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Package FDist
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<h1 class="epydoc">Source Code for <a href="Bio.PopGen.FDist-module.html">Package Bio.PopGen.FDist</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 class="py-docstring">"""</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">This module provides code to work with FDist.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">See http://www.rubic.rdg.ac.uk/~mab/software.html .</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring">Record Holds FDist data.</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">RecordParser Parses a FDist record (file) into a Record object.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring">_Scanner Scans a FDist record.</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring">_RecordConsumer Consumes FDist data to a Record object.</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">types</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Module Bio.File=Bio.File-module.html"><a title="Bio.File" class="py-name" href="#" onclick="return doclink('link-1', 'File', 'link-1');">File</a></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Module Bio.ParserSupport=Bio.ParserSupport-module.html"><a title="Bio.ParserSupport" class="py-name" href="#" onclick="return doclink('link-3', 'ParserSupport', 'link-3');">ParserSupport</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> </tt>
<a name="Record"></a><div id="Record-def"><a name="L29"></a><tt class="py-lineno"> 29</tt> <a class="py-toggle" href="#" id="Record-toggle" onclick="return toggle('Record');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Record-class.html">Record</a><tt class="py-op">:</tt> </tt>
</div><div id="Record-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Record-expanded"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-docstring">"""Holds information from a FDist record.</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"> Members:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> data_org Data organization (0 pops by rows, 1 alleles by rows).</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> The Record will behave as if data was 0 (converting if needed)</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> num_pops Number of populations</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> num_loci Number of loci</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> loci_data Loci data</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> loci_data is a list, where each element represents a locus. Each element</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> is a tuple, the first element is the number of alleles, the second</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> element a list. Each element of the list is the count of each allele</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> per population.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Record.__init__"></a><div id="Record.__init__-def"><a name="L48"></a><tt class="py-lineno"> 48</tt> <a class="py-toggle" href="#" id="Record.__init__-toggle" onclick="return toggle('Record.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Record-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__init__-expanded"><a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Method Bio.PopGen.FDist._RecordConsumer.data_org()=Bio.PopGen.FDist._RecordConsumer-class.html#data_org"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-4', 'data_org', 'link-4');">data_org</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method Bio.PopGen.FDist._RecordConsumer.num_pops()=Bio.PopGen.FDist._RecordConsumer-class.html#num_pops"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-5', 'num_pops', 'link-5');">num_pops</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.PopGen.FDist._RecordConsumer.num_loci()=Bio.PopGen.FDist._RecordConsumer-class.html#num_loci"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-6', 'num_loci', 'link-6');">num_loci</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">loci_data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> </tt>
