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<a href="Bio-module.html">Package Bio</a> ::
Package Application
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<h1 class="epydoc">Source Code for <a href="Bio.Application-module.html">Package Bio.Application</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""General mechanisms to access applications in biopython.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">popen2</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</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="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="generic_run"></a><div id="generic_run-def"><a name="L9"></a><tt class="py-lineno"> 9</tt> <a class="py-toggle" href="#" id="generic_run-toggle" onclick="return toggle('generic_run');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application-module.html#generic_run">generic_run</a><tt class="py-op">(</tt><tt class="py-param">commandline</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="generic_run-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="generic_run-expanded"><a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> <tt class="py-docstring">"""Run an application with the given commandline.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"> This expects a pre-built commandline that derives from </tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> AbstractCommandline, and returns a ApplicationResult object</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"> to get results from a program, along with handles of the</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> standard output and standard error.</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-comment"># print str(commandline)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">platform</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">'win'</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-comment"># Windows does not have popen2.Popen3</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">r</tt><tt class="py-op">,</tt> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Variable Bio.Affy.CelFile.e=Bio.Affy.CelFile-module.html#e,Variable Bio.LogisticRegression.e=Bio.LogisticRegression-module.html#e,Variable Bio.MarkovModel.e=Bio.MarkovModel-module.html#e,Variable Bio.MaxEntropy.e=Bio.MaxEntropy-module.html#e,Variable Bio.NaiveBayes.e=Bio.NaiveBayes-module.html#e,Variable Bio.Statistics.lowess.e=Bio.Statistics.lowess-module.html#e,Variable Bio.distance.e=Bio.distance-module.html#e,Variable Bio.kNN.e=Bio.kNN-module.html#e"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-2', 'e', 'link-2');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">popen2</tt><tt class="py-op">.</tt><tt class="py-name">popen3</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">commandline</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">r_out</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-3', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">e_out</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-4', 'e', 'link-2');">e</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-5', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">w</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-6', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-7', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt id="link-8" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-8', 'e', 'link-2');">e</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-9', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-comment"># No way to get the error code; setting it to a dummy variable</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">error_code</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">child</tt> <tt class="py-op">=</tt> <tt class="py-name">popen2</tt><tt class="py-op">.</tt><tt class="py-name">Popen3</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">commandline</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-comment"># get information and close the files, so if we call this function</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># repeatedly we won't end up with too many open files</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment"># here are the file descriptors</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt class="py-name">fromchild</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt class="py-name">tochild</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-10', 'e', 'link-2');">e</a></tt> <tt class="py-op">=</tt> <tt class="py-name">child</tt><tt class="py-op">.</tt><tt class="py-name">childerr</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-name">r_out</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-11', 'read', 'link-3');">read</a></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">e_out</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-12', 'e', 'link-2');">e</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-13', 'read', 'link-3');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">w</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-14', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-15', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt id="link-16" class="py-name"><a title="Bio.Affy.CelFile.e
Bio.LogisticRegression.e
Bio.MarkovModel.e
Bio.MaxEntropy.e
Bio.NaiveBayes.e
Bio.Statistics.lowess.e
Bio.distance.e
Bio.kNN.e" class="py-name" href="#" onclick="return doclink('link-16', 'e', 'link-2');">e</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-17', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-comment"># capture error code</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">error_code</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">WEXITSTATUS</tt><tt class="py-op">(</tt><tt class="py-name">child</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.WWW.RequestLimiter.wait()=Bio.WWW.RequestLimiter-class.html#wait"><a title="Bio.WWW.RequestLimiter.wait" class="py-name" href="#" onclick="return doclink('link-18', 'wait', 'link-18');">wait</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-19" class="py-name" targets="Class Bio.Application.ApplicationResult=Bio.Application.ApplicationResult-class.html"><a title="Bio.Application.ApplicationResult" class="py-name" href="#" onclick="return doclink('link-19', 'ApplicationResult', 'link-19');">ApplicationResult</a></tt><tt class="py-op">(</tt><tt class="py-name">commandline</tt><tt class="py-op">,</tt> <tt class="py-name">error_code</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt id="link-20" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-20', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Class Bio.File.UndoHandle=Bio.File.UndoHandle-class.html"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-21', 'UndoHandle', 'link-21');">UndoHandle</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">r_out</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt id="link-22" class="py-name"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-22', 'File', 'link-1');">File</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.File.UndoHandle" class="py-name" href="#" onclick="return doclink('link-23', 'UndoHandle', 'link-21');">UndoHandle</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">.</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">e_out</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="ApplicationResult"></a><div id="ApplicationResult-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="ApplicationResult-toggle" onclick="return toggle('ApplicationResult');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Application.ApplicationResult-class.html">ApplicationResult</a><tt class="py-op">:</tt> </tt>
