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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.AlignAce-module.html">Package AlignAce</a> ::
Module AlignAceStandalone
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<h1 class="epydoc">Source Code for <a href="Bio.AlignAce.AlignAceStandalone-module.html">Module Bio.AlignAce.AlignAceStandalone</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 AlignACE, </tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">for motif search in DNA sequences.</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">AlignACE 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">AlignACE Citations:</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring">Computational identification of cis-regulatory elements associated with </tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring">groups of functionally related genes in Saccharomyces cerevisiae, </tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring">Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular </tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"><tt class="py-docstring">Biology 2000 Mar 10;296(5):1205-14.</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring">Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences </tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring">Clustered by Whole-Genome mRNA Quantitation, </tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"><tt class="py-docstring">Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology </tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"><tt class="py-docstring">1998 Oct;16(10):939-45. </tt> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"><tt class="py-docstring">functions:</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"><tt class="py-docstring">AlignAce - runs the AlignACE standalone prgram and returns the </tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"><tt class="py-docstring">ApplicationResult object</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</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">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="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-3', 'ParserSupport', 'link-3');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" 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-4', 'Applications', 'link-4');">Applications</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.AlignAce.Applications.AlignAceCommandline=Bio.AlignAce.Applications.AlignAceCommandline-class.html"><a title="Bio.AlignAce.Applications.AlignAceCommandline" class="py-name" href="#" onclick="return doclink('link-5', 'AlignAceCommandline', 'link-5');">AlignAceCommandline</a></tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-6" 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-6', 'Scanner', 'link-6');">Scanner</a></tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-7" 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-7', 'Parser', 'link-7');">Parser</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> </tt>
<a name="AlignAce"></a><div id="AlignAce-def"><a name="L44"></a><tt class="py-lineno">44</tt> <a class="py-toggle" href="#" id="AlignAce-toggle" onclick="return toggle('AlignAce');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignAce.AlignAceStandalone-module.html#AlignAce">AlignAce</a><tt class="py-op">(</tt><tt class="py-param">infile</tt><tt class="py-op">,</tt> <tt class="py-param">cmd</tt><tt class="py-op">=</tt><tt class="py-string">"AlignACE"</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="AlignAce-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="AlignAce-expanded"><a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-docstring">"""Runs AlignACE and returns data.</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"><tt class="py-docstring"> cmd == AlignACE executable</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"><tt class="py-docstring"> infile == sequence file to process</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-docstring"> You may pass more parameters to **keywds to change the behavior of</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-docstring"> the search. Otherwise, optional values will be chosen by blastall.</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"><tt class="py-docstring"> numcols number of columns to align (10)</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"><tt class="py-docstring"> expect number of sites expected in model (10)</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"><tt class="py-docstring"> gcback background fractional GC content of input sequence (0.38)</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"><tt class="py-docstring"> minpass minimum number of non-improved passes in phase 1 (200)</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-docstring"> seed set seed for random number generator (time)</tt> </tt>
<a name="L58"></a><tt class="py-lineno">58</tt> <tt class="py-line"><tt class="py-docstring"> undersample possible sites / (expect * numcols * seedings) (1)</tt> </tt>
<a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"><tt class="py-docstring"> oversample 1/undersample (1)</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno">62</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-8" 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-8', 'exists', 'link-8');">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="L63"></a><tt class="py-lineno">63</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="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno">65</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-9" class="py-name"><a title="Bio.biblio.Biblio.exists
Bio.biblio.BiblioCollection.exists" class="py-name" href="#" onclick="return doclink('link-9', 'exists', 'link-8');">exists</a></tt><tt class="py-op">(</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno">66</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">"Input file does not exist at %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">infile</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-name">AlignCmd</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.AlignAce.Applications.AlignAceCommandline" class="py-name" href="#" onclick="return doclink('link-10', 'AlignAceCommandline', 'link-5');">AlignAceCommandline</a></tt><tt class="py-op">(</tt><tt class="py-name">cmd</tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"> <tt class="py-name">AlignCmd</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'set_parameter', 'link-11');">set_parameter</a></tt><tt class="py-op">(</tt><tt class="py-string">"input"</tt><tt class="py-op">,</tt><tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> </tt>
<a name="L72"></a><tt class="py-lineno">72</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="L73"></a><tt class="py-lineno">73</tt> <tt class="py-line"> <tt class="py-name">AlignCmd</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Application.AbstractCommandline.set_parameter" class="py-name" href="#" onclick="return doclink('link-12', 'set_parameter', 'link-11');">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="L74"></a><tt class="py-lineno">74</tt> <tt class="py-line"> </tt>
<a name="L75"></a><tt class="py-lineno">75</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">AlignCmd</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'run', 'link-13');">run</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L76"></a><tt class="py-lineno">76</tt> <tt class="py-line"> </tt><script type="text/javascript">
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