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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.PopGen-module.html">Package PopGen</a> ::
<a href="Bio.PopGen.FDist-module.html">Package FDist</a> ::
Module Controller
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<h1 class="epydoc">Source Code for <a href="Bio.PopGen.FDist.Controller-module.html">Module Bio.PopGen.FDist.Controller</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">This module allows to control fdist.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">This will allow to call fdist and associated program (cplot, datacal, pv).</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">http://www.rubic.rdg.ac.uk/~mab/software.html</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<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">tempfile</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">sys</tt> <tt class="py-keyword">import</tt> <tt class="py-name">platform</tt><tt class="py-op">,</tt> <tt class="py-name">maxint</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">shutil</tt> <tt class="py-keyword">import</tt> <tt class="py-name">copyfile</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">randint</tt><tt class="py-op">,</tt> <tt class="py-name">random</tt> </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="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-0', 'time', 'link-0');">time</a></tt> <tt class="py-keyword">import</tt> <tt class="py-name">strftime</tt><tt class="py-op">,</tt> <tt class="py-name">clock</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment">#from logging import debug</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="FDistController"></a><div id="FDistController-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="FDistController-toggle" onclick="return toggle('FDistController');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html">FDistController</a><tt class="py-op">:</tt> </tt>
</div><div id="FDistController-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="FDistController-expanded"><a name="FDistController.__init__"></a><div id="FDistController.__init__-def"><a name="L25"></a><tt class="py-lineno"> 25</tt> <a class="py-toggle" href="#" id="FDistController.__init__-toggle" onclick="return toggle('FDistController.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-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">fdist_dir</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-param">ext</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.__init__-expanded"><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-docstring">"""Initializes the controller.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> fdist_dir is the directory where fdist2 is.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> ext is the extension of binaries (.exe on windows, </tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> none on Unix)</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-docstring"> """</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmp_idx</tt> <tt class="py-op">=</tt> <tt class="py-number">0</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-name">fdist_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">fdist_dir</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">os_name</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-1" 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-1', 'name', 'link-1');">name</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">os_name</tt><tt class="py-op">==</tt><tt class="py-string">'nt'</tt> <tt class="py-keyword">or</tt> <tt class="py-name">platform</tt><tt class="py-op">==</tt><tt class="py-string">'cygwin'</tt><tt class="py-op">:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">py_ext</tt> <tt class="py-op">=</tt> <tt class="py-string">'.exe'</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">py_ext</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ext</tt> <tt class="py-op">==</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ext</tt> <tt class="py-op">=</tt> <tt class="py-name">py_ext</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-keyword">else</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">ext</tt> <tt class="py-op">=</tt> <tt class="py-name">ext</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">exec_counts</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt>
<a name="FDistController._get_path"></a><div id="FDistController._get_path-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="FDistController._get_path-toggle" onclick="return toggle('FDistController._get_path');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#_get_path">_get_path</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">app</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController._get_path-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController._get_path-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the path to an fdist application.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> Includes Path where fdist can be found plus executable extension.</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</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">fdist_dir</tt> <tt class="py-op">==</tt> <tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">app</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ext</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt><tt class="py-op">.</tt><tt class="py-name">join</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">fdist_dir</tt><tt class="py-op">,</tt> <tt class="py-name">app</tt><tt class="py-op">]</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">ext</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="FDistController._get_temp_file"></a><div id="FDistController._get_temp_file-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="FDistController._get_temp_file-toggle" onclick="return toggle('FDistController._get_temp_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#_get_temp_file">_get_temp_file</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="FDistController._get_temp_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController._get_temp_file-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-docstring">"""Gets a temporary file name.</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-docstring"> Returns a temporary file name, if executing inside jython</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> tries to replace unexisting tempfile.mkstemp().</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmp_idx</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">strftime</tt><tt class="py-op">(</tt><tt class="py-string">"%H%M%S"</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">clock</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tmp_idx</tt><tt class="py-op">)</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="FDistController.run_datacal"></a><div id="FDistController.run_datacal-def"><a name="L65"></a><tt class="py-lineno"> 65</tt> <a class="py-toggle" href="#" id="FDistController.run_datacal-toggle" onclick="return toggle('FDistController.run_datacal');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_datacal">run_datacal</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.run_datacal-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.run_datacal-expanded"><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-docstring">"""Executes datacal.