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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Wise-module.html">Package&nbsp;Wise</a> ::
        Module&nbsp;psw
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<h1 class="epydoc">Source Code for <a href="Bio.Wise.psw-module.html">Module Bio.Wise.psw</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</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 class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise contains modules for running and processing the output of</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># some of the models in the Wise2 package by Ewan Birney available from:</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># http://www.ebi.ac.uk/Wise2/</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># </tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise.psw is for protein Smith-Waterman alignments</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Bio.Wise.dnal is for Smith-Waterman DNA alignments</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-docstring">"$Revision: 1.5 $"</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">exceptions</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </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">sys</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</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="Package Bio.Wise=Bio.Wise-module.html"><a title="Bio.Wise" class="py-name" href="#" onclick="return doclink('link-1', 'Wise', 'link-1');">Wise</a></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 id="link-2" class="py-name" targets="Variable Bio.Wise.psw._CMDLINE_PSW=Bio.Wise.psw-module.html#_CMDLINE_PSW"><a title="Bio.Wise.psw._CMDLINE_PSW" class="py-name" href="#" onclick="return doclink('link-2', '_CMDLINE_PSW', 'link-2');">_CMDLINE_PSW</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"psw"</tt><tt class="py-op">,</tt> <tt class="py-string">"-l"</tt><tt class="py-op">,</tt> <tt class="py-string">"-F"</tt><tt class="py-op">]</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Bio.Wise.psw._OPTION_GAP_START=Bio.Wise.psw-module.html#_OPTION_GAP_START"><a title="Bio.Wise.psw._OPTION_GAP_START" class="py-name" href="#" onclick="return doclink('link-3', '_OPTION_GAP_START', 'link-3');">_OPTION_GAP_START</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"-g"</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable Bio.Wise.psw._OPTION_GAP_EXTENSION=Bio.Wise.psw-module.html#_OPTION_GAP_EXTENSION"><a title="Bio.Wise.psw._OPTION_GAP_EXTENSION" class="py-name" href="#" onclick="return doclink('link-4', '_OPTION_GAP_EXTENSION', 'link-4');">_OPTION_GAP_EXTENSION</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"-e"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Bio.Wise.psw._OPTION_SCORES=Bio.Wise.psw-module.html#_OPTION_SCORES"><a title="Bio.Wise.psw._OPTION_SCORES" class="py-name" href="#" onclick="return doclink('link-5', '_OPTION_SCORES', 'link-5');">_OPTION_SCORES</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"-m"</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"> </tt>
<a name="AlignmentColumnFullException"></a><div id="AlignmentColumnFullException-def"><a name="L28"></a><tt class="py-lineno"> 28</tt> <a class="py-toggle" href="#" id="AlignmentColumnFullException-toggle" onclick="return toggle('AlignmentColumnFullException');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumnFullException-class.html">AlignmentColumnFullException</a><tt class="py-op">(</tt><tt class="py-base-class">exceptions</tt><tt class="py-op">.</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentColumnFullException-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignmentColumnFullException-expanded"><a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="Alignment"></a><div id="Alignment-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="Alignment-toggle" onclick="return toggle('Alignment');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Wise.psw.Alignment-class.html">Alignment</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Alignment-expanded"><a name="Alignment.append"></a><div id="Alignment.append-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Alignment.append-toggle" onclick="return toggle('Alignment.append');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.Alignment-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">column_unit</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.append-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.append-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">            <tt class="py-name">self</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 id="link-6" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-6', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">column_unit</tt><tt class="py-op">)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">        <tt class="py-keyword">except</tt> <tt id="link-7" class="py-name" targets="Class Bio.Wise.psw.AlignmentColumnFullException=Bio.Wise.psw.AlignmentColumnFullException-class.html"><a title="Bio.Wise.psw.AlignmentColumnFullException" class="py-name" href="#" onclick="return doclink('link-7', 'AlignmentColumnFullException', 'link-7');">AlignmentColumnFullException</a></tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">            <tt id="link-8" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-8', 'list', 'link-8');">list</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-9', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-10" class="py-name" targets="Class Bio.Wise.psw.AlignmentColumn=Bio.Wise.psw.AlignmentColumn-class.html"><a title="Bio.Wise.psw.AlignmentColumn" class="py-name" href="#" onclick="return doclink('link-10', 'AlignmentColumn', 'link-10');">AlignmentColumn</a></tt><tt class="py-op">(</tt><tt class="py-name">column_unit</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">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">            <tt id="link-11" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-11', 'list', 'link-8');">list</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-12', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Bio.Wise.psw.AlignmentColumn" class="py-name" href="#" onclick="return doclink('link-13', 'AlignmentColumn', 'link-10');">AlignmentColumn</a></tt><tt class="py-op">(</tt><tt class="py-name">column_unit</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line"> </tt>
<a name="AlignmentColumn"></a><div id="AlignmentColumn-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="AlignmentColumn-toggle" onclick="return toggle('AlignmentColumn');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumn-class.html">AlignmentColumn</a><tt class="py-op">(</tt><tt class="py-base-class">list</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentColumn-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignmentColumn-expanded"><a name="AlignmentColumn._set_kind"></a><div id="AlignmentColumn._set_kind-def"><a name="L41"></a><tt class="py-lineno"> 41</tt> <a class="py-toggle" href="#" id="AlignmentColumn._set_kind-toggle" onclick="return toggle('AlignmentColumn._set_kind');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumn-class.html#_set_kind">_set_kind</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">column_unit</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentColumn._set_kind-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentColumn._set_kind-expanded"><a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> <tt class="py-op">==</tt> <tt class="py-string">"SEQUENCE"</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">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> <tt class="py-op">=</tt> <tt class="py-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="AlignmentColumn.__init__"></a><div id="AlignmentColumn.__init__-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="AlignmentColumn.__init__-toggle" onclick="return toggle('AlignmentColumn.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumn-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">column_unit</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentColumn.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentColumn.__init__-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">unit</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> <tt class="py-op">=</tt> <tt class="py-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">        <tt id="link-14" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-14', 'list', 'link-8');">list</a></tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method 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Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
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Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
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Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
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Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
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Martel.Generate.GeneratorState.__init__
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Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
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Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-15', '__init__', 'link-15');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">column</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="AlignmentColumn.__repr__"></a><div id="AlignmentColumn.__repr__-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="AlignmentColumn.__repr__-toggle" onclick="return toggle('AlignmentColumn.__repr__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumn-class.html#__repr__">__repr__</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="AlignmentColumn.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentColumn.__repr__-expanded"><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">"%s(%s, %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"> </tt>