<a name="Record.__str__"></a><div id="Record.__str__-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="Record.__str__-toggle" onclick="return toggle('Record.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Record-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Record.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Record.__str__-expanded"><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">rep</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'0\n'</tt><tt class="py-op">]</tt> <tt class="py-comment">#We only export in 0 format, even if originally was 1</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-7" 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-7', 'append', 'link-7');">append</a></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 id="link-8" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-8', 'num_pops', 'link-5');">num_pops</a></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="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-9', 'append', 'link-7');">append</a></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 id="link-10" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-10', 'num_loci', 'link-6');">num_loci</a></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="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-11', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">locus_data</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">loci_data</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">num_alleles</tt><tt class="py-op">,</tt> <tt class="py-name">pops_data</tt> <tt class="py-op">=</tt> <tt class="py-name">locus_data</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-12', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">num_alleles</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="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pop_data</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pops_data</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">allele_count</tt> <tt class="py-keyword">in</tt> <tt class="py-name">pop_data</tt><tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-13', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">allele_count</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-name">rep</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-14', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</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">rep</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-15', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">)</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">return</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">rep</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="RecordParser"></a><div id="RecordParser-def"><a name="L70"></a><tt class="py-lineno"> 70</tt> <a class="py-toggle" href="#" id="RecordParser-toggle" onclick="return toggle('RecordParser');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.FDist.RecordParser-class.html">RecordParser</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractParser</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordParser-expanded"><a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-docstring">"""Parses FDist data into a Record object.</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="RecordParser.__init__"></a><div id="RecordParser.__init__-def"><a name="L74"></a><tt class="py-lineno"> 74</tt> <a class="py-toggle" href="#" id="RecordParser.__init__-toggle" onclick="return toggle('RecordParser.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.RecordParser-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.__init__-expanded"><a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Class Bio.Blast.NCBIStandalone._Scanner=Bio.Blast.NCBIStandalone._Scanner-class.html,Class Bio.Blast.NCBIWWW._Scanner=Bio.Blast.NCBIWWW._Scanner-class.html,Class Bio.CDD._Scanner=Bio.CDD._Scanner-class.html,Class Bio.Compass._Scanner=Bio.Compass._Scanner-class.html,Class Bio.ECell._Scanner=Bio.ECell._Scanner-class.html,Class Bio.Enzyme._Scanner=Bio.Enzyme._Scanner-class.html,Class Bio.Gobase._Scanner=Bio.Gobase._Scanner-class.html,Class Bio.IntelliGenetics._Scanner=Bio.IntelliGenetics._Scanner-class.html,Class Bio.LocusLink._Scanner=Bio.LocusLink._Scanner-class.html,Class Bio.Medline._Scanner=Bio.Medline._Scanner-class.html,Class Bio.MetaTool._Scanner=Bio.MetaTool._Scanner-class.html,Class Bio.NBRF._Scanner=Bio.NBRF._Scanner-class.html,Class Bio.PopGen.FDist._Scanner=Bio.PopGen.FDist._Scanner-class.html,Class Bio.PopGen.GenePop._Scanner=Bio.PopGen.GenePop._Scanner-class.html,Class Bio.Prosite.Prodoc._Scanner=Bio.Prosite.Prodoc._Scanner-class.html,Class Bio.Prosite._Scanner=Bio.Prosite._Scanner-class.html,Class Bio.Rebase._Scanner=Bio.Rebase._Scanner-class.html,Class Bio.Saf._Scanner=Bio.Saf._Scanner-class.html,Class Bio.Sequencing.Ace._Scanner=Bio.Sequencing.Ace._Scanner-class.html,Class Bio.Sequencing.Phd._Scanner=Bio.Sequencing.Phd._Scanner-class.html,Class Bio.SwissProt.KeyWList._Scanner=Bio.SwissProt.KeyWList._Scanner-class.html,Class Bio.SwissProt.SProt._Scanner=Bio.SwissProt.SProt._Scanner-class.html,Class Bio.UniGene._Scanner=Bio.UniGene._Scanner-class.html"><a title="Bio.Blast.NCBIStandalone._Scanner
