<?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.SeqUtils.CodonUsage</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.SeqUtils-module.html">Package SeqUtils</a> ::
Module CodonUsage
</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.SeqUtils.CodonUsage-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils.CodonUsage-module.html">Module Bio.SeqUtils.CodonUsage</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">math</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Bio.SeqUtils.CodonUsageIndices=Bio.SeqUtils.CodonUsageIndices-module.html"><a title="Bio.SeqUtils.CodonUsageIndices" class="py-name" href="#" onclick="return doclink('link-0', 'CodonUsageIndices', 'link-0');">CodonUsageIndices</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Variable Bio.SeqUtils.CodonUsageIndices.SharpEcoliIndex=Bio.SeqUtils.CodonUsageIndices-module.html#SharpEcoliIndex"><a title="Bio.SeqUtils.CodonUsageIndices.SharpEcoliIndex" class="py-name" href="#" onclick="return doclink('link-1', 'SharpEcoliIndex', 'link-1');">SharpEcoliIndex</a></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-2');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Package Bio.Fasta=Bio.Fasta-module.html"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-3', 'Fasta', 'link-3');">Fasta</a></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable Bio.SeqUtils.CodonUsage.CodonsDict=Bio.SeqUtils.CodonUsage-module.html#CodonsDict"><a title="Bio.SeqUtils.CodonUsage.CodonsDict" class="py-name" href="#" onclick="return doclink('link-4', 'CodonsDict', 'link-4');">CodonsDict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'TTT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-string">'CTC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-string">'ATA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-string">'GTG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-string">'CAT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-string">'AAC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-string">'GAA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-string">'TCG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-string">'ACT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-string">'GCC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-string">'TGA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-string">'CGG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-string">'GGT'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">}</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"># this dictionary is used to know which codons encode the same AA.</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-5" class="py-name" targets="Variable Bio.SeqUtils.CodonUsage.SynonymousCodons=Bio.SeqUtils.CodonUsage-module.html#SynonymousCodons"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-5', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'CYS'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TGT'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'ASP'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'GAT'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-string">'SER'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TCT'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCC'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-string">'GLN'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'CAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'MET'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'ATG'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'ASN'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'AAC'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</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-string">'PRO'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'CCT'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'LYS'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'AAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</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-string">'STOP'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'THR'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'ACC'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-string">'PHE'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TTT'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'ALA'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'GCA'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-string">'GLY'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'GGT'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'ILE'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'ATC'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-string">'LEU'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TTA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'HIS'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'CAT'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-string">'ARG'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'CGA'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'TRP'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TGG'</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-string">'VAL'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'GTA'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'GLU'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'GAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">'TYR'</tt><tt