<a name="AlignmentColumn.append"></a><div id="AlignmentColumn.append-def"><a name="L53"></a><tt class="py-lineno"> 53</tt> <a class="py-toggle" href="#" id="AlignmentColumn.append-toggle" onclick="return toggle('AlignmentColumn.append');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.AlignmentColumn-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">column_unit</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentColumn.append-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentColumn.append-expanded"><a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</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="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt id="link-16" class="py-name"><a title="Bio.Wise.psw.AlignmentColumnFullException" class="py-name" href="#" onclick="return doclink('link-16', 'AlignmentColumnFullException', 'link-7');">AlignmentColumnFullException</a></tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">unit</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Wise.psw.AlignmentColumn._set_kind()=Bio.Wise.psw.AlignmentColumn-class.html#_set_kind"><a title="Bio.Wise.psw.AlignmentColumn._set_kind" class="py-name" href="#" onclick="return doclink('link-17', '_set_kind', 'link-17');">_set_kind</a></tt><tt class="py-op">(</tt><tt class="py-name">column_unit</tt><tt class="py-op">)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-name">self</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-name">column_unit</tt><tt class="py-op">.</tt><tt class="py-name">column</tt> </tt>
</div></div><a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">         </tt>
<a name="ColumnUnit"></a><div id="ColumnUnit-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="ColumnUnit-toggle" onclick="return toggle('ColumnUnit');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Wise.psw.ColumnUnit-class.html">ColumnUnit</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ColumnUnit-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ColumnUnit-expanded"><a name="ColumnUnit.__init__"></a><div id="ColumnUnit.__init__-def"><a name="L63"></a><tt class="py-lineno"> 63</tt> <a class="py-toggle" href="#" id="ColumnUnit.__init__-toggle" onclick="return toggle('ColumnUnit.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.ColumnUnit-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">unit</tt><tt class="py-op">,</tt> <tt class="py-param">column</tt><tt class="py-op">,</tt> <tt class="py-param">kind</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ColumnUnit.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ColumnUnit.__init__-expanded"><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unit</tt> <tt class="py-op">=</tt> <tt class="py-name">unit</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">column</tt> <tt class="py-op">=</tt> <tt class="py-name">column</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt> <tt class="py-op">=</tt> <tt class="py-name">kind</tt> </tt>
</div><a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"> </tt>
<a name="ColumnUnit.__str__"></a><div id="ColumnUnit.__str__-def"><a name="L68"></a><tt class="py-lineno"> 68</tt> <a class="py-toggle" href="#" id="ColumnUnit.__str__-toggle" onclick="return toggle('ColumnUnit.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw.ColumnUnit-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="ColumnUnit.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ColumnUnit.__str__-expanded"><a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-string">"ColumnUnit(unit=%s, column=%s, %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">unit</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">column</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">kind</tt><tt class="py-op">)</tt> </tt>
</div><a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"> </tt>
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Bio.SeqFeature.ExactPosition.__str__()=Bio.SeqFeature.ExactPosition-class.html#__str__,Method Bio.SeqFeature.FeatureLocation.__str__()=Bio.SeqFeature.FeatureLocation-class.html#__str__,Method Bio.SeqFeature.OneOfPosition.__str__()=Bio.SeqFeature.OneOfPosition-class.html#__str__,Method Bio.SeqFeature.PositionGap.__str__()=Bio.SeqFeature.PositionGap-class.html#__str__,Method Bio.SeqFeature.Reference.__str__()=Bio.SeqFeature.Reference-class.html#__str__,Method Bio.SeqFeature.SeqFeature.__str__()=Bio.SeqFeature.SeqFeature-class.html#__str__,Method Bio.SeqFeature.WithinPosition.__str__()=Bio.SeqFeature.WithinPosition-class.html#__str__,Method Bio.SeqRecord.SeqRecord.