Bio.Blast.NCBIWWW._Scanner
Bio.CDD._Scanner
Bio.Compass._Scanner
Bio.ECell._Scanner
Bio.Enzyme._Scanner
Bio.Gobase._Scanner
Bio.IntelliGenetics._Scanner
Bio.LocusLink._Scanner
Bio.Medline._Scanner
Bio.MetaTool._Scanner
Bio.NBRF._Scanner
Bio.PopGen.FDist._Scanner
Bio.PopGen.GenePop._Scanner
Bio.Prosite.Prodoc._Scanner
Bio.Prosite._Scanner
Bio.Rebase._Scanner
Bio.Saf._Scanner
Bio.Sequencing.Ace._Scanner
Bio.Sequencing.Phd._Scanner
Bio.SwissProt.KeyWList._Scanner
Bio.SwissProt.SProt._Scanner
Bio.UniGene._Scanner" class="py-name" href="#" onclick="return doclink('link-16', '_Scanner', 'link-16');">_Scanner</a></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">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Class Bio.CDD._RecordConsumer=Bio.CDD._RecordConsumer-class.html,Class Bio.ECell._RecordConsumer=Bio.ECell._RecordConsumer-class.html,Class Bio.Enzyme._RecordConsumer=Bio.Enzyme._RecordConsumer-class.html,Class Bio.GenBank._RecordConsumer=Bio.GenBank._RecordConsumer-class.html,Class Bio.Gobase._RecordConsumer=Bio.Gobase._RecordConsumer-class.html,Class Bio.IntelliGenetics._RecordConsumer=Bio.IntelliGenetics._RecordConsumer-class.html,Class Bio.LocusLink._RecordConsumer=Bio.LocusLink._RecordConsumer-class.html,Class Bio.Medline._RecordConsumer=Bio.Medline._RecordConsumer-class.html,Class Bio.MetaTool._RecordConsumer=Bio.MetaTool._RecordConsumer-class.html,Class Bio.NBRF._RecordConsumer=Bio.NBRF._RecordConsumer-class.html,Class Bio.PopGen.FDist._RecordConsumer=Bio.PopGen.FDist._RecordConsumer-class.html,Class Bio.PopGen.GenePop._RecordConsumer=Bio.PopGen.GenePop._RecordConsumer-class.html,Class Bio.Prosite.Prodoc._RecordConsumer=Bio.Prosite.Prodoc._RecordConsumer-class.html,Class Bio.Prosite._RecordConsumer=Bio.Prosite._RecordConsumer-class.html,Class Bio.Rebase._RecordConsumer=Bio.Rebase._RecordConsumer-class.html,Class Bio.Saf._RecordConsumer=Bio.Saf._RecordConsumer-class.html,Class Bio.Sequencing.Ace._RecordConsumer=Bio.Sequencing.Ace._RecordConsumer-class.html,Class Bio.Sequencing.Phd._RecordConsumer=Bio.Sequencing.Phd._RecordConsumer-class.html,Class Bio.SwissProt.SProt._RecordConsumer=Bio.SwissProt.SProt._RecordConsumer-class.html,Class Bio.UniGene._RecordConsumer=Bio.UniGene._RecordConsumer-class.html"><a title="Bio.CDD._RecordConsumer
Bio.ECell._RecordConsumer
Bio.Enzyme._RecordConsumer
Bio.GenBank._RecordConsumer
Bio.Gobase._RecordConsumer
Bio.IntelliGenetics._RecordConsumer
Bio.LocusLink._RecordConsumer
Bio.Medline._RecordConsumer
Bio.MetaTool._RecordConsumer
Bio.NBRF._RecordConsumer
Bio.PopGen.FDist._RecordConsumer
Bio.PopGen.GenePop._RecordConsumer
Bio.Prosite.Prodoc._RecordConsumer
Bio.Prosite._RecordConsumer
Bio.Rebase._RecordConsumer
Bio.Saf._RecordConsumer
Bio.Sequencing.Ace._RecordConsumer
Bio.Sequencing.Phd._RecordConsumer
Bio.SwissProt.SProt._RecordConsumer
Bio.UniGene._RecordConsumer" class="py-name" href="#" onclick="return doclink('link-17', '_RecordConsumer', 'link-17');">_RecordConsumer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="RecordParser.parse"></a><div id="RecordParser.parse-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="RecordParser.parse-toggle" onclick="return toggle('RecordParser.parse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.RecordParser-class.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordParser.parse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordParser.parse-expanded"><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scanner</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.Affy.CelFile.CelScanner.feed()=Bio.Affy.CelFile.CelScanner-class.html#feed,Method Bio.AlignAce.Scanner.AlignAceScanner.feed()=Bio.AlignAce.Scanner.AlignAceScanner-class.html#feed,Method Bio.AlignAce.Scanner.CompareAceScanner.feed()=Bio.AlignAce.Scanner.CompareAceScanner-class.html#feed,Method Bio.Blast.NCBIStandalone._Scanner.feed()=Bio.Blast.NCBIStandalone._Scanner-class.html#feed,Method Bio.Blast.NCBIWWW._Scanner.feed()=Bio.Blast.NCBIWWW._Scanner-class.html#feed,Method Bio.CDD._Scanner.feed()=Bio.CDD._Scanner-class.html#feed,Method Bio.Compass._Scanner.feed()=Bio.Compass._Scanner-class.html#feed,Method Bio.ECell._Scanner.feed()=Bio.ECell._Scanner-class.html#feed,Method