<?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.AlignAce.CompareAceStandalone</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.AlignAce-module.html">Package AlignAce</a> :: Module CompareAceStandalone </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.AlignAce.CompareAceStandalone-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.AlignAce.CompareAceStandalone-module.html">Module Bio.AlignAce.CompareAceStandalone</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2003 by Bartek Wilczynski. All rights reserved.</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with the standalone version of CompareAce, </tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">for motif comparison</tt> </tt> <a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-docstring">CompareACE homepage:</tt> </tt> <a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">http://atlas.med.harvard.edu/</tt> </tt> <a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-docstring">functions:</tt> </tt> <a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring">CompareAce - runs the AlignACE standalone prgram and returns the ApplicationResult object</tt> </tt> <a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt> <a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> </tt> <a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt> <a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt> <a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"> </tt> <a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt> <a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.AlignAce.Applications=Bio.AlignAce.Applications-module.html,Module Bio.Blast.Applications=Bio.Blast.Applications-module.html,Module Bio.Emboss.Applications=Bio.Emboss.Applications-module.html"><a title="Bio.AlignAce.Applications Bio.Blast.Applications Bio.Emboss.Applications" class="py-name" href="#" onclick="return doclink('link-2', 'Applications', 'link-2');">Applications</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.AlignAce.Applications.CompareAceCommandline=Bio.AlignAce.Applications.CompareAceCommandline-class.html"><a title="Bio.AlignAce.Applications.CompareAceCommandline" class="py-name" href="#" onclick="return doclink('link-3', 'CompareAceCommandline', 'link-3');">CompareAceCommandline</a></tt> </tt> <a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt> <a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.AlignAce.Scanner=Bio.AlignAce.Scanner-module.html,Module Bio.GenBank.Scanner=Bio.GenBank.Scanner-module.html"><a title="Bio.AlignAce.Scanner Bio.GenBank.Scanner" class="py-name" href="#" onclick="return doclink('link-4', 'Scanner', 'link-4');">Scanner</a></tt> </tt> <a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Module Bio.AlignAce.Parser=Bio.AlignAce.Parser-module.html,Module Bio.Entrez.Parser=Bio.Entrez.Parser-module.html,Module Bio.MEME.Parser=Bio.MEME.Parser-module.html,Class Bio.SCOP.Cla.Parser=Bio.SCOP.Cla.Parser-class.html,Class Bio.SCOP.Des.Parser=Bio.SCOP.Des.Parser-class.html,Class Bio.SCOP.Dom.Parser=Bio.SCOP.Dom.Parser-class.html,Class Bio.SCOP.Hie.Parser=Bio.SCOP.Hie.Parser-class.html,Class Bio.SCOP.Raf.Parser=Bio.SCOP.Raf.Parser-class.html,Module Martel.Parser=Martel.Parser-module.html,Class Martel.Parser.Parser=Martel.Parser.Parser-class.html"><a title="Bio.AlignAce.Parser Bio.Entrez.Parser Bio.MEME.Parser Bio.SCOP.Cla.Parser Bio.SCOP.Des.Parser Bio.SCOP.Dom.Parser Bio.SCOP.Hie.Parser Bio.SCOP.Raf.Parser Martel.Parser Martel.Parser.Parser" class="py-name" href="#" onclick="return doclink('link-5', 'Parser', 'link-5');">Parser</a></tt> </tt> <a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> </tt> <a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> </tt> <a name="CompareAce"></a><div id="CompareAce-def"><a name="L30"></a><tt class="py-lineno">30</tt> <a class="py-toggle" href="#" id="CompareAce-toggle" onclick="return toggle('CompareAce');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.CompareAceStandalone-module.html#CompareAce">CompareAce</a><tt class="py-op">(</tt> <tt class="py-param">cmd</tt><tt class="py-op">=</tt><tt class="py-string">"CompareACE"</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="CompareAce-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="CompareAce-expanded"><a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-docstring">"""Runs CompareACE and returns data.</tt> </tt> <a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-docstring"> motif1, motif2 == files containing AlignACE motifs</tt> </tt> <a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> </tt> <a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.biblio.Biblio.exists()=Bio.biblio.Biblio-class.html#exists,Method Bio.biblio.BiblioCollection.exists()=Bio.biblio.BiblioCollection-class.html#exists"><a title="Bio.biblio.Biblio.exists Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-6', 'exists', 'link-6');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">cmd</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IOError</tt><tt class="py-op">,</tt> <tt class="py-string">"Executable does not exist at %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">cmd</tt> </tt> <a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> </tt> <a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">CompareCmd</tt> <tt class="py-op">=</tt> <tt id="link-7" class="py-name"><a title="Bio.AlignAce.Applications.CompareAceCommandline" class="py-name" href="#" onclick="return doclink('link-7', 'CompareAceCommandline', 'link-3');">CompareAceCommandline</a></tt><tt class="py-op">(</tt><tt class="py-name">cmd</tt><tt class="py-op">)</tt> </tt> <a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> </tt> <a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">par</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">keywds</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-name">CompareCmd</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Method Bio.Application.AbstractCommandline.set_parameter()=Bio.Application.AbstractCommandline-class.html#set_parameter"><a title="Bio.Application.AbstractCommandline.set_parameter" class="py-name" href="#" onclick="return doclink('link-8', 'set_parameter', 'link-8');">set_parameter</a></tt><tt class="py-op">(</tt><tt class="py-name">par</tt><tt class="py-op">,</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> </tt> <a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> </tt> <a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">CompareCmd</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.AlignAce.Applications.AlignAceCommandline.run()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#run,Method Bio.AlignAce.Applications.CompareAceCommandline.run()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#run,Method Bio.Entrez.Parser.DataHandler.run()=Bio.Entrez.Parser.DataHandler-class.html#run,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#run,Method Martel.setup.my_install.run()=Martel.setup.my_install-class.html#run,Method Martel.setup.run_install_tests.run()=Martel.setup.run_install_tests-class.html#run,Method Martel.setup.run_local_tests.run()=Martel.setup.run_local_tests-class.html#run"><a title="Bio.AlignAce.Applications.AlignAceCommandline.run Bio.AlignAce.Applications.CompareAceCommandline.run Bio.Entrez.Parser.DataHandler.run Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.run Martel.setup.my_install.run Martel.setup.run_install_tests.run Martel.setup.run_local_tests.run" class="py-name" href="#" onclick="return doclink('link-9', 'run', 'link-9');">run</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <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 Mon Sep 15 09:28:17 2008 </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 // 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