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<a href="Bio-module.html">Package Bio</a> ::
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<a href="Bio.Align.Applications._Muscle-module.html" onclick="show_private();">Module _Muscle</a> ::
Class MuscleCommandline
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class MuscleCommandline</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Align.Applications._Muscle-pysrc.html#MuscleCommandline">source code</a></span></p>
<pre class="base-tree">
object --+
|
<a href="Bio.Application.AbstractCommandline-class.html">Application.AbstractCommandline</a> --+
|
<strong class="uidshort">MuscleCommandline</strong>
</pre>
<hr />
<p>Command line wrapper for the multiple alignment program MUSCLE.</p>
<p>http://www.drive5.com/muscle/</p>
<p>Example:</p>
<pre class="py-doctest">
<span class="py-prompt">>>> </span><span class="py-keyword">from</span> Bio.Align.Applications <span class="py-keyword">import</span> MuscleCommandline
<span class="py-prompt">>>> </span>muscle_exe = r<span class="py-string">"C:\Program Files\Aligments\muscle3.8.31_i86win32.exe"</span>
<span class="py-prompt">>>> </span>in_file = r<span class="py-string">"C:\My Documents\unaligned.fasta"</span>
<span class="py-prompt">>>> </span>out_file = r<span class="py-string">"C:\My Documents\aligned.fasta"</span>
<span class="py-prompt">>>> </span>muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file)
<span class="py-prompt">>>> </span><span class="py-keyword">print</span> muscle_cline
<span class="py-output">C:\Program Files\Aligments\muscle3.8.31_i86win32.exe -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta"</span></pre>
<p>You would typically run the command line with muscle_cline() or via
the Python subprocess module, as described in the Biopython tutorial.</p>
<p>Citations:</p>
<p>Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high
accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.</p>
<p>Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with
reduced time and space complexity. BMC Bioinformatics 5(1): 113.</p>
<p>Last checked against version: 3.7, briefly against 3.8</p>
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<td><span class="summary-sig"><a href="Bio.Align.Applications._Muscle.MuscleCommandline-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">cmd</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">muscle</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">**kwargs</span>)</span><br />
Create a new instance of a command line wrapper object.</td>
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<span class="codelink"><a href="Bio.Align.Applications._Muscle-pysrc.html#MuscleCommandline.__init__">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Application.AbstractCommandline-class.html">Application.AbstractCommandline</a></code></b>:
<code><a href="Bio.Application.AbstractCommandline-class.html#__call__">__call__</a></code>,
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<code><a href="Bio.Application.AbstractCommandline-class.html#set_parameter">set_parameter</a></code>
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<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Application.AbstractCommandline-class.html">Application.AbstractCommandline</a></code></b> (private):
<code><a href="Bio.Application.AbstractCommandline-class.html#_check_value" onclick="show_private();">_check_value</a></code>,
<code><a href="Bio.Application.AbstractCommandline-class.html#_clear_parameter" onclick="show_private();">_clear_parameter</a></code>,
<code><a href="Bio.Application.AbstractCommandline-class.html#_get_parameter" onclick="show_private();">_get_parameter</a></code>,
<code><a href="Bio.Application.AbstractCommandline-class.html#_validate" onclick="show_private();">_validate</a></code>
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<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>__sizeof__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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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">cmd</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">muscle</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">**kwargs</span>)</span>
<br /><em class="fname">(Constructor)</em>
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</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Applications._Muscle-pysrc.html#MuscleCommandline.__init__">source code</a></span>
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<p>Create a new instance of a command line wrapper object.</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
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