Bio.Emboss.Primer._Primer3Scanner.feed()=Bio.Emboss.Primer._Primer3Scanner-class.html#feed,Method Bio.Emboss.Primer._PrimerSearchScanner.feed()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#feed,Method Bio.Enzyme._Scanner.feed()=Bio.Enzyme._Scanner-class.html#feed,Method Bio.GenBank.Scanner.InsdcScanner.feed()=Bio.GenBank.Scanner.InsdcScanner-class.html#feed,Method Bio.Gobase._Scanner.feed()=Bio.Gobase._Scanner-class.html#feed,Method Bio.IntelliGenetics._Scanner.feed()=Bio.IntelliGenetics._Scanner-class.html#feed,Method Bio.InterPro.InterProParser.feed()=Bio.InterPro.InterProParser-class.html#feed,Method Bio.LocusLink._Scanner.feed()=Bio.LocusLink._Scanner-class.html#feed,Method Bio.LocusLink.web_parse.LocusLinkParser.feed()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#feed,Method Bio.MEME.Parser._MASTScanner.feed()=Bio.MEME.Parser._MASTScanner-class.html#feed,Method Bio.MEME.Parser._MEMEScanner.feed()=Bio.MEME.Parser._MEMEScanner-class.html#feed,Method Bio.Medline._Scanner.feed()=Bio.Medline._Scanner-class.html#feed,Method Bio.MetaTool._Scanner.feed()=Bio.MetaTool._Scanner-class.html#feed,Method Bio.NBRF._Scanner.feed()=Bio.NBRF._Scanner-class.html#feed,Method Bio.Ndb.NdbParser.feed()=Bio.Ndb.NdbParser-class.html#feed,Method Bio.NetCatch.ExtractUrls.feed()=Bio.NetCatch.ExtractUrls-class.html#feed,Method Bio.PopGen.FDist._Scanner.feed()=Bio.PopGen.FDist._Scanner-class.html#feed,Method Bio.PopGen.GenePop._Scanner.feed()=Bio.PopGen.GenePop._Scanner-class.html#feed,Method Bio.Prosite.Prodoc._Scanner.feed()=Bio.Prosite.Prodoc._Scanner-class.html#feed,Method Bio.Prosite._Scanner.feed()=Bio.Prosite._Scanner-class.html#feed,Method Bio.Rebase._Scanner.feed()=Bio.Rebase._Scanner-class.html#feed,Method Bio.Saf._Scanner.feed()=Bio.Saf._Scanner-class.html#feed,Method Bio.Sequencing.Ace._Scanner.feed()=Bio.Sequencing.Ace._Scanner-class.html#feed,Method Bio.Sequencing.Phd._Scanner.feed()=Bio.Sequencing.Phd._Scanner-class.html#feed,Method Bio.SwissProt.KeyWList._Scanner.feed()=Bio.SwissProt.KeyWList._Scanner-class.html#feed,Method Bio.SwissProt.SProt._Scanner.feed()=Bio.SwissProt.SProt._Scanner-class.html#feed,Method Bio.UniGene._Scanner.feed()=Bio.UniGene._Scanner-class.html#feed"><a title="Bio.Affy.CelFile.CelScanner.feed
Bio.AlignAce.Scanner.AlignAceScanner.feed
Bio.AlignAce.Scanner.CompareAceScanner.feed
Bio.Blast.NCBIStandalone._Scanner.feed
Bio.Blast.NCBIWWW._Scanner.feed
Bio.CDD._Scanner.feed
Bio.Compass._Scanner.feed
Bio.ECell._Scanner.feed
Bio.Emboss.Primer._Primer3Scanner.feed
Bio.Emboss.Primer._PrimerSearchScanner.feed
Bio.Enzyme._Scanner.feed
Bio.GenBank.Scanner.InsdcScanner.feed
Bio.Gobase._Scanner.feed
Bio.IntelliGenetics._Scanner.feed
Bio.InterPro.InterProParser.feed
Bio.LocusLink._Scanner.feed
Bio.LocusLink.web_parse.LocusLinkParser.feed
Bio.MEME.Parser._MASTScanner.feed
Bio.MEME.Parser._MEMEScanner.feed
Bio.Medline._Scanner.feed
Bio.MetaTool._Scanner.feed
Bio.NBRF._Scanner.feed
Bio.Ndb.NdbParser.feed
Bio.NetCatch.ExtractUrls.feed
Bio.PopGen.FDist._Scanner.feed
Bio.PopGen.GenePop._Scanner.feed
Bio.Prosite.Prodoc._Scanner.feed
Bio.Prosite._Scanner.feed
Bio.Rebase._Scanner.feed
Bio.Saf._Scanner.feed
Bio.Sequencing.Ace._Scanner.feed
Bio.Sequencing.Phd._Scanner.feed
Bio.SwissProt.KeyWList._Scanner.feed
Bio.SwissProt.SProt._Scanner.feed
Bio.UniGene._Scanner.feed" class="py-name" href="#" onclick="return doclink('link-18', 'feed', 'link-18');">feed</a></tt><tt class="py-op">(</tt><tt id="link-19" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-19', 'handle', 'link-19');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_consumer</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-20', 'data', 'link-20');">data</a></tt> </tt>
</div></div><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="_Scanner"></a><div id="_Scanner-def"><a name="L82"></a><tt class="py-lineno"> 82</tt> <a class="py-toggle" href="#" id="_Scanner-toggle" onclick="return toggle('_Scanner');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.FDist._Scanner-class.html">_Scanner</a><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_Scanner-expanded"><a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-docstring">"""Scans a FDist record.</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> There is only one record per file.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> </tt>