class="py-op">:</tt> <tt class="py-op">[</tt><tt class="py-string">'TAT'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</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>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="CodonAdaptationIndex"></a><div id="CodonAdaptationIndex-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex-toggle" onclick="return toggle('CodonAdaptationIndex');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html">CodonAdaptationIndex</a><tt class="py-op">:</tt> </tt>
</div><div id="CodonAdaptationIndex-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CodonAdaptationIndex-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-docstring">"""</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"> This class implements the codon adaptaion index (CAI) described by Sharp and</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> Li (Nucleic Acids Res. 1987 Feb 11;15(3):1281-95).</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> methods:</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> set_cai_index(Index):</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> This mehtod sets-up an index to be used when calculating CAI for a gene.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> Just pass a dictionary similar to the SharpEcoliIndex in CodonUsageIndices</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> module.</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"> generate_index(FastaFile):</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> This method takes a location of a FastaFile and generates an index. This</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> index can later be used to calculate CAI of a gene.</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> cai_for_gene(DNAsequence):</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> This mehtod uses the Index (either the one you set or the one you generated)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> and returns the CAI for the DNA sequence.</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> print_index():</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> This method prints out the index you used.</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-docstring"> """</tt> </tt>
<a name="CodonAdaptationIndex.__init__"></a><div id="CodonAdaptationIndex.__init__-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex.__init__-toggle" onclick="return toggle('CodonAdaptationIndex.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-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="CodonAdaptationIndex.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex.__init__-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-6', 'index', 'link-6');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</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">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># use this method with predefined CAI index</tt> </tt>
<a name="CodonAdaptationIndex.set_cai_index"></a><div id="CodonAdaptationIndex.set_cai_index-def"><a name="L66"></a><tt class="py-lineno"> 66</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex.set_cai_index-toggle" onclick="return toggle('CodonAdaptationIndex.set_cai_index');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#set_cai_index">set_cai_index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">Index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CodonAdaptationIndex.set_cai_index-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex.set_cai_index-expanded"><a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-7', 'index', 'link-6');">index</a></tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Module Bio.Index=Bio.Index-module.html,Class Bio.SCOP.Cla.Index=Bio.SCOP.Cla.Index-class.html"><a title="Bio.Index
Bio.SCOP.Cla.Index" class="py-name" href="#" onclick="return doclink('link-8', 'Index', 'link-8');">Index</a></tt> </tt>
</div><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="CodonAdaptationIndex.generate_index"></a><div id="CodonAdaptationIndex.generate_index-def"><a name="L69"></a><tt class="py-lineno"> 69</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex.generate_index-toggle" onclick="return toggle('CodonAdaptationIndex.generate_index');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#generate_index">generate_index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">FastaFile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CodonAdaptationIndex.generate_index-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex.generate_index-expanded"><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># first make sure i am not overwriting an existing index:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-9', 'index', 'link-6');">index</a></tt> <tt class="py-op">!=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">!=</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-10" class="py-name" targets="Class Bio.Crystal.Error=Bio.Crystal.Error-class.html,Class Bio.ECell.Error=Bio.ECell.Error-class.html"><a title="Bio.Crystal.Error
