<?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.GFF.binning</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.GFF-module.html">Package GFF</a> ::
Module binning
</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.GFF.binning-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.GFF.binning-module.html">Module Bio.GFF.binning</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</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"># Copyright 2002 by Michael Hoffman. All rights reserved.</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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># note:</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># I used Lincoln Stein's perl Bio::DB::GFF::Util::Binning as a model for this</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-comment"></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">Binning support for Bio.GFF</tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"><tt class="py-name">__version__</tt> <tt class="py-op">=</tt> <tt class="py-string">"$Revision: 1.1 $"</tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"><tt class="py-comment"># $Source: /home/repository/biopython/biopython/Bio/GFF/binning.py,v $</tt> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Meta"></a><div id="Meta-def"><a name="L18"></a><tt class="py-lineno">18</tt> <a class="py-toggle" href="#" id="Meta-toggle" onclick="return toggle('Meta');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.GFF.binning.Meta-class.html">Meta</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Meta-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="Meta-expanded"><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> <tt id="link-0" class="py-name" targets="Variable Bio.GFF.binning.Meta.MIN_BIN=Bio.GFF.binning.Meta-class.html#MIN_BIN"><a title="Bio.GFF.binning.Meta.MIN_BIN" class="py-name" href="#" onclick="return doclink('link-0', 'MIN_BIN', 'link-0');">MIN_BIN</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1000</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt> <tt class="py-line"> <tt id="link-1" class="py-name" targets="Variable Bio.GFF.binning.Meta.MAX_BIN=Bio.GFF.binning.Meta-class.html#MAX_BIN"><a title="Bio.GFF.binning.Meta.MAX_BIN" class="py-name" href="#" onclick="return doclink('link-1', 'MAX_BIN', 'link-1');">MAX_BIN</a></tt> <tt class="py-op">=</tt> <tt class="py-number">100000000</tt> </tt>
</div><a name="L21"></a><tt class="py-lineno">21</tt> <tt class="py-line"> </tt>
<a name="query"></a><div id="query-def"><a name="L22"></a><tt class="py-lineno">22</tt> <a class="py-toggle" href="#" id="query-toggle" onclick="return toggle('query');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GFF.binning-module.html#query">query</a><tt class="py-op">(</tt><tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">stop</tt><tt class="py-op">=</tt><tt id="link-2" class="py-name" targets="Class Bio.GFF.binning.Meta=Bio.GFF.binning.Meta-class.html"><a title="Bio.GFF.binning.Meta" class="py-name" href="#" onclick="return doclink('link-2', 'Meta', 'link-2');">Meta</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.GFF.binning.Meta.MAX_BIN" class="py-name" href="#" onclick="return doclink('link-3', 'MAX_BIN', 'link-1');">MAX_BIN</a></tt><tt class="py-op">,</tt> <tt class="py-param">minbin</tt><tt class="py-op">=</tt><tt id="link-4" class="py-name"><a title="Bio.GFF.binning.Meta" class="py-name" href="#" onclick="return doclink('link-4', 'Meta', 'link-2');">Meta</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.GFF.binning.Meta.MIN_BIN" class="py-name" href="#" onclick="return doclink('link-5', 'MIN_BIN', 'link-0');">MIN_BIN</a></tt><tt class="py-op">,</tt> <tt class="py-param">maxbin</tt><tt class="py-op">=</tt><tt id="link-6" class="py-name"><a title="Bio.GFF.binning.Meta" class="py-name" href="#" onclick="return doclink('link-6', 'Meta', 'link-2');">Meta</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.GFF.binning.Meta.MAX_BIN" class="py-name" href="#" onclick="return doclink('link-7', 'MAX_BIN', 'link-1');">MAX_BIN</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="query-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="query-expanded"><a name="L23"></a><tt class="py-lineno">23</tt> <tt class="py-line"> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L24"></a><tt class="py-lineno">24</tt> <tt class="py-line"> <tt class="py-name">bins</tt> <tt class="py-op">=</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 class="py-name">tier</tt> <tt class="py-op">=</tt> <tt class="py-name">maxbin</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 class="py-keyword">if</tt> <tt id="link-8" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-8', 'start', 'link-8');">start</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L28"></a><tt class="py-lineno">28</tt> <tt class="py-line"> <tt id="link-9" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-9', 'start', 'link-8');">start</a></tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L29"></a><tt class="py-lineno">29</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stop</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</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">stop</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.GFF.binning.Meta" class="py-name" href="#" onclick="return doclink('link-10', 'Meta', 'link-2');">Meta</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.GFF.binning.Meta.MAX_BIN" class="py-name" href="#" onclick="return doclink('link-11', 'MAX_BIN', 'link-1');">MAX_BIN</a></tt> </tt>
<a name="L31"></a><tt class="py-lineno">31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno">32</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">tier</tt> <tt class="py-op">>=</tt> <tt class="py-name">minbin</tt><tt class="py-op">:</tt> </tt>
<a name="L33"></a><tt class="py-lineno">33</tt> <tt class="py-line"> <tt class="py-name">tier_start</tt><tt class="py-op">,</tt> <tt class="py-name">tier_stop</tt> <tt class="py-op">=</tt> <tt class="py-name">bot</tt><tt class="py-op">(</tt><tt class="py-name">tier</tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-12', 'start', 'link-8');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">top</tt><tt class="py-op">(</tt><tt class="py-name">tier</tt><tt class="py-op">,</tt> <tt class="py-name">stop</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">if</tt> <tt class="py-op">(</tt><tt class="py-name">tier_start</tt> <tt class="py-op">==</tt> <tt class="py-name">tier_stop</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-name">bins</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-string">'fbin=%s'</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">args</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-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">tier_start</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno">37</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno">38</tt> <tt class="py-line"> <tt class="py-name">bins</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-13');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'fbin BETWEEN %s AND %s'</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">args</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.extend()=Bio.EUtils.POM.ElementNode-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.EUtils.POM.ElementNode.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-16', 'extend', 'link-16');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">tier_start</tt><tt class="py-op">,</tt> <tt class="py-name">tier_stop</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-name">tier</tt> <tt class="py-op">/=</tt> <tt class="py-number">10</tt> </tt>