<a name="_Scanner.feed"></a><div id="_Scanner.feed-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="_Scanner.feed-toggle" onclick="return toggle('_Scanner.feed');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._Scanner-class.html#feed">feed</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">consumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_Scanner.feed-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_Scanner.feed-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-docstring">"""feed(self, handle, consumer)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> Feed in a FDist unit record for scanning. handle is a file-like</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> object that contains a FDist record. consumer is a</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> Consumer object that will receive events as the report is scanned.</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Medline._RecordConsumer.start_record()=Bio.Medline._RecordConsumer-class.html#start_record,Method Bio.PopGen.FDist._RecordConsumer.start_record()=Bio.PopGen.FDist._RecordConsumer-class.html#start_record,Method Bio.PopGen.GenePop._RecordConsumer.start_record()=Bio.PopGen.GenePop._RecordConsumer-class.html#start_record,Method Bio.Prosite.Prodoc._RecordConsumer.start_record()=Bio.Prosite.Prodoc._RecordConsumer-class.html#start_record,Method Bio.Prosite._RecordConsumer.start_record()=Bio.Prosite._RecordConsumer-class.html#start_record,Method Bio.SwissProt.SProt._RecordConsumer.start_record()=Bio.SwissProt.SProt._RecordConsumer-class.html#start_record,Method Bio.SwissProt.SProt._SequenceConsumer.start_record()=Bio.SwissProt.SProt._SequenceConsumer-class.html#start_record,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.start_record()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#start_record"><a title="Bio.Medline._RecordConsumer.start_record
Bio.PopGen.FDist._RecordConsumer.start_record
Bio.PopGen.GenePop._RecordConsumer.start_record
Bio.Prosite.Prodoc._RecordConsumer.start_record
Bio.Prosite._RecordConsumer.start_record
Bio.SwissProt.SProt._RecordConsumer.start_record
Bio.SwissProt.SProt._SequenceConsumer.start_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.start_record" class="py-name" href="#" onclick="return doclink('link-21', 'start_record', 'link-21');">start_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-22', 'num_pops', 'link-5');">num_pops</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-23', 'num_loci', 'link-6');">num_loci</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">loci_data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt id="link-24" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-24', 'data_org', 'link-4');">data_org</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-25', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-26" 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-26', 'readline', 'link-26');">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>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-27', 'data_org', 'link-4');">data_org</a></tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-28', 'data_org', 'link-4');">data_org</a></tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt id="link-29" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-29', 'num_pops', 'link-5');">num_pops</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-30', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'readline', 'link-26');">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>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-32', 'num_pops', 'link-5');">num_pops</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-33', 'num_pops', 'link-5');">num_pops</a></tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt id="link-34" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-34', 'num_loci', 'link-6');">num_loci</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-35" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-35', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-36" 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-36', 'readline', 'link-26');">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>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-37', 'num_loci', 'link-6');">num_loci</a></tt><tt class="py-op">(</tt><tt id="link-38" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-38', 'num_loci', 'link-6');">num_loci</a></tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-39" 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-39', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-40', 'num_loci', 'link-6');">num_loci</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-41', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-42" 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-42', 