</div><div id="ApplicationResult-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ApplicationResult-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-docstring">"""Make results of a program available through a standard interface.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> This tries to pick up output information available from the program</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> and make it available programmatically.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ApplicationResult.__init__"></a><div id="ApplicationResult.__init__-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="ApplicationResult.__init__-toggle" onclick="return toggle('ApplicationResult.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.ApplicationResult-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">application_cl</tt><tt class="py-op">,</tt> <tt class="py-param">return_code</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ApplicationResult.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ApplicationResult.__init__-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-docstring">"""Intialize with the commandline from the program.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cl</tt> <tt class="py-op">=</tt> <tt class="py-name">application_cl</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-comment"># provide the return code of the application</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">return_code</tt> <tt class="py-op">=</tt> <tt class="py-name">return_code</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-comment"># get the application dependent results we can provide</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># right now the only results we handle are output files</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_results</tt> <tt class="py-op">=</tt> <tt class="py-op">{</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 id="link-24" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.parameter()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#parameter"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-24', 'parameter', 'link-24');">parameter</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cl</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.parameters()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#parameters,Variable Bio.expressions.blast.wublast.parameters=Bio.expressions.blast.wublast-module.html#parameters"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-25', 'parameters', 'link-25');">parameters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"file"</tt> <tt class="py-keyword">in</tt> <tt id="link-26" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-26', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">param_types</tt> <tt class="py-keyword">and</tt> \ </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-string">"output"</tt> <tt class="py-keyword">in</tt> <tt id="link-27" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-27', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">param_types</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-28" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-28', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">is_set</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_results</tt><tt class="py-op">[</tt><tt id="link-29" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-29', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method Bio.Compass._Consumer.names()=Bio.Compass._Consumer-class.html#names"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-30', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-31', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-32', 'value', 'link-32');">value</a></tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="ApplicationResult.get_result"></a><div id="ApplicationResult.get_result-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="ApplicationResult.get_result-toggle" onclick="return toggle('ApplicationResult.get_result');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.ApplicationResult-class.html#get_result">get_result</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">output_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ApplicationResult.get_result-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ApplicationResult.get_result-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve result information for the given output.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_results</tt><tt class="py-op">[</tt><tt class="py-name">output_name</tt><tt class="py-op">]</tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="ApplicationResult.available_results"></a><div id="ApplicationResult.available_results-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="ApplicationResult.available_results-toggle" onclick="return toggle('ApplicationResult.available_results');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.ApplicationResult-class.html#available_results">available_results</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ApplicationResult.available_results-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ApplicationResult.available_results-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve a list of all available results.</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">result_names</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_results</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-33', 'keys', 'link-33');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-name">result_names</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-34', 'sort', 'link-34');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result_names</tt> </tt>
</div></div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> </tt>
<a name="AbstractCommandline"></a><div id="AbstractCommandline-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="AbstractCommandline-toggle" onclick="return toggle('AbstractCommandline');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Application.AbstractCommandline-class.html">AbstractCommandline</a><tt class="py-op">:</tt> </tt>
</div><div id="AbstractCommandline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AbstractCommandline-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-docstring">"""Generic interface for running applications from biopython.</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> This class shouldn't be called directly; it should be subclassed to</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> provide an implementation for a specific application.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="AbstractCommandline.__init__"></a><div id="AbstractCommandline.__init__-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="AbstractCommandline.__init__-toggle" onclick="return toggle('AbstractCommandline.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.AbstractCommandline-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractCommandline.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractCommandline.__init__-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program_name</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-35', 'parameters', 'link-25');">parameters</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="AbstractCommandline.__str__"></a><div id="AbstractCommandline.__str__-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="AbstractCommandline.__str__-toggle" onclick="return toggle('AbstractCommandline.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.AbstractCommandline-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractCommandline.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractCommandline.__str__-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-docstring">"""Make the commandline with the currently set options.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">commandline</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">program_name</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-36" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-36', 'parameter', 'link-24');">parameter</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-37', 'parameters', 'link-25');">parameters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-38" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-38', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">is_required</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt><tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-39', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">is_set</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Parameter %s is not set."