seen on FDistController.run_fdist.</p>
<p>It will split a single execution in several parts and create separated
data directories.</p>
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