Bio.ECell.Error" class="py-name" href="#" onclick="return doclink('link-10', 'Error', 'link-10');">Error</a></tt><tt class="py-op">(</tt><tt class="py-string">"an index has already been set or a codon count has been done. cannot overwrite either."</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># count codon occurances in the file.</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method Bio.SeqUtils.CodonUsage.CodonAdaptationIndex._count_codons()=Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#_count_codons"><a title="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex._count_codons" class="py-name" href="#" onclick="return doclink('link-11', '_count_codons', 'link-11');">_count_codons</a></tt><tt class="py-op">(</tt><tt class="py-name">FastaFile</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment"># now to calculate the index we first need to sum the number of times</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># synonymous codons were used all together.</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">AA</tt> <tt class="py-keyword">in</tt> <tt id="link-12" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-12', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-13', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">Sum</tt><tt class="py-op">=</tt><tt class="py-number">0.0</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">RCSU</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># RCSU values are equal to CodonCount/((1/num of synonymous codons) * sum of all synonymous codons)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt id="link-14" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-14', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">[</tt><tt class="py-name">AA</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">Sum</tt> <tt class="py-op">+=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-comment"># calculate the RSCU value for each of the codons</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt id="link-15" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-15', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">[</tt><tt class="py-name">AA</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">RCSU</tt><tt class="py-op">.</tt><tt id="link-16" 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-16', 'append', 'link-16');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-17', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">[</tt><tt class="py-name">AA</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-name">Sum</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-comment"># now generate the index W=RCSUi/RCSUmax:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">RCSUmax</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">RCSU</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-18" 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-18', 'i', 'link-18');">i</a></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 id="link-19" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-19', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">[</tt><tt class="py-name">AA</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-20', 'index', 'link-6');">index</a></tt><tt class="py-op">[</tt><tt id="link-21" class="py-name"><a title="Bio.SeqUtils.CodonUsage.SynonymousCodons" class="py-name" href="#" onclick="return doclink('link-21', 'SynonymousCodons', 'link-5');">SynonymousCodons</a></tt><tt class="py-op">[</tt><tt class="py-name">AA</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-22" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-22', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">=</tt> <tt class="py-name">RCSU</tt><tt class="py-op">[</tt><tt id="link-23" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-23', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">/</tt><tt class="py-name">RCSUmax</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="CodonAdaptationIndex.cai_for_gene"></a><div id="CodonAdaptationIndex.cai_for_gene-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex.cai_for_gene-toggle" onclick="return toggle('CodonAdaptationIndex.cai_for_gene');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#cai_for_gene">cai_for_gene</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">DNAsequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CodonAdaptationIndex.cai_for_gene-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex.cai_for_gene-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">caiValue</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">LengthForCai</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-comment"># if no index is set or generated, the default SharpEcoliIndex will be used.