<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Bio.PopGen.FDist.Utils</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
<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 Utils
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>] | <a href="Bio.PopGen.FDist.Utils-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.PopGen.FDist.Utils-module.html">Module Bio.PopGen.FDist.Utils</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-keyword">import</tt> <tt class="py-name">os</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</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-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.PopGen=Bio.PopGen-module.html"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-1', 'PopGen', 'link-1');">PopGen</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package Bio.PopGen.GenePop=Bio.PopGen.GenePop-module.html"><a title="Bio.PopGen.GenePop" class="py-name" href="#" onclick="return doclink('link-2', 'GenePop', 'link-2');">GenePop</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-4', 'PopGen', 'link-1');">PopGen</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.PopGen.FDist=Bio.PopGen.FDist-module.html"><a title="Bio.PopGen.FDist" class="py-name" href="#" onclick="return doclink('link-5', 'FDist', 'link-5');">FDist</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"><tt class="py-comment"># Quite a few utility functions could be done (like remove pop,</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># add locus, etc...). The recommended strategy is convert back</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and forth from/to GenePop and use GenePop Utils</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="convert_genepop_to_fdist"></a><div id="convert_genepop_to_fdist-def"><a name="L15"></a><tt class="py-lineno">15</tt> <a class="py-toggle" href="#" id="convert_genepop_to_fdist-toggle" onclick="return toggle('convert_genepop_to_fdist');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Utils-module.html#convert_genepop_to_fdist">convert_genepop_to_fdist</a><tt class="py-op">(</tt><tt class="py-param">gp_rec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="convert_genepop_to_fdist-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="convert_genepop_to_fdist-expanded"><a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-docstring">"""Converts a GenePop record to a FDist one.</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"><tt class="py-docstring"> Parameters:</tt> </tt>
<a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"><tt class="py-docstring"> gp_rec - Genepop Record</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-docstring"> Returns:</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt> <tt class="py-line"><tt class="py-docstring"> FDist record.</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">fd_rec</tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.PopGen" class="py-name" href="#" onclick="return doclink('link-7', 'PopGen', 'link-1');">PopGen</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.PopGen.FDist" class="py-name" href="#" onclick="return doclink('link-8', 'FDist', 'link-5');">FDist</a></tt><tt class="py-op">.</tt><tt id="link-9" 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-9', 'Record', 'link-9');">Record</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt> <tt class="py-line"> </tt>
<a name="L26"></a><tt class="py-lineno">26</tt> <tt class="py-line"> <tt class="py-name">fd_rec</tt><tt class="py-op">.</tt><tt id="link-10" 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-10', 'data_org', 'link-10');">data_org</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L27"></a><tt class="py-lineno">27</tt> <tt class="py-line"> <tt class="py-name">fd_rec</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'num_loci', 'link-11');">num_loci</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">loci_list</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt class="py-name">fd_rec</tt><tt class="py-op">.</tt><tt id="link-12" 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-12', 'num_pops', 'link-12');">num_pops</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">populations</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">lc_i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">loci_list</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno">30</tt> <tt class="py-line"> <tt class="py-name">alleles</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> <tt class="py-name">pop_data</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pop_i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">populations</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">indiv</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">populations</tt><tt class="py-op">[</tt><tt class="py-name">pop_i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno">34</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">al</tt> <tt class="py-keyword">in</tt> <tt class="py-name">indiv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">lc_i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno">35</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">al</tt><tt class="py-op"><></tt><tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">al</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alleles</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno">36</tt> <tt class="py-line"> <tt class="py-name">alleles</tt><tt class="py-op">.</tt><tt id="link-13" 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-13', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">al</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-comment">#here we go again (necessary...)</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">pop_i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">populations</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno">39</tt> <tt class="py-line"> <tt class="py-name">allele_counts</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L40"></a><tt class="py-lineno">40</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">indiv</tt> <tt class="py-keyword">in</tt> <tt class="py-name">gp_rec</tt><tt class="py-op">.</tt><tt class="py-name">populations</tt><tt class="py-op">[</tt><tt class="py-name">pop_i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">al</tt> <tt class="py-keyword">in</tt> <tt class="py-name">indiv</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">lc_i</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">al</tt><tt class="py-op"><></tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt id="link-14" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-14', 'count', 'link-14');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-name">allele_counts</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-15', 'get', 'link-15');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">al</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> <tt class="py-name">allele_counts</tt><tt class="py-op">[</tt><tt class="py-name">al</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-16', 'count', 'link-14');">count</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L45"></a><tt class="py-lineno">45</tt> <tt class="py-line"> <tt class="py-name">allele_array</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment">#We need the same order as in alleles</tt> </tt>
<a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">allele</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alleles</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-name">allele_array</tt><tt class="py-op">.</tt><tt id="link-17" 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-17', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">allele_counts</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-18', 'get', 'link-15');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">allele</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno">48</tt> <tt class="py-line"> <tt class="py-name">pop_data</tt><tt class="py-op">.</tt><tt id="link-19" 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-19', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">allele_array</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-comment">#if lc_i==3:</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># print alleles, allele_counts#, pop_data</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fd_rec</tt><tt class="py-op">.</tt><tt class="py-name">loci_data</tt><tt class="py-op">.</tt><tt id="link-20" 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-20', 'append', 'link-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">alleles</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">pop_data</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">fd_rec</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> </tt>
<a name="approximate_fst"></a><div id="approximate_fst-def"><a name="L54"></a><tt class="py-lineno">54</tt> <a class="py-toggle" href="#" id="approximate_fst-toggle" onclick="return toggle('approximate_fst');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.PopGen.FDist.Utils-module.html#approximate_fst">approximate_fst</a><tt class="py-op">(</tt><tt class="py-param">desired_fst</tt><tt class="py-op">,</tt> <tt class="py-param">simulated_fst</tt><tt class="py-op">,</tt> <tt class="py-param">parameter_fst</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-param">max_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">min_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">limit</tt> <tt class="py-op">=</tt> <tt class="py-number">0.005</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="approximate_fst-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="approximate_fst-expanded"><a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-docstring">"""Calculates the next Fst attempt in order to approximate a</tt> </tt>
<a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"><tt class="py-docstring"> desired Fst.</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"> """</tt> </tt>
<a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-21" 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-21', 'abs', 'link-21');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">simulated_fst</tt> <tt class="py-op">-</tt> <tt class="py-name">desired_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="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">parameter_fst</tt><tt class="py-op">,</tt> <tt class="py-name">max_run_fst</tt><tt class="py-op">,</tt> <tt class="py-name">min_run_fst</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">simulated_fst</tt> <tt class="py-op">></tt> <tt class="py-name">desired_fst</tt><tt class="py-op">:</tt> </tt>
<a name="L63"></a><tt class="py-lineno">63</tt> <tt class="py-line"> <tt class="py-name">max_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">parameter_fst</tt> </tt>
<a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-name">next_parameter_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">parameter_fst</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> <tt class="py-keyword">else</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">min_run_fst</tt> <tt class="py-op">=</tt> <tt class="py-name">parameter_fst</tt> </tt>
<a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-name">next_parameter_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">parameter_fst</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-number">2</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">next_parameter_fst</tt><tt class="py-op">,</tt> <tt class="py-name">max_run_fst</tt><tt class="py-op">,</tt> <tt class="py-name">min_run_fst</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Tree link -->
<th> <a
href="module-tree.html">Trees</a> </th>
<!-- Index link -->
<th> <a
href="identifier-index.html">Indices</a> </th>
<!-- Help link -->
<th> <a
href="help.html">Help</a> </th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Mon Sep 15 09:27:17 2008
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