__str__()=Bio.SeqRecord.SeqRecord-class.html#__str__,Method Bio.StdHandler.Feature.__str__()=Bio.StdHandler.Feature-class.html#__str__,Method Bio.SubsMat.BadMatrix.__str__()=Bio.SubsMat.BadMatrix-class.html#__str__,Method Bio.Translate.Translator.__str__()=Bio.Translate.Translator-class.html#__str__,Method Bio.Wise.dnal.Statistics.__str__()=Bio.Wise.dnal.Statistics-class.html#__str__,Method Bio.Wise.psw.ColumnUnit.__str__()=Bio.Wise.psw.ColumnUnit-class.html#__str__,Method Bio.config.Registry.Registry.__str__()=Bio.config.Registry.Registry-class.html#__str__,Method BioSQL.BioSeq.DBSeq.__str__()=BioSQL.BioSeq.DBSeq-class.html#__str__,Method Martel.Expression.Alt.__str__()=Martel.Expression.Alt-class.html#__str__,Method Martel.Expression.Any.__str__()=Martel.Expression.Any-class.html#__str__,Method Martel.Expression.AnyEol.__str__()=Martel.Expression.AnyEol-class.html#__str__,Method Martel.Expression.Assert.__str__()=Martel.Expression.Assert-class.html#__str__,Method Martel.Expression.AtBeginning.__str__()=Martel.Expression.AtBeginning-class.html#__str__,Method Martel.Expression.AtEnd.__str__()=Martel.Expression.AtEnd-class.html#__str__,Method Martel.Expression.Debug.__str__()=Martel.Expression.Debug-class.html#__str__,Method Martel.Expression.Dot.__str__()=Martel.Expression.Dot-class.html#__str__,Method Martel.Expression.Expression.__str__()=Martel.Expression.Expression-class.html#__str__,Method Martel.Expression.Group.__str__()=Martel.Expression.Group-class.html#__str__,Method Martel.Expression.GroupRef.__str__()=Martel.Expression.GroupRef-class.html#__str__,Method Martel.Expression.Literal.__str__()=Martel.Expression.Literal-class.html#__str__,Method Martel.Expression.MaxRepeat.__str__()=Martel.Expression.MaxRepeat-class.html#__str__,Method Martel.Expression.NullOp.__str__()=Martel.Expression.NullOp-class.html#__str__,Method Martel.Expression.PassThrough.__str__()=Martel.Expression.PassThrough-class.html#__str__,Method Martel.Expression.Seq.__str__()=Martel.Expression.Seq-class.html#__str__,Method Martel.Expression.Str.__str__()=Martel.Expression.Str-class.html#__str__,Method Martel.Parser.HeaderFooterParser.__str__()=Martel.Parser.HeaderFooterParser-class.html#__str__,Method Martel.Parser.MartelAttributeList.__str__()=Martel.Parser.MartelAttributeList-class.html#__str__,Method Martel.Parser.Parser.__str__()=Martel.Parser.Parser-class.html#__str__,Method Martel.Parser.RecordParser.__str__()=Martel.Parser.RecordParser-class.html#__str__"><a title="Bio.Align.AlignInfo.PSSM.__str__
Bio.Align.Generic.Alignment.__str__
Bio.AlignAce.Motif.Motif.__str__
Bio.Application.AbstractCommandline.__str__
Bio.Application._Argument.__str__
Bio.Application._Option.__str__
Bio.Blast.Record.Alignment.__str__
Bio.Blast.Record.Description.__str__
Bio.CDD.Record.Record.__str__
Bio.Clustalw.ClustalAlignment.__str__
Bio.Clustalw.MultipleAlignCL.__str__
Bio.Crystal.Chain.__str__
Bio.Crystal.Crystal.__str__
Bio.Crystal.Hetero.__str__
Bio.DBXRef.DBXRef.__str__
Bio.Data.CodonTable.CodonTable.__str__
Bio.Decode.Function.__str__
Bio.Decode.ValueToken.__str__
Bio.ECell.Record.Record.__str__
Bio.EUtils.Datatypes.And.__str__
Bio.EUtils.Datatypes.Date.__str__
Bio.EUtils.Datatypes.EUtilsSearchError.__str__
Bio.EUtils.Datatypes.Not.__str__
Bio.EUtils.Datatypes.Or.__str__
Bio.EUtils.Datatypes.Problem.__str__
Bio.EUtils.Datatypes.Range.__str__
Bio.EUtils.Datatypes.Summary.__str__
Bio.EUtils.Datatypes.Term.__str__
Bio.EUtils.MultiDict._BaseMultiDict.__str__
Bio.EUtils.POM.AttributeList.__str__
Bio.EUtils.POM.Comment.__str__
Bio.EUtils.POM.ElementNode.__str__
Bio.EUtils.POM.Fragments.__str__
Bio.EUtils.POM.IndentedText.__str__
Bio.EUtils.POM.POMDocument.__str__
Bio.EUtils.POM.Text.__str__
Bio.EUtils.sourcegen.ClassHolder.__str__
Bio.EUtils.sourcegen.FunctionHolder.__str__
Bio.EUtils.sourcegen.MethodHolder.__str__
Bio.EUtils.sourcegen.SourceFile.__str__
Bio.Emboss.Primer.PrimerSearchInputRecord.__str__
Bio.Enzyme.DataRecord.__str__
Bio.Enzyme.EnzymeRecord.__str__
Bio.Fasta.FastaAlign.FastaAlignment.__str__
Bio.Fasta.Record.__str__
Bio.GA.Organism.Organism.__str__
Bio.GFF.Feature.__str__
Bio.GFF.GenericTools.VerboseDict.__str__
Bio.GFF.GenericTools.VerboseList.__str__
Bio.GFF.easy.Location.__str__
Bio.GenBank.LocationParser.Integer.__str__
Bio.GenBank.LocationParser.Symbol.__str__
Bio.GenBank.Record.Feature.__str__
Bio.GenBank.Record.Record.__str__
Bio.GenBank.Record.Reference.__str__
Bio.Geo.Record.Record.__str__
Bio.IntelliGenetics.Record.Record.__str__
Bio.InterPro.Record.__str__
Bio.KEGG.Compound.Record.__str__
Bio.KEGG.Enzyme.Record.__str__
Bio.LocusLink.Record.__str__
Bio.LocusLink.web_parse.Record.__str__
Bio.LocusLink.web_parse.Token.__str__
Bio.LocusLink.web_parse.Url.__str__
Bio.MarkovModel.MarkovModel.__str__
Bio.MetaTool.Record.Metabolite.__str__
Bio.MetaTool.Record.MetaboliteRole.__str__
Bio.MetaTool.Record.PathwayTransform.__str__
Bio.MetaTool.Record.Record.__str__
