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biopython-doc-1.47-2mdv2008.1.x86_64.rpm

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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
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<h1 class="epydoc">Source Code for <a href="Bio.Wise-module.html">Package Bio.Wise</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: 1.16 $"</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">os</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">sys</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">tempfile</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</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.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-1', 'SeqIO', 'link-1');">SeqIO</a></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>
<a name="_build_align_cmdline"></a><div id="_build_align_cmdline-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="_build_align_cmdline-toggle" onclick="return toggle('_build_align_cmdline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise-module.html#_build_align_cmdline">_build_align_cmdline</a><tt class="py-op">(</tt><tt class="py-param">cmdline</tt><tt class="py-op">,</tt> <tt class="py-param">pair</tt><tt class="py-op">,</tt> <tt class="py-param">output_filename</tt><tt class="py-op">,</tt> <tt class="py-param">kbyte</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">force_type</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">quiet</tt><tt class="py-op">=</tt><tt id="link-2" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-2', 'False', 'link-2');">False</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_build_align_cmdline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_build_align_cmdline-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; os.environ["WISE_KBYTE"]="300000"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; _build_align_cmdline(["dnal"], ("seq1.fna", "seq2.fna"), "/tmp/output", kbyte=100000)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-docstring">    'dnal -kbyte 100000 seq1.fna seq2.fna &gt; /tmp/output'</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; _build_align_cmdline(["psw"], ("seq1.faa", "seq2.faa"), "/tmp/output_aa")</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"><tt class="py-docstring">    'psw -kbyte 300000 seq1.faa seq2.faa &gt; /tmp/output_aa'</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-name">cmdline</tt> <tt class="py-op">=</tt> <tt class="py-name">cmdline</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-comment">### XXX: force_type ignored</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-keyword">if</tt> <tt class="py-name">kbyte</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</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">try</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">            <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-3" 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-3', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"-kbyte"</tt><tt class="py-op">,</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_KBYTE"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</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="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">            <tt class="py-keyword">pass</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-keyword">else</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">cmdline</tt><tt class="py-op">.</tt><tt id="link-4" 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-4', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"-kbyte"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">kbyte</tt><tt class="py-op">)</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>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">isatty</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">.</tt><tt class="py-name">fileno</tt><tt class="py-op">(</tt><tt class="py-op">)</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 class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'append', 'link-5');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"-quiet"</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-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-6" 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-6', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-name">pair</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"&gt;"</tt><tt class="py-op">,</tt> <tt class="py-name">output_filename</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 class="py-keyword">if</tt> <tt class="py-name">quiet</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-name">cmdline</tt><tt class="py-op">.</tt><tt id="link-8" 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-8', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"2&gt;"</tt><tt class="py-op">,</tt> <tt class="py-string">"/dev/null"</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 class="py-name">cmdline_str</tt> <tt class="py-op">=</tt> <tt class="py-string">' '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">cmdline_str</tt> </tt>
</div><a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"> </tt>
<a name="align"></a><div id="align-def"><a name="L55"></a><tt class="py-lineno"> 55</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-module.html#align">align</a><tt class="py-op">(</tt><tt class="py-param">cmdline</tt><tt class="py-op">,</tt> <tt class="py-param">pair</tt><tt class="py-op">,</tt> <tt class="py-param">kbyte</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">force_type</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">dry_run</tt><tt class="py-op">=</tt><tt id="link-9" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-9', 'False', 'link-2');">False</a></tt><tt class="py-op">,</tt> <tt class="py-param">quiet</tt><tt class="py-op">=</tt><tt id="link-10" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-10', 'False', 'link-2');">False</a></tt><tt class="py-op">,</tt> <tt class="py-param">debug</tt><tt class="py-op">=</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-11', 'False', 'link-2');">False</a></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="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">    Returns a filehandle</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">len</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-number">2</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">     </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line">    <tt class="py-name">output_file</tt> <tt class="py-op">=</tt> <tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">NamedTemporaryFile</tt><tt class="py-op">(</tt><tt class="py-name">mode</tt><tt class="py-op">=</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-name">input_files</tt> <tt class="py-op">=</tt> <tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">NamedTemporaryFile</tt><tt class="py-op">(</tt><tt class="py-name">mode</tt><tt class="py-op">=</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">tempfile</tt><tt class="py-op">.</tt><tt class="py-name">NamedTemporaryFile</tt><tt class="py-op">(</tt><tt class="py-name">mode</tt><tt class="py-op">=</tt><tt class="py-string">"w"</tt><tt class="py-op">)</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">dry_run</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt id="link-12" class="py-name" targets="Function Bio.Wise._build_align_cmdline()=Bio.Wise-module.html#_build_align_cmdline"><a title="Bio.Wise._build_align_cmdline" class="py-name" href="#" onclick="return doclink('link-12', '_build_align_cmdline', 'link-12');">_build_align_cmdline</a></tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">,</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">                                   <tt class="py-name">pair</tt><tt class="py-op">,</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">                                   <tt class="py-name">output_file</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'name', 'link-13');">name</a></tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">                                   <tt class="py-name">kbyte</tt><tt class="py-op">,</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">                                   <tt class="py-name">force_type</tt><tt class="py-op">,</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">                                   <tt class="py-name">quiet</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> </tt>