</tt> <tt class="py-op">%</tt> <tt id="link-40" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-40', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-41', 'names', 'link-30');">names</a></tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-42" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-42', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">is_set</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">commandline</tt> <tt class="py-op">+=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-43', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">commandline</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="AbstractCommandline.set_parameter"></a><div id="AbstractCommandline.set_parameter-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="AbstractCommandline.set_parameter-toggle" onclick="return toggle('AbstractCommandline.set_parameter');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.AbstractCommandline-class.html#set_parameter">set_parameter</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractCommandline.set_parameter-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractCommandline.set_parameter-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-docstring">"""Set a commandline option for a program.</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">set_option</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-44" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-44', 'parameter', 'link-24');">parameter</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameters
Bio.expressions.blast.wublast.parameters" class="py-name" href="#" onclick="return doclink('link-45', 'parameters', 'link-25');">parameters</a></tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-46" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-46', 'name', 'link-46');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-47" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-47', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-48', 'names', 'link-30');">names</a></tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-49" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-49', 'value', 'link-32');">value</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name" targets="Method Bio.Application.AbstractCommandline._check_value()=Bio.Application.AbstractCommandline-class.html#_check_value"><a title="Bio.Application.AbstractCommandline._check_value" class="py-name" href="#" onclick="return doclink('link-50', '_check_value', 'link-50');">_check_value</a></tt><tt class="py-op">(</tt><tt id="link-51" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-51', 'value', 'link-32');">value</a></tt><tt class="py-op">,</tt> <tt id="link-52" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-52', 'name', 'link-46');">name</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-53', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">checker_function</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-54', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-55', 'value', 'link-32');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-56', 'value', 'link-32');">value</a></tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-57" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.parameter" class="py-name" href="#" onclick="return doclink('link-57', 'parameter', 'link-24');">parameter</a></tt><tt class="py-op">.</tt><tt class="py-name">is_set</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">set_option</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">set_option</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Option name %s was not found."</tt> <tt class="py-op">%</tt> <tt id="link-58" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-58', 'name', 'link-46');">name</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="AbstractCommandline._check_value"></a><div id="AbstractCommandline._check_value-def"><a name="L127"></a><tt class="py-lineno">127</tt> <a class="py-toggle" href="#" id="AbstractCommandline._check_value-toggle" onclick="return toggle('AbstractCommandline._check_value');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application.AbstractCommandline-class.html#_check_value">_check_value</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">check_function</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AbstractCommandline._check_value-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AbstractCommandline._check_value-expanded"><a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-docstring">"""Check whether the given value is valid.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> This uses the passed function 'check_function', which can either</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> return a [0, 1] (bad, good) value or raise an error. Either way</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> this function will raise an error if the value is not valid, or</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> finish silently otherwise.</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">check_function</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">is_good</tt> <tt class="py-op">=</tt> <tt class="py-name">check_function</tt><tt class="py-op">(</tt><tt id="link-59" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-59', 'value', 'link-32');">value</a></tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">is_good</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> <tt class="py-comment"># if we are dealing with a good/bad check</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt><tt class="py-op">(</tt><tt class="py-name">is_good</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-string">"Invalid parameter value %r for parameter %s"</tt> <tt class="py-op">%</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-60', 'value', 'link-32');">value</a></tt><tt class="py-op">,</tt> <tt id="link-61" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-61', 'name', 'link-46');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt>
<a name="_AbstractParameter"></a><div id="_AbstractParameter-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="_AbstractParameter-toggle" onclick="return toggle('_AbstractParameter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Application._AbstractParameter-class.html">_AbstractParameter</a><tt class="py-op">:</tt> </tt>
</div><div id="_AbstractParameter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_AbstractParameter-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-docstring">"""A class to hold information about a parameter for a commandline.</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> Do not use this directly, instead use one of the subclasses.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> o names -- a list of string names by which the parameter can be</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> referenced (ie. ["-a", "--append", "append"]). The first name in</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> the list is considered to be the one that goes on the commandline,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> for those parameters that print the option. The last name in the list</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> is assumed to be a "human readable" name describing the option in one</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> word.