'readline', 'link-26');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">num_alleles</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-43', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-44" 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-44', 'readline', 'link-26');">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>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">pops_data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-45" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-45', 'data_org', 'link-4');">data_org</a></tt><tt class="py-op">==</tt><tt class="py-number">0</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">for</tt> <tt class="py-name">j</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt id="link-46" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-46', 'num_pops', 'link-5');">num_pops</a></tt><tt class="py-op">)</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">line_comp</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-47', 'handle', 'link-19');">handle</a></tt><tt class="py-op">.</tt><tt id="link-48" 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-48', 'readline', 'link-26');">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-49" 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-49', 'split', 'link-49');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-name">pop_dist</tt> <tt class="py-op">=</tt> <tt id="link-50" 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-50', 'map', 'link-50');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-51" 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-51', 'x', 'link-51');">x</a></tt><tt class="py-op">:</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-52" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-52', 'x', 'link-51');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">line_comp</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-name">pops_data</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-53', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">pop_dist</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">'1/alleles by rows not implemented'</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.PopGen.FDist._RecordConsumer.new_locus()=Bio.PopGen.FDist._RecordConsumer-class.html#new_locus"><a title="Bio.PopGen.FDist._RecordConsumer.new_locus" class="py-name" href="#" onclick="return doclink('link-54', 'new_locus', 'link-54');">new_locus</a></tt><tt class="py-op">(</tt><tt class="py-name">num_alleles</tt><tt class="py-op">,</tt> <tt class="py-name">pops_data</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">consumer</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Method Bio.Emboss.Primer._Primer3RecordConsumer.end_record()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#end_record,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#end_record,Method Bio.Medline._RecordConsumer.end_record()=Bio.Medline._RecordConsumer-class.html#end_record,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#end_record,Method Bio.PopGen.FDist._RecordConsumer.end_record()=Bio.PopGen.FDist._RecordConsumer-class.html#end_record,Method Bio.PopGen.GenePop._RecordConsumer.end_record()=Bio.PopGen.GenePop._RecordConsumer-class.html#end_record,Method Bio.Prosite.Prodoc._RecordConsumer.end_record()=Bio.Prosite.Prodoc._RecordConsumer-class.html#end_record,Method Bio.Prosite._RecordConsumer.end_record()=Bio.Prosite._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._RecordConsumer.end_record()=Bio.SwissProt.SProt._RecordConsumer-class.html#end_record,Method Bio.SwissProt.SProt._SequenceConsumer.end_record()=Bio.SwissProt.SProt._SequenceConsumer-class.html#end_record,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#end_record"><a title="Bio.Emboss.Primer._Primer3RecordConsumer.end_record
Bio.Emboss.Primer._PrimerSearchRecordConsumer.end_record
Bio.Medline._RecordConsumer.end_record
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.end_record
Bio.PopGen.FDist._RecordConsumer.end_record
Bio.PopGen.GenePop._RecordConsumer.end_record
Bio.Prosite.Prodoc._RecordConsumer.end_record
Bio.Prosite._RecordConsumer.end_record
Bio.SwissProt.SProt._RecordConsumer.end_record
Bio.SwissProt.SProt._SequenceConsumer.end_record