<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 class="py-keyword">for</tt> <tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">input_file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">pair</tt><tt class="py-op">,</tt> <tt class="py-name">input_files</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-comment"># Pipe the file through Biopython's Fasta parser/writer</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># to make sure it conforms to the Fasta standard (in particular,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-comment"># Wise2 may choke on long lines in the Fasta file)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-comment"></tt>        <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-14', 'SeqIO', 'link-1');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-15" 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-15', 'parse', 'link-15');">parse</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-16', 'open', 'link-16');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">filename</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'fasta'</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt id="link-17" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-17', 'SeqIO', 'link-1');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-18', 'write', 'link-18');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">records</tt><tt class="py-op">,</tt> <tt class="py-name">input_file</tt><tt class="py-op">,</tt> <tt class="py-string">'fasta'</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-name">input_file</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.Mindy.BerkeleyDB.BerkeleyDB.flush()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#flush,Method Bio.Mindy.FlatDB.MemoryFlatDB.flush()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#flush"><a title="Bio.Mindy.BerkeleyDB.BerkeleyDB.flush
Bio.Mindy.FlatDB.MemoryFlatDB.flush" class="py-name" href="#" onclick="return doclink('link-19', 'flush', 'link-19');">flush</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">    <tt class="py-name">input_file_names</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">input_file</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-13');">name</a></tt> <tt class="py-keyword">for</tt> <tt class="py-name">input_file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">input_files</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-name">cmdline_str</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Wise._build_align_cmdline" class="py-name" href="#" onclick="return doclink('link-21', '_build_align_cmdline', 'link-12');">_build_align_cmdline</a></tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">,</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">                                       <tt class="py-name">input_file_names</tt><tt class="py-op">,</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">                                       <tt class="py-name">output_file</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-22', 'name', 'link-13');">name</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-name">kbyte</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">force_type</tt><tt class="py-op">,</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">                                       <tt class="py-name">quiet</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line"> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</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="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">        <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-name">cmdline_str</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt class="py-name">status</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-name">cmdline_str</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;&gt;</tt> <tt class="py-number">8</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">status</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">kbyte</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-comment"># possible memory problem; could be None</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">            <tt class="py-keyword">print</tt> <tt class="py-op">&gt;&gt;</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stderr</tt><tt class="py-op">,</tt> <tt class="py-string">"INFO trying again with the linear model"</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt id="link-23" 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-23', 'align', 'link-23');">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-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">force_type</tt><tt class="py-op">,</tt> <tt class="py-name">dry_run</tt><tt class="py-op">,</tt> <tt class="py-name">quiet</tt><tt class="py-op">,</tt> <tt class="py-name">debug</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">OSError</tt><tt class="py-op">,</tt> <tt class="py-string">"%s returned %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">cmdline</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">status</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">     </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">output_file</tt> </tt>
</div><a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"> </tt>
<a name="all_pairs"></a><div id="all_pairs-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="all_pairs-toggle" onclick="return toggle('all_pairs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Wise-module.html#all_pairs">all_pairs</a><tt class="py-op">(</tt><tt class="py-param">singles</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="all_pairs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="all_pairs-expanded"><a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">    Generate pairs list for all-against-all alignments</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; all_pairs(range(4))</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    [(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">    <tt class="py-name">pairs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</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-name">singles</tt> <tt class="py-op">=</tt> <tt id="link-24" 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-24', 'list', 'link-24');">list</a></tt><tt class="py-op">(</tt><tt class="py-name">singles</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    <tt class="py-keyword">while</tt> <tt class="py-name">singles</tt><tt class="py-op">:</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">        <tt class="py-name">suitor</tt> <tt class="py-op">=</tt> <tt class="py-name">singles</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.Seq.MutableSeq.pop()=Bio.Seq.MutableSeq-class.html#pop"><a title="Bio.Seq.MutableSeq.pop" class="py-name" href="#" onclick="return doclink('link-25', 'pop', 'link-25');">pop</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-comment"># if sorted, stay sorted</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">        <tt class="py-name">pairs</tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'extend', 'link-3');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">suitor</tt><tt class="py-op">,</tt> <tt class="py-name">single</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">single</tt> <tt class="py-keyword">in</tt> <tt class="py-name">singles</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">pairs</tt> </tt>
</div><a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line"> </tt>
<a name="main"></a><div id="main-def"><a name="L120"></a><tt class="py-lineno">120</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-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="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L123"></a><tt class="py-lineno">123</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-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="L124"></a><tt class="py-lineno">124</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="L125"></a><tt class="py-lineno">125</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="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</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="L128"></a><tt class="py-lineno">128</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="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">        <tt id="link-27" 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-27', '_test', 'link-27');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt id="link-28" 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-28', 'main', 'link-28');">main</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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