</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-24', 'index', 'link-6');">index</a></tt><tt class="py-op">==</tt><tt class="py-op">{</tt><tt class="py-op">}</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.set_cai_index()=Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#set_cai_index"><a title="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.set_cai_index" class="py-name" href="#" onclick="return doclink('link-25', 'set_cai_index', 'link-25');">set_cai_index</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Bio.SeqUtils.CodonUsageIndices.SharpEcoliIndex" class="py-name" href="#" onclick="return doclink('link-26', 'SharpEcoliIndex', 'link-1');">SharpEcoliIndex</a></tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">DNAsequence</tt><tt class="py-op">.</tt><tt class="py-name">islower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">DNAsequence</tt> <tt class="py-op">=</tt> <tt class="py-name">DNAsequence</tt><tt class="py-op">.</tt><tt class="py-name">upper</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 class="py-keyword">for</tt> <tt id="link-27" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-27', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt> <tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">DNAsequence</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">DNAsequence</tt><tt class="py-op">[</tt><tt id="link-28" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-28', 'i', 'link-18');">i</a></tt><tt class="py-op">:</tt><tt id="link-29" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-29', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-30', 'index', 'link-6');">index</a></tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-31', 'has_key', 'link-31');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">codon</tt><tt class="py-op">!=</tt><tt class="py-string">'ATG'</tt> <tt class="py-keyword">and</tt> <tt class="py-name">codon</tt><tt class="py-op">!=</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-comment">#these two codons are always one, exclude them.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">caiValue</tt> <tt class="py-op">+=</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Variable Bio.Affy.CelFile.log=Bio.Affy.CelFile-module.html#log,Variable Bio.LogisticRegression.log=Bio.LogisticRegression-module.html#log,Variable Bio.MarkovModel.log=Bio.MarkovModel-module.html#log,Variable Bio.MaxEntropy.log=Bio.MaxEntropy-module.html#log,Variable Bio.NaiveBayes.log=Bio.NaiveBayes-module.html#log,Variable Bio.Statistics.lowess.log=Bio.Statistics.lowess-module.html#log,Variable Bio.distance.log=Bio.distance-module.html#log,Variable Bio.kNN.log=Bio.kNN-module.html#log"><a title="Bio.Affy.CelFile.log
Bio.LogisticRegression.log
Bio.MarkovModel.log
Bio.MaxEntropy.log
Bio.NaiveBayes.log
Bio.Statistics.lowess.log
Bio.distance.log
Bio.kNN.log" class="py-name" href="#" onclick="return doclink('link-32', 'log', 'link-32');">log</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-33', 'index', 'link-6');">index</a></tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">LengthForCai</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'TGA'</tt><tt class="py-op">,</tt><tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> <tt class="py-comment"># some indices you will use may not include stop codons.</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"illegal codon in sequence: %s.\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-34', 'index', 'link-6');">index</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 class="py-keyword">return</tt> <tt class="py-name">math</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Variable Bio.Affy.CelFile.exp=Bio.Affy.CelFile-module.html#exp,Variable Bio.LogisticRegression.exp=Bio.LogisticRegression-module.html#exp,Variable Bio.MarkovModel.exp=Bio.MarkovModel-module.html#exp,Variable Bio.MaxEntropy.exp=Bio.MaxEntropy-module.html#exp,Variable Bio.NaiveBayes.exp=Bio.NaiveBayes-module.html#exp,Variable Bio.Statistics.lowess.exp=Bio.Statistics.lowess-module.html#exp,Variable Bio.distance.exp=Bio.distance-module.html#exp,Variable Bio.kNN.exp=Bio.kNN-module.html#exp"><a title="Bio.Affy.CelFile.exp
Bio.LogisticRegression.exp
Bio.MarkovModel.exp
Bio.MaxEntropy.exp
Bio.NaiveBayes.exp
Bio.Statistics.lowess.exp
Bio.distance.exp
Bio.kNN.exp" class="py-name" href="#" onclick="return doclink('link-35', 'exp', 'link-35');">exp</a></tt><tt class="py-op">(</tt><tt class="py-name">caiValue</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-number">1.0</tt><tt class="py-op">/</tt><tt class="py-op">(</tt><tt class="py-name">LengthForCai</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> </tt>
