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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Phylo-module.html">Package Phylo</a> ::
<a href="Bio.Phylo.PAML-module.html">Package PAML</a> ::
<a href="Bio.Phylo.PAML.codeml-module.html">Module codeml</a> ::
Class Codeml
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Codeml</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Phylo.PAML._paml.Paml-class.html">_paml.Paml</a> --+
|
<strong class="uidshort">Codeml</strong>
</pre>
<hr />
<p>This class implements an interface to CODEML, part of the PAML
package.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Phylo.PAML.codeml.Codeml-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alignment</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">tree</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">working_dir</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">out_file</span>=<span class="summary-sig-default">None</span>)</span><br />
Initialize the codeml instance.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.__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.Phylo.PAML.codeml.Codeml-class.html#write_ctl_file" class="summary-sig-name">write_ctl_file</a>(<span class="summary-sig-arg">self</span>)</span><br />
Dynamically build a CODEML control file from the options.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.write_ctl_file">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.Phylo.PAML.codeml.Codeml-class.html#read_ctl_file" class="summary-sig-name">read_ctl_file</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ctl_file</span>)</span><br />
Parse a control file and load the options into the Codeml instance.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.read_ctl_file">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.Phylo.PAML.codeml.Codeml-class.html#print_options" class="summary-sig-name">print_options</a>(<span class="summary-sig-arg">self</span>)</span><br />
Print out all of the options and their current settings.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.print_options">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.Phylo.PAML.codeml.Codeml-class.html#_set_rel_paths" class="summary-sig-name" onclick="show_private();">_set_rel_paths</a>(<span class="summary-sig-arg">self</span>)</span><br />
Convert all file/directory locations to paths relative to the current
working directory.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml._set_rel_paths">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.Phylo.PAML.codeml.Codeml-class.html#run" class="summary-sig-name">run</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">ctl_file</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">verbose</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">command</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">codeml</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">parse</span>=<span class="summary-sig-default">True</span>)</span><br />
Run codeml using the current configuration and then parse the
results.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.run">source code</a></span>
</td>
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</td>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Phylo.PAML._paml.Paml-class.html">_paml.Paml</a></code></b>:
<code><a href="Bio.Phylo.PAML._paml.Paml-class.html#get_all_options">get_all_options</a></code>,
<code><a href="Bio.Phylo.PAML._paml.Paml-class.html#get_option">get_option</a></code>,
<code><a href="Bio.Phylo.PAML._paml.Paml-class.html#set_options">set_options</a></code>
</p>
<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>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
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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">alignment</span>=<span class="sig-default">None</span>,
<span class="sig-arg">tree</span>=<span class="sig-default">None</span>,
<span class="sig-arg">working_dir</span>=<span class="sig-default">None</span>,
<span class="sig-arg">out_file</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.Phylo.PAML.codeml-pysrc.html#Codeml.__init__">source code</a></span>
</td>
</tr></table>
<p>Initialize the codeml instance.</p>
<p>The user may optionally pass in strings specifying the locations of
the input alignment and tree files, the working directory and the final
output file. Other options found in the CODEML control have typical
settings by default to run site class models 0, 1 and 2 on a nucleotide
alignment.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="write_ctl_file"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">write_ctl_file</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.write_ctl_file">source code</a></span>
</td>
</tr></table>
<p>Dynamically build a CODEML control file from the options.</p>
<p>The control file is written to the location specified by the ctl_file
property of the codeml class.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.PAML._paml.Paml-class.html#write_ctl_file">_paml.Paml.write_ctl_file</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="read_ctl_file"></a>
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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">read_ctl_file</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">ctl_file</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.read_ctl_file">source code</a></span>
</td>
</tr></table>
<p>Parse a control file and load the options into the Codeml
instance.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.PAML._paml.Paml-class.html#read_ctl_file">_paml.Paml.read_ctl_file</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="print_options"></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">print_options</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.print_options">source code</a></span>
</td>
</tr></table>
<p>Print out all of the options and their current settings.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.PAML._paml.Paml-class.html#print_options">_paml.Paml.print_options</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_set_rel_paths"></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">_set_rel_paths</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml._set_rel_paths">source code</a></span>
</td>
</tr></table>
<p>Convert all file/directory locations to paths relative to the current
working directory.</p>
<p>CODEML requires that all paths specified in the control file be
relative to the directory from which it is called rather than absolute
paths.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.PAML._paml.Paml-class.html#_set_rel_paths" onclick="show_private();">_paml.Paml._set_rel_paths</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="run"></a>
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<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">run</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">ctl_file</span>=<span class="sig-default">None</span>,
<span class="sig-arg">verbose</span>=<span class="sig-default">False</span>,
<span class="sig-arg">command</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">codeml</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">parse</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Phylo.PAML.codeml-pysrc.html#Codeml.run">source code</a></span>
</td>
</tr></table>
<p>Run codeml using the current configuration and then parse the
results.</p>
<p>Return a process signal so the user can determine if the execution was
successful (return code 0 is successful, -N indicates a failure). The
arguments may be passed as either absolute or relative paths, despite the
fact that CODEML requires relative paths.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.Phylo.PAML._paml.Paml-class.html#run">_paml.Paml.run</a>
</dt>
</dl>
</td></tr></table>
</div>
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