<a name="L41"></a><tt class="py-lineno">41</tt> <tt class="py-line"> <tt id="link-17" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.query()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#query,Function Bio.Entrez.query()=Bio.Entrez-module.html#query,Function Bio.WWW.NCBI.query()=Bio.WWW.NCBI-module.html#query"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-17', 'query', 'link-17');">query</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"\n\t OR "</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">bins</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno">42</tt> <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno">43</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-18" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.query
Bio.Entrez.query
Bio.WWW.NCBI.query" class="py-name" href="#" onclick="return doclink('link-18', 'query', 'link-17');">query</a></tt> <tt class="py-op">%</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">args</tt><tt class="py-op">)</tt> </tt>
</div><a name="L44"></a><tt class="py-lineno">44</tt> <tt class="py-line"> </tt>
<a name="bin"></a><div id="bin-def"><a name="L45"></a><tt class="py-lineno">45</tt> <a class="py-toggle" href="#" id="bin-toggle" onclick="return toggle('bin');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GFF.binning-module.html#bin">bin</a><tt class="py-op">(</tt><tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">stop</tt><tt class="py-op">,</tt> <tt class="py-param">min</tt><tt class="py-op">,</tt> <tt class="py-param">wantarray</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bin-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="bin-expanded"><a name="L46"></a><tt class="py-lineno">46</tt> <tt class="py-line"> <tt class="py-name">tier</tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt> </tt>
<a name="L47"></a><tt class="py-lineno">47</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</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">bin_start</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt id="link-19" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-19', 'start', 'link-8');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">tier</tt><tt class="py-op">)</tt> </tt>
<a name="L49"></a><tt class="py-lineno">49</tt> <tt class="py-line"> <tt class="py-name">bin_end</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">stop</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">tier</tt><tt class="py-op">)</tt> </tt>
<a name="L50"></a><tt class="py-lineno">50</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">bin_start</tt> <tt class="py-op">==</tt> <tt class="py-name">bin_end</tt><tt class="py-op">:</tt> </tt>
<a name="L51"></a><tt class="py-lineno">51</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L52"></a><tt class="py-lineno">52</tt> <tt class="py-line"> <tt class="py-name">tier</tt> <tt class="py-op">*=</tt> <tt class="py-number">10</tt> </tt>
<a name="L53"></a><tt class="py-lineno">53</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">wantarray</tt><tt class="py-op">:</tt> </tt>
<a name="L54"></a><tt class="py-lineno">54</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tier</tt><tt class="py-op">,</tt> <tt class="py-name">bin_start</tt> </tt>
<a name="L55"></a><tt class="py-lineno">55</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L56"></a><tt class="py-lineno">56</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">bin_name</tt><tt class="py-op">(</tt><tt class="py-name">tier</tt><tt class="py-op">,</tt> <tt class="py-name">bin_start</tt><tt class="py-op">)</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno">57</tt> <tt class="py-line"> </tt>
<a name="bot"></a><div id="bot-def"><a name="L58"></a><tt class="py-lineno">58</tt> <a class="py-toggle" href="#" id="bot-toggle" onclick="return toggle('bot');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GFF.binning-module.html#bot">bot</a><tt class="py-op">(</tt><tt class="py-param">tier</tt><tt class="py-op">,</tt> <tt class="py-param">pos</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bot-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="bot-expanded"><a name="L59"></a><tt class="py-lineno">59</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-20" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-20', 'name', 'link-20');">name</a></tt><tt class="py-op">(</tt><tt class="py-name">tier</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">/</tt><tt class="py-name">tier</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L60"></a><tt class="py-lineno">60</tt> <tt class="py-line"> </tt>
<a name="L61"></a><tt class="py-lineno">61</tt> <tt class="py-line"><tt class="py-name">top</tt> <tt class="py-op">=</tt> <tt class="py-name">bot</tt> </tt>
<a name="L62"></a><tt class="py-lineno">62</tt> <tt class="py-line"> </tt>
<a name="name"></a><div id="name-def"><a name="L63"></a><tt class="py-lineno">63</tt> <a class="py-toggle" href="#" id="name-toggle" onclick="return toggle('name');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GFF.binning-module.html#name">name</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="name-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="name-expanded"><a name="L64"></a><tt class="py-lineno">64</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%d.%06d"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-21" 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-21', 'x', 'link-21');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt>
</div><a name="L65"></a><tt class="py-lineno">65</tt> <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L66"></a><tt class="py-lineno">66</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.GFF.binning-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywds</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_test-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="_test-expanded"><a name="L67"></a><tt class="py-lineno">67</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L68"></a><tt class="py-lineno">68</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">modules</tt><tt class="py-op">[</tt><tt class="py-name">__name__</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-name">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">keywds</tt><tt class="py-op">)</tt> </tt>
</div><a name="L69"></a><tt class="py-lineno">69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno">70</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno">71</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">__debug__</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno">72</tt> <tt class="py-line"> <tt id="link-22" class="py-name" targets="Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.EUtils.MultiDict._test()=Bio.EUtils.MultiDict-module.html#_test,Function Bio.GFF._test()=Bio.GFF-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.DocSQL._test
Bio.EUtils.MultiDict._test
Bio.GFF._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-22', '_test', 'link-22');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno">73</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 09:28:11 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>