</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> o param_type -- a list of string describing the type of parameter, </tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> which can help let programs know how to use it. Example descriptions</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> include 'input', 'output', 'file'</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> o checker_function -- a reference to a function that will determine</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"> if a given value is valid for this parameter. This function can either</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> raise an error when given a bad value, or return a [0, 1] decision on</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> whether the value is correct.</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> o description -- a description of the option.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> o is_required -- a flag to indicate if the parameter must be set for</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> the program to be run.</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> o is_set -- if the parameter has been set</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> o value -- the value of a parameter</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_AbstractParameter.__init__"></a><div id="_AbstractParameter.__init__-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_AbstractParameter.__init__-toggle" onclick="return toggle('_AbstractParameter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application._AbstractParameter-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">types</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-param">checker_function</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-param">is_required</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">description</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_AbstractParameter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_AbstractParameter.__init__-expanded"><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-62', 'names', 'link-30');">names</a></tt> <tt class="py-op">=</tt> <tt id="link-63" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-63', 'names', 'link-30');">names</a></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">param_types</tt> <tt class="py-op">=</tt> <tt class="py-name">types</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">checker_function</tt> <tt class="py-op">=</tt> <tt class="py-name">checker_function</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Enzyme._RecordConsumer.description()=Bio.Enzyme._RecordConsumer-class.html#description,Method Bio.Prosite._RecordConsumer.description()=Bio.Prosite._RecordConsumer-class.html#description,Function Bio.Std.description()=Bio.Std-module.html#description,Method Bio.SwissProt.SProt._RecordConsumer.description()=Bio.SwissProt.SProt._RecordConsumer-class.html#description,Method Bio.SwissProt.SProt._SequenceConsumer.description()=Bio.SwissProt.SProt._SequenceConsumer-class.html#description,Variable Martel.setup.run_local_tests.description=Martel.setup.run_local_tests-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-64', 'description', 'link-64');">description</a></tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Enzyme._RecordConsumer.description
Bio.Prosite._RecordConsumer.description
Bio.Std.description
Bio.SwissProt.SProt._RecordConsumer.description
Bio.SwissProt.SProt._SequenceConsumer.description
Martel.setup.run_local_tests.description" class="py-name" href="#" onclick="return doclink('link-65', 'description', 'link-64');">description</a></tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_required</tt> <tt class="py-op">=</tt> <tt class="py-name">is_required</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">is_set</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-66', 'value', 'link-32');">value</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div></div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="_Option"></a><div id="_Option-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="_Option-toggle" onclick="return toggle('_Option');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Application._Option-class.html">_Option</a><tt class="py-op">(</tt><tt class="py-base-class">_AbstractParameter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Option-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Option-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent an option that can be set for a program.</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> This holds UNIXish options like --append=yes and -a yes</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Option.__str__"></a><div id="_Option.__str__-def"><a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="_Option.__str__-toggle" onclick="return toggle('_Option.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application._Option-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Option.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Option.__str__-expanded"><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the value of this option for the commandline.</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-comment"># first deal with long options</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-67', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-68', 'find', 'link-68');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"--"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-69', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-70', 'value', 'link-32');">value</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"=%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-71', 'value', 'link-32');">value</a></tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">" "</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># now short options</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-72', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-73', 'find', 'link-68');">find</a></tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-74', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-75', 'value', 'link-32');">value</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">output</tt> <tt class="py-op">+=</tt> <tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-76', 'value', 'link-32');">value</a></tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Unrecognized option type: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-77', 'names', 'link-30');">names</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">output</tt> </tt>
</div></div><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
<a name="_Argument"></a><div id="_Argument-def"><a name="L211"></a><tt class="py-lineno">211</tt> <a class="py-toggle" href="#" id="_Argument-toggle" onclick="return toggle('_Argument');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Application._Argument-class.html">_Argument</a><tt class="py-op">(</tt><tt class="py-base-class">_AbstractParameter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Argument-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Argument-expanded"><a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent an argument on a commandline.</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_Argument.__str__"></a><div id="_Argument.__str__-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="_Argument.__str__-toggle" onclick="return toggle('_Argument.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Application._Argument-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Argument.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Argument.__str__-expanded"><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-78', 'value', 'link-32');">value</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s "</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-79', 'value', 'link-32');">value</a></tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">" "</tt> </tt>
</div></div><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt><script type="text/javascript">
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