Bio.Mindy.Location.Location.__str__
Bio.NBRF.Record.Record.__str__
Bio.Ndb.Record.__str__
Bio.NetCatch.ExtractUrls.__str__
Bio.NetCatch.NetCatch.__str__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__str__
Bio.Nexus.Trees.Tree.__str__
Bio.Pathway.Interaction.__str__
Bio.Pathway.Network.__str__
Bio.Pathway.Reaction.__str__
Bio.Pathway.Rep.Graph.Graph.__str__
Bio.Pathway.Rep.HashSet.HashSet.__str__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__str__
Bio.Pathway.System.__str__
Bio.PopGen.FDist.Record.__str__
Bio.PopGen.GenePop.Record.__str__
Bio.Prosite.Pattern.Prosite.__str__
Bio.Prosite.Pattern.PrositeMatch.__str__
Bio.Prosite.Pattern.PrositeTerm.__str__
Bio.Prosite.PatternHit.__str__
Bio.Restriction.Restriction.RestrictionBatch.__str__
Bio.Restriction.Restriction.RestrictionType.__str__
Bio.SCOP.Cla.Record.__str__
Bio.SCOP.Des.Record.__str__
Bio.SCOP.Dom.Record.__str__
Bio.SCOP.Domain.__str__
Bio.SCOP.Hie.Record.__str__
Bio.SCOP.Node.__str__
Bio.SCOP.Residues'.Residues.__str__
Bio.Saf.Record.Record.__str__
Bio.Seq.MutableSeq.__str__
Bio.Seq.Seq.__str__
Bio.SeqFeature.AfterPosition.__str__
Bio.SeqFeature.BeforePosition.__str__
Bio.SeqFeature.BetweenPosition.__str__
Bio.SeqFeature.ExactPosition.__str__
Bio.SeqFeature.FeatureLocation.__str__
Bio.SeqFeature.OneOfPosition.__str__
Bio.SeqFeature.PositionGap.__str__
Bio.SeqFeature.Reference.__str__
Bio.SeqFeature.SeqFeature.__str__
Bio.SeqFeature.WithinPosition.__str__
Bio.SeqRecord.SeqRecord.__str__
Bio.StdHandler.Feature.__str__
Bio.SubsMat.BadMatrix.__str__
Bio.Translate.Translator.__str__
Bio.Wise.dnal.Statistics.__str__
Bio.Wise.psw.ColumnUnit.__str__
Bio.config.Registry.Registry.__str__
BioSQL.BioSeq.DBSeq.__str__
Martel.Expression.Alt.__str__
Martel.Expression.Any.__str__
Martel.Expression.AnyEol.__str__
Martel.Expression.Assert.__str__
Martel.Expression.AtBeginning.__str__
Martel.Expression.AtEnd.__str__
Martel.Expression.Debug.__str__
Martel.Expression.Dot.__str__
Martel.Expression.Expression.__str__
Martel.Expression.Group.__str__
Martel.Expression.GroupRef.__str__
Martel.Expression.Literal.__str__
Martel.Expression.MaxRepeat.__str__
Martel.Expression.NullOp.__str__
Martel.Expression.PassThrough.__str__
Martel.Expression.Seq.__str__
Martel.Expression.Str.__str__
Martel.Parser.HeaderFooterParser.__str__
Martel.Parser.MartelAttributeList.__str__
Martel.Parser.Parser.__str__
Martel.Parser.RecordParser.__str__" class="py-name" href="#" onclick="return doclink('link-19', '__str__', 'link-19');">__str__</a></tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt id="link-20" class="py-name" targets="Variable Bio.Wise.psw._re_unit=Bio.Wise.psw-module.html#_re_unit"><a title="Bio.Wise.psw._re_unit" class="py-name" href="#" onclick="return doclink('link-20', '_re_unit', 'link-20');">_re_unit</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-21', 'compile', 'link-21');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$"</tt><tt class="py-op">)</tt> </tt>
<a name="parse_line"></a><div id="parse_line-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="parse_line-toggle" onclick="return toggle('parse_line');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw-module.html#parse_line">parse_line</a><tt class="py-op">(</tt><tt class="py-param">line</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_line-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_line-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; print parse_line("Column 0:")</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-docstring">    None</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; parse_line("Unit  0- [  -1-   0] [SEQUENCE]")</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-docstring">    ColumnUnit(unit=0, column=0, SEQUENCE)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; parse_line("Unit  1- [  85-  86] [SEQUENCE]")</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">    ColumnUnit(unit=1, column=86, SEQUENCE)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt id="link-22" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-22', 'match', 'link-22');">match</a></tt> <tt class="py-op">=</tt> <tt id="link-23" class="py-name"><a title="Bio.Wise.psw._re_unit" class="py-name" href="#" onclick="return doclink('link-23', '_re_unit', 'link-20');">_re_unit</a></tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-24', 'match', 'link-22');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line"> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-25" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-25', 'match', 'link-22');">match</a></tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line"> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-26" class="py-name" targets="Class Bio.Wise.psw.ColumnUnit=Bio.Wise.psw.ColumnUnit-class.html"><a title="Bio.Wise.psw.ColumnUnit" class="py-name" href="#" onclick="return doclink('link-26', 'ColumnUnit', 