<?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.Align.Applications._Prank.PrankCommandline</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.Align-module.html">Package Align</a> :: <a href="Bio.Align.Applications-module.html">Package Applications</a> :: <a href="Bio.Align.Applications._Prank-module.html" onclick="show_private();">Module _Prank</a> :: Class PrankCommandline </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.Align.Applications._Prank.PrankCommandline-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class PrankCommandline</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Align.Applications._Prank-pysrc.html#PrankCommandline">source code</a></span></p> <pre class="base-tree"> object --+ | <a href="Bio.Application.AbstractCommandline-class.html">Application.AbstractCommandline</a> --+ | <strong class="uidshort">PrankCommandline</strong> </pre> <hr /> <p>Command line wrapper for the multiple alignment program PRANK.</p> <p>http://www.ebi.ac.uk/goldman-srv/prank/prank/</p> <p>Example:</p> <p>To align a FASTA file (unaligned.fasta) with the output in aligned FASTA format with the output filename starting with "aligned" (you can't pick the filename explicitly), no tree ouput and no XML output, use:</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> PrankCommandline <span class="py-prompt">>>> </span>prank_cline = PrankCommandline(d=<span class="py-string">"unaligned.fasta"</span>, <span class="py-more">... </span> o=<span class="py-string">"aligned"</span>, <span class="py-comment">#prefix only!</span> <span class="py-more">... </span> f=8, <span class="py-comment">#FASTA output</span> <span class="py-more">... </span> notree=True, noxml=True) <span class="py-prompt">>>> </span><span class="py-keyword">print</span> prank_cline <span class="py-output">prank -d=unaligned.fasta -o=aligned -f=8 -noxml -notree</span></pre> <p>You would typically run the command line with prank_cline() or via the Python subprocess module, as described in the Biopython tutorial.</p> <p>Citations:</p> <p>Loytynoja, A. and Goldman, N. 2005. An algorithm for progressive multiple alignment of sequences with insertions. Proceedings of the National Academy of Sciences, 102: 10557--10562.</p> <p>Loytynoja, A. and Goldman, N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science, 320: 1632.</p> <p>Last checked agains version: 081202</p> <!-- ==================== 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.Align.Applications._Prank.PrankCommandline-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">prank</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> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Align.Applications._Prank-pysrc.html#PrankCommandline.__init__">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td colspan="2" class="summary"> <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>, <code><a href="Bio.Application.AbstractCommandline-class.html#__repr__">__repr__</a></code>, <code><a href="Bio.Application.AbstractCommandline-class.html#__setattr__">__setattr__</a></code>, <code><a href="Bio.Application.AbstractCommandline-class.html#__str__">__str__</a></code>, <code><a href="Bio.Application.AbstractCommandline-class.html#set_parameter">set_parameter</a></code> </p> <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> </p></div> <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> </p> </td> </tr> </table> <!-- ==================== PROPERTIES ==================== --> <a name="section-Properties"></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">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> </tr> </table> </td> </tr> <tr> <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> <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">cmd</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">prank</code><code class="variable-quote">'</code></span>, <span class="sig-arg">**kwargs</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Align.Applications._Prank-pysrc.html#PrankCommandline.__init__">source code</a></span> </td> </tr></table> <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> </dt> </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 Thu Aug 18 18:19:23 2011 </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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