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> data_dir - Where the data is found.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-name">in_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.PopGen.FDist.Controller.FDistController._get_temp_file()=Bio.PopGen.FDist.Controller.FDistController-class.html#_get_temp_file"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-2', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">out_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-3', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-4" 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-4', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-5" 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-5', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'a\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-6', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">curr_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">system</tt><tt class="py-op">(</tt><tt class="py-string">'cd '</tt> <tt class="py-op">+</tt> <tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-string">' && '</tt> <tt class="py-op">+</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.PopGen.FDist.Controller.FDistController._get_path()=Bio.PopGen.FDist.Controller.FDistController-class.html#_get_path"><a title="Bio.PopGen.FDist.Controller.FDistController._get_path" class="py-name" href="#" onclick="return doclink('link-7', '_get_path', 'link-7');">_get_path</a></tt><tt class="py-op">(</tt><tt class="py-string">'datacal'</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">in_name</tt> <tt class="py-op">+</tt> <tt class="py-string">' > '</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-8', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</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">fst_line</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-9', 'readline', 'link-9');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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 id="link-10" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-10', 'split', 'link-10');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">fst</tt> <tt class="py-op">=</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">fst_line</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">sample_line</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-11', 'readline', 'link-9');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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 id="link-12" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-12', 'split', 'link-10');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">sample</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">sample_line</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-13', 'close', 'link-6');">close</a></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 class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-14', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</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">os</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-15', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</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 class="py-name">fst</tt><tt class="py-op">,</tt> <tt class="py-name">sample</tt> </tt>
</div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="FDistController._generate_intfile"></a><div id="FDistController._generate_intfile-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="FDistController._generate_intfile-toggle" onclick="return toggle('FDistController._generate_intfile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#_generate_intfile">_generate_intfile</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController._generate_intfile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController._generate_intfile-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Generates an INTFILE.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> Parameter:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> data_dir - data directory</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-name">inf</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-16', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'INTFILE'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-17" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-17', 'i', 'link-17');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">98</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">inf</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><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-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">randint</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">maxint</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-name">maxint</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-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">inf</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><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-19', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'8\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">inf</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-20', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="FDistController.run_fdist"></a><div id="FDistController.run_fdist-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="FDistController.run_fdist-toggle" onclick="return toggle('FDistController.run_fdist');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_fdist">run_fdist</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">npops</tt><tt class="py-op">,</tt> <tt class="py-param">nsamples</tt><tt class="py-op">,</tt> <tt class="py-param">fst</tt><tt class="py-op">,</tt> <tt class="py-param">sample_size</tt><tt class="py-op">,</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-param">mut</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">num_sims</tt> <tt class="py-op">=</tt> <tt class="py-number">20000</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.run_fdist-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.run_fdist-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-docstring">"""Executes fdist.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> Parameters:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> npops - Number of populations</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> nsamples - Number of populations sampled</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> fst - expected Fst</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> sample_size - Sample size per population</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> mut - 1=Stepwise, 0=Infinite allele</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> num_sims - number of simulations</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> data_dir - Where the data is found</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> fst - Average Fst</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> Important Note: This can take quite a while to run!