Bio.builders.SeqRecord.sequence.BuildSeqRecord.end_record" class="py-name" href="#" onclick="return doclink('link-55', 'end_record', 'link-55');">end_record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer"></a><div id="_RecordConsumer-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="_RecordConsumer-toggle" onclick="return toggle('_RecordConsumer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html">_RecordConsumer</a><tt class="py-op">(</tt><tt class="py-base-class">AbstractConsumer</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_RecordConsumer-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-docstring">"""Consumer that converts a FDist record to a Record object.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> Members:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> data Record with FDist data.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="_RecordConsumer.__init__"></a><div id="_RecordConsumer.__init__-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="_RecordConsumer.__init__-toggle" onclick="return toggle('_RecordConsumer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.__init__-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-56', 'data', 'link-20');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.start_record"></a><div id="_RecordConsumer.start_record-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="_RecordConsumer.start_record-toggle" onclick="return toggle('_RecordConsumer.start_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#start_record">start_record</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="_RecordConsumer.start_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.start_record-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-57', 'data', 'link-20');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-58" class="py-name" targets="Module Bio.Blast.Record=Bio.Blast.Record-module.html,Module Bio.CDD.Record=Bio.CDD.Record-module.html,Class Bio.CDD.Record.Record=Bio.CDD.Record.Record-class.html,Class Bio.Cluster.Record=Bio.Cluster.Record-class.html,Class Bio.Compass.Record=Bio.Compass.Record-class.html,Module Bio.ECell.Record=Bio.ECell.Record-module.html,Class Bio.ECell.Record.Record=Bio.ECell.Record.Record-class.html,Class Bio.Fasta.Record=Bio.Fasta.Record-class.html,Module Bio.GenBank.Record=Bio.GenBank.Record-module.html,Class Bio.GenBank.Record.Record=Bio.GenBank.Record.Record-class.html,Module Bio.Geo.Record=Bio.Geo.Record-module.html,Class Bio.Geo.Record.Record=Bio.Geo.Record.Record-class.html,Class Bio.Gobase.Record=Bio.Gobase.Record-class.html,Module Bio.IntelliGenetics.Record=Bio.IntelliGenetics.Record-module.html,Class Bio.IntelliGenetics.Record.Record=Bio.IntelliGenetics.Record.Record-class.html,Class Bio.InterPro.Record=Bio.InterPro.Record-class.html,Class Bio.KEGG.Compound.Record=Bio.KEGG.Compound.Record-class.html,Class Bio.KEGG.Enzyme.Record=Bio.KEGG.Enzyme.Record-class.html,Class Bio.LocusLink.Record=Bio.LocusLink.Record-class.html,Class Bio.LocusLink.web_parse.Record=Bio.LocusLink.web_parse.Record-class.html,Class Bio.Medline.Record=Bio.Medline.Record-class.html,Module Bio.MetaTool.Record=Bio.MetaTool.Record-module.html,Class Bio.MetaTool.Record.Record=Bio.MetaTool.Record.Record-class.html,Module Bio.NBRF.Record=Bio.NBRF.Record-module.html,Class Bio.NBRF.Record.Record=Bio.NBRF.Record.Record-class.html,Class Bio.Ndb.Record=Bio.Ndb.Record-class.html,Class Bio.PopGen.FDist.Record=Bio.PopGen.FDist.Record-class.html,Class Bio.PopGen.GenePop.Record=Bio.PopGen.GenePop.Record-class.html,Class Bio.Prosite.Prodoc.Record=Bio.Prosite.Prodoc.Record-class.html,Class Bio.Prosite.Record=Bio.Prosite.Record-class.html,Class Bio.Rebase.Record=Bio.Rebase.Record-class.html,Class Bio.SCOP.Cla.Record=Bio.SCOP.Cla.Record-class.html,Class Bio.SCOP.Des.Record=Bio.SCOP.Des.Record-class.html,Class Bio.SCOP.Dom.Record=Bio.SCOP.Dom.Record-class.html,Class Bio.SCOP.Hie.Record=Bio.SCOP.Hie.Record-class.html,Module Bio.Saf.Record=Bio.Saf.Record-module.html,Class Bio.Saf.Record.Record=Bio.Saf.Record.Record-class.html,Class Bio.Sequencing.Phd.Record=Bio.Sequencing.Phd.Record-class.html,Class Bio.SwissProt.KeyWList.Record=Bio.SwissProt.KeyWList.Record-class.html,Class Bio.SwissProt.SProt.Record=Bio.SwissProt.SProt.Record-class.html"><a title="Bio.Blast.Record
Bio.CDD.Record
Bio.CDD.Record.Record
Bio.Cluster.Record
Bio.Compass.Record
Bio.ECell.Record
Bio.ECell.Record.Record
Bio.Fasta.Record
Bio.GenBank.Record
Bio.GenBank.Record.Record
Bio.Geo.Record
Bio.Geo.Record.Record
Bio.Gobase.Record
Bio.IntelliGenetics.Record
Bio.IntelliGenetics.Record.Record
Bio.InterPro.Record
Bio.KEGG.Compound.Record
Bio.KEGG.Enzyme.Record
Bio.LocusLink.Record
Bio.LocusLink.web_parse.Record
Bio.Medline.Record
Bio.MetaTool.Record
Bio.MetaTool.Record.Record
Bio.NBRF.Record
Bio.NBRF.Record.Record
Bio.Ndb.Record