<a name="CodonAdaptationIndex._count_codons"></a><div id="CodonAdaptationIndex._count_codons-def"><a name="L112"></a><tt class="py-lineno">112</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex._count_codons-toggle" onclick="return toggle('CodonAdaptationIndex._count_codons');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#_count_codons">_count_codons</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">FastaFile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CodonAdaptationIndex._count_codons-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex._count_codons-expanded"><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">InputFile</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-36', 'open', 'link-36');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">FastaFile</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-comment"># set up the fasta parser</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-37', 'Fasta', 'link-3');">Fasta</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Class Bio.CDD.RecordParser=Bio.CDD.RecordParser-class.html,Class Bio.Compass.RecordParser=Bio.Compass.RecordParser-class.html,Class Bio.ECell.RecordParser=Bio.ECell.RecordParser-class.html,Class Bio.Enzyme.RecordParser=Bio.Enzyme.RecordParser-class.html,Class Bio.Fasta.RecordParser=Bio.Fasta.RecordParser-class.html,Class Bio.GenBank.RecordParser=Bio.GenBank.RecordParser-class.html,Class Bio.Gobase.RecordParser=Bio.Gobase.RecordParser-class.html,Class Bio.IntelliGenetics.RecordParser=Bio.IntelliGenetics.RecordParser-class.html,Class Bio.LocusLink.RecordParser=Bio.LocusLink.RecordParser-class.html,Class Bio.Medline.RecordParser=Bio.Medline.RecordParser-class.html,Class Bio.MetaTool.RecordParser=Bio.MetaTool.RecordParser-class.html,Class Bio.NBRF.RecordParser=Bio.NBRF.RecordParser-class.html,Class Bio.PopGen.FDist.RecordParser=Bio.PopGen.FDist.RecordParser-class.html,Class Bio.PopGen.GenePop.RecordParser=Bio.PopGen.GenePop.RecordParser-class.html,Class Bio.Prosite.Prodoc.RecordParser=Bio.Prosite.Prodoc.RecordParser-class.html,Class Bio.Prosite.RecordParser=Bio.Prosite.RecordParser-class.html,Class Bio.Rebase.RecordParser=Bio.Rebase.RecordParser-class.html,Class Bio.Saf.RecordParser=Bio.Saf.RecordParser-class.html,Class Bio.Sequencing.Ace.RecordParser=Bio.Sequencing.Ace.RecordParser-class.html,Class Bio.Sequencing.Phd.RecordParser=Bio.Sequencing.Phd.RecordParser-class.html,Class Bio.SwissProt.SProt.RecordParser=Bio.SwissProt.SProt.RecordParser-class.html,Class Bio.UniGene.RecordParser=Bio.UniGene.RecordParser-class.html,Class Martel.Parser.RecordParser=Martel.Parser.RecordParser-class.html"><a title="Bio.CDD.RecordParser
Bio.Compass.RecordParser
Bio.ECell.RecordParser
Bio.Enzyme.RecordParser
Bio.Fasta.RecordParser
Bio.GenBank.RecordParser
Bio.Gobase.RecordParser
Bio.IntelliGenetics.RecordParser
Bio.LocusLink.RecordParser
Bio.Medline.RecordParser
Bio.MetaTool.RecordParser
Bio.NBRF.RecordParser
Bio.PopGen.FDist.RecordParser
Bio.PopGen.GenePop.RecordParser
Bio.Prosite.Prodoc.RecordParser
Bio.Prosite.RecordParser
Bio.Rebase.RecordParser
Bio.Saf.RecordParser
Bio.Sequencing.Ace.RecordParser
Bio.Sequencing.Phd.RecordParser
Bio.SwissProt.SProt.RecordParser
Bio.UniGene.RecordParser
Martel.Parser.RecordParser" class="py-name" href="#" onclick="return doclink('link-38', 'RecordParser', 'link-38');">RecordParser</a></tt><tt class="py-op">(</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">iterator</tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Bio.Fasta" class="py-name" href="#" onclick="return doclink('link-39', 'Fasta', 'link-3');">Fasta</a></tt><tt class="py-op">.</tt><tt id="link-40" class="py-name" targets="Class Bio.Blast.NCBIStandalone.Iterator=Bio.Blast.NCBIStandalone.Iterator-class.html,Class Bio.CDD.Iterator=Bio.CDD.Iterator-class.html,Class Bio.Compass.Iterator=Bio.Compass.Iterator-class.html,Class Bio.ECell.Iterator=Bio.ECell.Iterator-class.html,Class Bio.Enzyme.Iterator=Bio.Enzyme.Iterator-class.html,Class Bio.Fasta.Iterator=Bio.Fasta.Iterator-class.html,Class Bio.GenBank.Iterator=Bio.GenBank.Iterator-class.html,Class Bio.Gobase.Iterator=Bio.Gobase.Iterator-class.html,Class Bio.IntelliGenetics.Iterator=Bio.IntelliGenetics.Iterator-class.html,Class Bio.LocusLink.Iterator=Bio.LocusLink.Iterator-class.html,Class Bio.Medline.Iterator=Bio.Medline.Iterator-class.html,Class Bio.MetaTool.Iterator=Bio.MetaTool.Iterator-class.html,Class Bio.NBRF.Iterator=Bio.NBRF.Iterator-class.html,Class Bio.Prosite.Iterator=Bio.Prosite.Iterator-class.html,Class Bio.Prosite.Prodoc.Iterator=Bio.Prosite.Prodoc.Iterator-class.html,Class Bio.Rebase.Iterator=Bio.Rebase.Iterator-class.html,Class Bio.SCOP.Cla.Iterator=Bio.SCOP.Cla.Iterator-class.html,Class Bio.SCOP.Des.Iterator=Bio.SCOP.Des.Iterator-class.html,Class Bio.SCOP.Dom.Iterator=Bio.SCOP.Dom.Iterator-class.html,Class Bio.SCOP.Hie.Iterator=Bio.SCOP.Hie.Iterator-class.html,Class Bio.SCOP.Raf.Iterator=Bio.SCOP.Raf.Iterator-class.html,Class Bio.Saf.Iterator=Bio.Saf.Iterator-class.html,Class Bio.Sequencing.Ace.Iterator=Bio.Sequencing.Ace.Iterator-class.html,Class Bio.Sequencing.Phd.Iterator=Bio.Sequencing.Phd.Iterator-class.html,Class Bio.SwissProt.SProt.Iterator=Bio.SwissProt.SProt.Iterator-class.html,Class Bio.UniGene.Iterator=Bio.UniGene.Iterator-class.html,Module Martel.Iterator=Martel.Iterator-module.html,Class Martel.Iterator.Iterator=Martel.Iterator.Iterator-class.html"><a title="Bio.Blast.NCBIStandalone.Iterator