</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fst</tt> <tt class="py-op">>=</tt> <tt class="py-number">0.9</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment">#Lets not joke</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fst</tt> <tt class="py-op">=</tt> <tt class="py-number">0.899</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fst</tt> <tt class="py-op"><=</tt> <tt class="py-number">0.0</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-comment">#0 will make fdist run forever</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fst</tt> <tt class="py-op">=</tt> <tt class="py-number">0.001</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">in_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'input.fd'</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">out_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'output.fd'</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment">#print 'writing', data_dir + os.sep + in_name</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-21', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</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">f</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><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-22', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'y\n\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-23', 'close', 'link-6');">close</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 class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-24', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'fdist_params2.dat'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><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-25', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">npops</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><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-26', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">nsamples</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><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-27', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">fst</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><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-28', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">sample_size</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><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-29', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">mut</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><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-30', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">num_sims</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-31', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method Bio.PopGen.FDist.Controller.FDistController._generate_intfile()=Bio.PopGen.FDist.Controller.FDistController-class.html#_generate_intfile"><a title="Bio.PopGen.FDist.Controller.FDistController._generate_intfile" class="py-name" href="#" onclick="return doclink('link-32', '_generate_intfile', 'link-32');">_generate_intfile</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <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-string">'cd '</tt> <tt class="py-op">+</tt> <tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-string">' && '</tt> <tt class="py-op">+</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_path" class="py-name" href="#" onclick="return doclink('link-33', '_get_path', 'link-7');">_get_path</a></tt><tt class="py-op">(</tt><tt class="py-string">'fdist2'</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">in_name</tt> <tt class="py-op">+</tt> <tt class="py-string">' > '</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-34', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readlines()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readlines,Method Bio.File.SGMLHandle.readlines()=Bio.File.SGMLHandle-class.html#readlines,Method Bio.File.UndoHandle.readlines()=Bio.File.UndoHandle-class.html#readlines,Method Bio.SGMLExtractor.SGMLExtractorHandle.readlines()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readlines"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-35', 'readlines', 'link-35');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-36', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</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">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'average Fst'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">fst</tt> <tt class="py-op">=</tt> <tt class="py-name">float</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 id="link-37" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-37', 'split', 'link-10');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-38', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-39', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fst</tt> </tt>
</div><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> </tt>
<a name="FDistController.run_fdist_force_fst"></a><div id="FDistController.run_fdist_force_fst-def"><a name="L152"></a><tt class="py-lineno">152</tt> <a class="py-toggle" href="#" id="FDistController.run_fdist_force_fst-toggle" onclick="return toggle('FDistController.run_fdist_force_fst');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_fdist_force_fst">run_fdist_force_fst</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">npops</tt><tt class="py-op">,</tt> <tt class="py-param">nsamples</tt><tt class="py-op">,</tt> <tt class="py-param">fst</tt><tt class="py-op">,</tt> <tt class="py-param">sample_size</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-param">mut</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">num_sims</tt> <tt class="py-op">=</tt> <tt class="py-number">20000</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">,</tt> <tt class="py-param">try_runs</tt> <tt class="py-op">=</tt> <tt class="py-number">5000</tt><tt class="py-op">,</tt> <tt class="py-param">limit</tt><tt class="py-op">=</tt><tt class="py-number">0.001</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.run_fdist_force_fst-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.run_fdist_force_fst-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-docstring">"""Exectues fdist trying to force Fst.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> Parameters:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"> try_runs - Number of simulations on the part trying to get</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> Fst correct</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> limit - Interval limit</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> Other parameters can be seen on run_fdist.</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">max_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">min_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">current_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">fst</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">old_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">fst</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-40" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-40', 'True', 'link-40');">True</a></tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment">#debug('testing fst ' + str(current_run_fst))</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">real_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.PopGen.FDist.Async.SplitFDist.run_fdist()=Bio.PopGen.FDist.Async.SplitFDist-class.html#run_fdist,Method Bio.PopGen.FDist.Controller.FDistController.run_fdist()=Bio.PopGen.FDist.Controller.FDistController-class.html#run_fdist"><a title="Bio.PopGen.FDist.Async.SplitFDist.run_fdist