'link-26');">ColumnUnit</a></tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-27', 'match', 'link-22');">match</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-28', 'group', 'link-28');">group</a></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 class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-29', 'match', 'link-22');">match</a></tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-30', 'group', 'link-28');">group</a></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-op">,</tt> <tt id="link-31" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-31', 'match', 'link-22');">match</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-32', 'group', 'link-28');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">     </tt>
<a name="parse"></a><div id="parse-def"><a name="L90"></a><tt class="py-lineno"> 90</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">iterable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-docstring">    format</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">    Column 0:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">    Unit  0- [  -1-   0] [SEQUENCE]</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-docstring">    Unit  1- [  85-  86] [SEQUENCE]</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-docstring">    means that seq1[0] == seq2[86] (0-based)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt id="link-33" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-33', 'alignment', 'link-33');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-34', 'Alignment', 'link-34');">Alignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">iterable</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">environ</tt><tt class="py-op">[</tt><tt class="py-string">"WISE_PY_DEBUG"</tt><tt class="py-op">]</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">print</tt> <tt class="py-name">line</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">except</tt> <tt class="py-name">KeyError</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">pass</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">             </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-name">column_unit</tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name" targets="Function Bio.Wise.psw.parse_line()=Bio.Wise.psw-module.html#parse_line"><a title="Bio.Wise.psw.parse_line" class="py-name" href="#" onclick="return doclink('link-35', 'parse_line', 'link-35');">parse_line</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">column_unit</tt><tt class="py-op">:</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt id="link-36" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-36', 'alignment', 'link-33');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-37', 'append', 'link-6');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">column_unit</tt><tt class="py-op">)</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-38" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-38', 'alignment', 'link-33');">alignment</a></tt> </tt>
</div><a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"> </tt>
<a name="align"></a><div id="align-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="align-toggle" onclick="return toggle('align');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw-module.html#align">align</a><tt class="py-op">(</tt><tt class="py-param">pair</tt><tt class="py-op">,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">          <tt class="py-param">scores</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">          <tt class="py-param">gap_start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">          <tt class="py-param">gap_extension</tt><tt class="py-op">=</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-op">*</tt><tt class="py-param">args</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="align-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="align-expanded"><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">     </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">    <tt class="py-name">cmdline</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Bio.Wise.psw._CMDLINE_PSW" class="py-name" href="#" onclick="return doclink('link-39', '_CMDLINE_PSW', 'link-2');">_CMDLINE_PSW</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-40" class="py-name" targets="Method Bio.Compass._Consumer.scores()=Bio.Compass._Consumer-class.html#scores"><a title="Bio.Compass._Consumer.scores" class="py-name" href="#" onclick="return doclink('link-40', 'scores', 'link-40');">scores</a></tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">        <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-41', 'extend', 'link-41');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Bio.Wise.psw._OPTION_SCORES" class="py-name" href="#" onclick="return doclink('link-42', '_OPTION_SCORES', 