Bio.PopGen.FDist.Record
Bio.PopGen.GenePop.Record
Bio.Prosite.Prodoc.Record
Bio.Prosite.Record
Bio.Rebase.Record
Bio.SCOP.Cla.Record
Bio.SCOP.Des.Record
Bio.SCOP.Dom.Record
Bio.SCOP.Hie.Record
Bio.Saf.Record
Bio.Saf.Record.Record
Bio.Sequencing.Phd.Record
Bio.SwissProt.KeyWList.Record
Bio.SwissProt.SProt.Record" class="py-name" href="#" onclick="return doclink('link-58', 'Record', 'link-58');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.end_record"></a><div id="_RecordConsumer.end_record-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="_RecordConsumer.end_record-toggle" onclick="return toggle('_RecordConsumer.end_record');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#end_record">end_record</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="_RecordConsumer.end_record-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.end_record-expanded"><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.data_org"></a><div id="_RecordConsumer.data_org-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="_RecordConsumer.data_org-toggle" onclick="return toggle('_RecordConsumer.data_org');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#data_org">data_org</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data_org</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.data_org-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.data_org-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-59', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-60', 'data_org', 'link-4');">data_org</a></tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.data_org" class="py-name" href="#" onclick="return doclink('link-61', 'data_org', 'link-4');">data_org</a></tt> </tt>
</div><a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_pops"></a><div id="_RecordConsumer.num_pops-def"><a name="L142"></a><tt class="py-lineno">142</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_pops-toggle" onclick="return toggle('_RecordConsumer.num_pops');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#num_pops">num_pops</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_pops</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_pops-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_pops-expanded"><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-62', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-63', 'num_pops', 'link-5');">num_pops</a></tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_pops" class="py-name" href="#" onclick="return doclink('link-64', 'num_pops', 'link-5');">num_pops</a></tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.num_loci"></a><div id="_RecordConsumer.num_loci-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="_RecordConsumer.num_loci-toggle" onclick="return toggle('_RecordConsumer.num_loci');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#num_loci">num_loci</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_loci</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.num_loci-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.num_loci-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-65', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-66', 'num_loci', 'link-6');">num_loci</a></tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.PopGen.FDist._RecordConsumer.num_loci" class="py-name" href="#" onclick="return doclink('link-67', 'num_loci', 'link-6');">num_loci</a></tt> </tt>
</div><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt>
<a name="_RecordConsumer.new_locus"></a><div id="_RecordConsumer.new_locus-def"><a name="L148"></a><tt class="py-lineno">148</tt> <a class="py-toggle" href="#" id="_RecordConsumer.new_locus-toggle" onclick="return toggle('_RecordConsumer.new_locus');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist._RecordConsumer-class.html#new_locus">new_locus</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">num_alleles</tt><tt class="py-op">,</tt> <tt class="py-param">pop_data</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_RecordConsumer.new_locus-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_RecordConsumer.new_locus-expanded"><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-20');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">loci_data</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-69', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">num_alleles</tt><tt class="py-op">,</tt> <tt class="py-name">pop_data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt><script type="text/javascript">
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