Bio.PopGen.FDist.Controller.FDistController.run_fdist" class="py-name" href="#" onclick="return doclink('link-41', 'run_fdist', 'link-41');">run_fdist</a></tt><tt class="py-op">(</tt><tt class="py-name">npops</tt><tt class="py-op">,</tt> <tt class="py-name">nsamples</tt><tt class="py-op">,</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">,</tt> <tt class="py-name">sample_size</tt><tt class="py-op">,</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">mut</tt><tt class="py-op">,</tt> <tt class="py-name">try_runs</tt><tt class="py-op">,</tt> <tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-comment">#debug('got real fst ' + str(real_fst))</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-42" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-42', 'abs', 'link-42');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">real_fst</tt> <tt class="py-op">-</tt> <tt class="py-name">fst</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">limit</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-comment">#debug('We are OK')</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="Bio.PopGen.FDist.Async.SplitFDist.run_fdist
Bio.PopGen.FDist.Controller.FDistController.run_fdist" class="py-name" href="#" onclick="return doclink('link-43', 'run_fdist', 'link-41');">run_fdist</a></tt><tt class="py-op">(</tt><tt class="py-name">npops</tt><tt class="py-op">,</tt> <tt class="py-name">nsamples</tt><tt class="py-op">,</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">,</tt> <tt class="py-name">sample_size</tt><tt class="py-op">,</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">mut</tt><tt class="py-op">,</tt> <tt class="py-name">num_sims</tt><tt class="py-op">,</tt> <tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">old_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">current_run_fst</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">real_fst</tt> <tt class="py-op">></tt> <tt class="py-name">fst</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">max_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">current_run_fst</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_run_fst</tt> <tt class="py-op"><</tt> <tt class="py-name">min_run_fst</tt> <tt class="py-op">+</tt> <tt class="py-name">limit</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment">#we can do no better</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#debug('Lower limit is ' + str(min_run_fst))</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.PopGen.FDist.Async.SplitFDist.run_fdist
Bio.PopGen.FDist.Controller.FDistController.run_fdist" class="py-name" href="#" onclick="return doclink('link-44', 'run_fdist', 'link-41');">run_fdist</a></tt><tt class="py-op">(</tt><tt class="py-name">npops</tt><tt class="py-op">,</tt> <tt class="py-name">nsamples</tt><tt class="py-op">,</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">,</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">sample_size</tt><tt class="py-op">,</tt> <tt class="py-name">mut</tt><tt class="py-op">,</tt> <tt class="py-name">num_sims</tt><tt class="py-op">,</tt> <tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">current_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">min_run_fst</tt> <tt class="py-op">+</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">min_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">current_run_fst</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">current_run_fst</tt> <tt class="py-op">></tt> <tt class="py-name">max_run_fst</tt> <tt class="py-op">-</tt> <tt class="py-name">limit</tt><tt class="py-op">:</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-comment">#we can do no better</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#debug('Upper limit is ' + str(max_run_fst))</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.PopGen.FDist.Async.SplitFDist.run_fdist
Bio.PopGen.FDist.Controller.FDistController.run_fdist" class="py-name" href="#" onclick="return doclink('link-45', 'run_fdist', 'link-41');">run_fdist</a></tt><tt class="py-op">(</tt><tt class="py-name">npops</tt><tt class="py-op">,</tt> <tt class="py-name">nsamples</tt><tt class="py-op">,</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">,</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">sample_size</tt><tt class="py-op">,</tt> <tt class="py-name">mut</tt><tt class="py-op">,</tt> <tt class="py-name">num_sims</tt><tt class="py-op">,</tt> <tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">current_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">max_run_fst</tt> <tt class="py-op">+</tt> <tt class="py-name">current_run_fst</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
</div><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> </tt>
<a name="FDistController.run_cplot"></a><div id="FDistController.run_cplot-def"><a name="L193"></a><tt class="py-lineno">193</tt> <a class="py-toggle" href="#" id="FDistController.run_cplot-toggle" onclick="return toggle('FDistController.run_cplot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_cplot">run_cplot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">ci</tt><tt class="py-op">=</tt> <tt class="py-number">0.95</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.run_cplot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.run_cplot-expanded"><a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-docstring">"""Executes cplot.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> ci - Confidence interval.</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> data_dir - Where the data is found.