Bio.CDD.Iterator
Bio.Compass.Iterator
Bio.ECell.Iterator
Bio.Enzyme.Iterator
Bio.Fasta.Iterator
Bio.GenBank.Iterator
Bio.Gobase.Iterator
Bio.IntelliGenetics.Iterator
Bio.LocusLink.Iterator
Bio.Medline.Iterator
Bio.MetaTool.Iterator
Bio.NBRF.Iterator
Bio.Prosite.Iterator
Bio.Prosite.Prodoc.Iterator
Bio.Rebase.Iterator
Bio.SCOP.Cla.Iterator
Bio.SCOP.Des.Iterator
Bio.SCOP.Dom.Iterator
Bio.SCOP.Hie.Iterator
Bio.SCOP.Raf.Iterator
Bio.Saf.Iterator
Bio.Sequencing.Ace.Iterator
Bio.Sequencing.Phd.Iterator
Bio.SwissProt.SProt.Iterator
Bio.UniGene.Iterator
Martel.Iterator
Martel.Iterator.Iterator" class="py-name" href="#" onclick="return doclink('link-40', 'Iterator', 'link-40');">Iterator</a></tt><tt class="py-op">(</tt><tt class="py-name">InputFile</tt><tt class="py-op">,</tt> <tt class="py-name">parser</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">cur_record</tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-41', 'next', 'link-41');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment"># make the codon dictionary local</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt> <tt class="py-op">=</tt> <tt id="link-42" class="py-name"><a title="Bio.SeqUtils.CodonUsage.CodonsDict" class="py-name" href="#" onclick="return doclink('link-42', 'CodonsDict', 'link-4');">CodonsDict</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method Bio.Crystal.Crystal.copy()=Bio.Crystal.Crystal-class.html#copy,Method Bio.GA.Organism.Organism.copy()=Bio.GA.Organism.Organism-class.html#copy,Method Bio.GenBank.NCBIDictionary.copy()=Bio.GenBank.NCBIDictionary-class.html#copy,Method Bio.PDB.Vector'.Vector.copy()=Bio.PDB.Vector%27.Vector-class.html#copy,Method Bio.Prosite.ExPASyDictionary.copy()=Bio.Prosite.ExPASyDictionary-class.html#copy,Method Bio.Prosite.Pattern.PrositeTerm.copy()=Bio.Prosite.Pattern.PrositeTerm-class.html#copy,Method Bio.Prosite.Prodoc.ExPASyDictionary.copy()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#copy,Method Bio.PubMed.Dictionary.copy()=Bio.PubMed.Dictionary-class.html#copy,Method Bio.SwissProt.SProt.ExPASyDictionary.copy()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#copy,Method Martel.Expression.Any.copy()=Martel.Expression.Any-class.html#copy,Method Martel.Expression.AnyEol.copy()=Martel.Expression.AnyEol-class.html#copy,Method Martel.Expression.Assert.copy()=Martel.Expression.Assert-class.html#copy,Method Martel.Expression.AtBeginning.copy()=Martel.Expression.AtBeginning-class.html#copy,Method Martel.Expression.AtEnd.copy()=Martel.Expression.AtEnd-class.html#copy,Method Martel.Expression.Debug.copy()=Martel.Expression.Debug-class.html#copy,Method Martel.Expression.Dot.copy()=Martel.Expression.Dot-class.html#copy,Method Martel.Expression.Expression.copy()=Martel.Expression.Expression-class.html#copy,Method Martel.Expression.ExpressionList.copy()=Martel.Expression.ExpressionList-class.html#copy,Method Martel.Expression.FastFeature.copy()=Martel.Expression.FastFeature-class.html#copy,Method Martel.Expression.Group.copy()=Martel.Expression.Group-class.html#copy,Method Martel.Expression.GroupRef.copy()=Martel.Expression.GroupRef-class.html#copy,Method Martel.Expression.HeaderFooter.copy()=Martel.Expression.HeaderFooter-class.html#copy,Method Martel.Expression.Literal.copy()=Martel.Expression.Literal-class.html#copy,Method Martel.Expression.MaxRepeat.copy()=Martel.Expression.MaxRepeat-class.html#copy,Method Martel.Expression.NullOp.copy()=Martel.Expression.NullOp-class.html#copy,Method Martel.Expression.ParseRecords.copy()=Martel.Expression.ParseRecords-class.html#copy,Method Martel.Expression.PassThrough.copy()=Martel.Expression.PassThrough-class.html#copy,Method Martel.Expression.Str.copy()=Martel.Expression.Str-class.html#copy,Method Martel.IterParser.IterHeaderFooter.copy()=Martel.IterParser.IterHeaderFooter-class.html#copy,Method Martel.IterParser.IterRecords.copy()=Martel.IterParser.IterRecords-class.html#copy,Method Martel.Iterator.IteratorRecords.copy()=Martel.Iterator.IteratorRecords-class.html#copy,Method Martel.Parser.HeaderFooterParser.copy()=Martel.Parser.HeaderFooterParser-class.html#copy,Method Martel.Parser.Parser.copy()=Martel.Parser.Parser-class.html#copy,Method Martel.Parser.RecordParser.copy()=Martel.Parser.RecordParser-class.html#copy"><a title="Bio.Crystal.Crystal.copy
Bio.GA.Organism.Organism.copy
Bio.GenBank.NCBIDictionary.copy
Bio.PDB.Vector'.Vector.copy
Bio.Prosite.ExPASyDictionary.copy
Bio.Prosite.Pattern.PrositeTerm.copy
Bio.Prosite.Prodoc.ExPASyDictionary.copy
Bio.PubMed.Dictionary.copy
Bio.SwissProt.SProt.ExPASyDictionary.copy
Martel.Expression.Any.copy
Martel.Expression.AnyEol.copy
Martel.Expression.Assert.copy
Martel.Expression.AtBeginning.copy
Martel.Expression.AtEnd.copy
Martel.Expression.Debug.copy
Martel.Expression.Dot.copy
Martel.Expression.Expression.copy
Martel.Expression.ExpressionList.copy