'link-5');">_OPTION_SCORES</a></tt><tt class="py-op">,</tt> <tt id="link-43" class="py-name"><a title="Bio.Compass._Consumer.scores" class="py-name" href="#" onclick="return doclink('link-43', 'scores', 'link-40');">scores</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </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">gap_start</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">        <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-44', 'extend', 'link-41');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Bio.Wise.psw._OPTION_GAP_START" class="py-name" href="#" onclick="return doclink('link-45', '_OPTION_GAP_START', 'link-3');">_OPTION_GAP_START</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">gap_start</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">gap_extension</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-46', 'extend', 'link-41');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-47" class="py-name"><a title="Bio.Wise.psw._OPTION_GAP_EXTENSION" class="py-name" href="#" onclick="return doclink('link-47', '_OPTION_GAP_EXTENSION', 'link-4');">_OPTION_GAP_EXTENSION</a></tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">gap_extension</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">    <tt class="py-name">temp_file</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Wise" class="py-name" href="#" onclick="return doclink('link-48', 'Wise', 'link-1');">Wise</a></tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.align()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#align,Class Bio.FSSP.fssp_rec.align=Bio.FSSP.fssp_rec.align-class.html,Function Bio.Wise.align()=Bio.Wise-module.html#align,Function Bio.Wise.dnal.align()=Bio.Wise.dnal-module.html#align,Function Bio.Wise.psw.align()=Bio.Wise.psw-module.html#align,Variable Bio.pairwise2.align=Bio.pairwise2-module.html#align"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-49', 'align', 'link-49');">align</a></tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">,</tt> <tt class="py-name">pair</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt id="link-50" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-50', 'parse', 'link-50');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">temp_file</tt><tt class="py-op">)</tt> </tt>
</div><a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="main-toggle" onclick="return toggle('main');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw-module.html#main">main</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="main-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="main-expanded"><a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt id="link-51" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.align
Bio.FSSP.fssp_rec.align
Bio.Wise.align
Bio.Wise.dnal.align
Bio.Wise.psw.align
Bio.pairwise2.align" class="py-name" href="#" onclick="return doclink('link-51', 'align', 'link-49');">align</a></tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L134"></a><tt class="py-lineno">134</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise.psw-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-param">args</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="_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_test-expanded"><a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">    <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line"> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</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">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt id="link-52" class="py-name" targets="Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.EUtils.MultiDict._test()=Bio.EUtils.MultiDict-module.html#_test,Function Bio.GFF._test()=Bio.GFF-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.DocSQL._test
Bio.EUtils.MultiDict._test
Bio.GFF._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-52', '_test', 'link-52');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">    <tt id="link-53" class="py-name" targets="Function Bio.EUtils.dtd2py.main()=Bio.EUtils.dtd2py-module.html#main,Function Bio.Mindy.main()=Bio.Mindy-module.html#main,Function Bio.Wise.dnal.main()=Bio.Wise.dnal-module.html#main,Function Bio.Wise.main()=Bio.Wise-module.html#main,Function Bio.Wise.psw.main()=Bio.Wise.psw-module.html#main,Function Bio.biblio.main()=Bio.biblio-module.html#main,Function Bio.expressions.blast.wublast.main()=Bio.expressions.blast.wublast-module.html#main,Function Martel.test.run_tests.main()=Martel.test.run_tests-module.html#main"><a title="Bio.EUtils.dtd2py.main
Bio.Mindy.main
Bio.Wise.dnal.main
Bio.Wise.main
Bio.Wise.psw.main
Bio.biblio.main
Bio.expressions.blast.wublast.main
Martel.test.run_tests.main" class="py-name" href="#" onclick="return doclink('link-53', 'main', 'link-53');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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