</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">in_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-46', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">out_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-47', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-48', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><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-49', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'out.dat out.cpl\n'</tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">ci</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-50', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-name">curr_dir</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._generate_intfile" class="py-name" href="#" onclick="return doclink('link-51', '_generate_intfile', 'link-32');">_generate_intfile</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <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-string">'cd '</tt> <tt class="py-op">+</tt> <tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-string">' && '</tt> <tt class="py-op">+</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_path" class="py-name" href="#" onclick="return doclink('link-52', '_get_path', 'link-7');">_get_path</a></tt><tt class="py-op">(</tt><tt class="py-string">'cplot'</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">in_name</tt> <tt class="py-op">+</tt> <tt class="py-string">' > '</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-53', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-54', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-55" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-55', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-string">'out.cpl'</tt><tt class="py-op">)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-name">conf_lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-56', 'readline', 'link-9');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">l</tt><tt class="py-op"><></tt><tt class="py-string">''</tt><tt class="py-op">:</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-name">conf_lines</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'append', 'link-57');">append</a></tt><tt class="py-op">(</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-58', 'map', 'link-58');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-59" class="py-name" targets="Variable Bio.MarkovModel.x=Bio.MarkovModel-module.html#x,Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-59', 'x', 'link-59');">x</a></tt> <tt class="py-op">:</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-60" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-60', 'x', 'link-59');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">l</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 id="link-61" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-61', 'split', 'link-10');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-62', 'readline', 'link-9');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-63', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-64', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">conf_lines</tt> </tt>
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="FDistController.run_pv"></a><div id="FDistController.run_pv-def"><a name="L225"></a><tt class="py-lineno">225</tt> <a class="py-toggle" href="#" id="FDistController.run_pv-toggle" onclick="return toggle('FDistController.run_pv');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Controller.FDistController-class.html#run_pv">run_pv</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">out_file</tt><tt class="py-op">=</tt><tt class="py-string">'probs.dat'</tt><tt class="py-op">,</tt> <tt class="py-param">data_dir</tt><tt class="py-op">=</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="FDistController.run_pv-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="FDistController.run_pv-expanded"><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-docstring">"""Executes pv.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> out_file - Name of output file.</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> data_dir - Where the data is found.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">in_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-65', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-name">out_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_temp_file" class="py-name" href="#" onclick="return doclink('link-66', '_get_temp_file', 'link-2');">_get_temp_file</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-67', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><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-68', 'write', 'link-5');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'data_fst_outfile '</tt> <tt class="py-op">+</tt> <tt class="py-name">out_file</tt> <tt class="py-op">+</tt> <tt class="py-string">' out.dat\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">f</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-69', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._generate_intfile" class="py-name" href="#" onclick="return doclink('link-70', '_generate_intfile', 'link-32');">_generate_intfile</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <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-string">'cd '</tt> <tt class="py-op">+</tt> <tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-string">' && '</tt> <tt class="py-op">+</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.PopGen.FDist.Controller.FDistController._get_path" class="py-name" href="#" onclick="return doclink('link-71', '_get_path', 'link-7');">_get_path</a></tt><tt class="py-op">(</tt><tt class="py-string">'pv'</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">in_name</tt> <tt class="py-op">+</tt> <tt class="py-string">' > '</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">pvf</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-72', 'open', 'link-4');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_file</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt id="link-73" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-73', 'map', 'link-58');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-74" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-74', 'x', 'link-59');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-75', 'map', 'link-58');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">y</tt><tt class="py-op">:</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">y</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-76" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-76', 'x', 'link-59');">x</a></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 id="link-77" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-77', 'split', 'link-10');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">pvf</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readlines
Bio.File.SGMLHandle.readlines
Bio.File.UndoHandle.readlines
Bio.SGMLExtractor.SGMLExtractorHandle.readlines" class="py-name" href="#" onclick="return doclink('link-78', 'readlines', 'link-35');">readlines</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">pvf</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-79', 'close', 'link-6');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-80', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">in_name</tt><tt class="py-op">)</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-81', 'remove', 'link-14');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">data_dir</tt> <tt class="py-op">+</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">sep</tt> <tt class="py-op">+</tt> <tt class="py-name">out_name</tt><tt class="py-op">)</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div></div><a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> </tt><script type="text/javascript">
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