Martel.Expression.FastFeature.copy
Martel.Expression.Group.copy
Martel.Expression.GroupRef.copy
Martel.Expression.HeaderFooter.copy
Martel.Expression.Literal.copy
Martel.Expression.MaxRepeat.copy
Martel.Expression.NullOp.copy
Martel.Expression.ParseRecords.copy
Martel.Expression.PassThrough.copy
Martel.Expression.Str.copy
Martel.IterParser.IterHeaderFooter.copy
Martel.IterParser.IterRecords.copy
Martel.Iterator.IteratorRecords.copy
Martel.Parser.HeaderFooterParser.copy
Martel.Parser.Parser.copy
Martel.Parser.RecordParser.copy" class="py-name" href="#" onclick="return doclink('link-43', 'copy', 'link-43');">copy</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-comment"># iterate over sequence and count all the codons in the FastaFile.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">cur_record</tt><tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment"># make sure the sequence is lower case</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-44', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">.</tt><tt class="py-name">islower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-name">DNAsequence</tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-45', 'sequence', 'link-44');">sequence</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-name">DNAsequence</tt> <tt class="py-op">=</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-46', 'sequence', 'link-44');">sequence</a></tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-47" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-47', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">DNAsequence</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">DNAsequence</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-18');">i</a></tt><tt class="py-op">:</tt><tt id="link-49" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-49', 'i', 'link-18');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-50', 'has_key', 'link-31');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">codon_count</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"illegal codon %s in gene: %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">,</tt> <tt class="py-name">cur_record</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-51', 'title', 'link-51');">title</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">cur_record</tt> <tt class="py-op">=</tt> <tt class="py-name">iterator</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-52', 'next', 'link-41');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-name">InputFile</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.FilteredReader.FilteredReader.close()=Bio.FilteredReader.FilteredReader-class.html#close,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.close()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#close,Method Bio.Mindy.FlatDB.MemoryFlatDB.close()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method Martel.Parser.Parser.close()=Martel.Parser.Parser-class.html#close,Method Martel.Parser.RecordParser.close()=Martel.Parser.RecordParser-class.html#close"><a title="Bio.FilteredReader.FilteredReader.close
Bio.Mindy.BerkeleyDB.BerkeleyDB.close
Bio.Mindy.FlatDB.MemoryFlatDB.close
BioSQL.BioSeqDatabase.Adaptor.close
Martel.Parser.Parser.close
Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-53', 'close', 'link-53');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-comment"># this just gives the index when the objects is printed.</tt> </tt>
<a name="CodonAdaptationIndex.print_index"></a><div id="CodonAdaptationIndex.print_index-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="CodonAdaptationIndex.print_index-toggle" onclick="return toggle('CodonAdaptationIndex.print_index');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#print_index">print_index</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="CodonAdaptationIndex.print_index-collapsed" style="display:none;" pad="+++" indent="++++++++++++"></div><div id="CodonAdaptationIndex.print_index-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">X</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-54', 'index', 'link-6');">index</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-55', 'keys', 'link-13');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">X</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-56', 'sort', 'link-56');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-57', 'i', 'link-18');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">X</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s\t%.3f"</tt> <tt class="py-op">%</tt><tt class="py-op">(</tt><tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-18');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-59', 'index', 'link-6');">index</a></tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-60', 'i', 'link-18');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L146"></a><tt class="py-lineno">146</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 09:27:00 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>
