<?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.Restriction._Update.RestrictionCompiler</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.Restriction-module.html">Package Restriction</a> :: <a href="Bio.Restriction._Update-module.html">Package _Update</a> :: Module RestrictionCompiler </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.Restriction._Update.RestrictionCompiler-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.Restriction._Update.RestrictionCompiler-module.html">Module Bio.Restriction._Update.RestrictionCompiler</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"># Restriction Analysis Libraries.</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"># Copyright (C) 2004. Frederic Sohm.</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">#</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"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</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"># as part of this package.</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">#</tt> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># this script is used to produce the dictionary which will contains the data</tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># about the restriction enzymes from the Emboss/Rebase data files</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># namely</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># emboss_e.### (description of the sites),</tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># emboss_r.### (origin, methylation, references)</tt> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># emboss_s.### (suppliers)</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># where ### is a number of three digits : 1 for the year two for the month</tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># very dirty implementation but it does the job, so...</tt> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Not very quick either but you are not supposed to use it frequently.</tt> </tt> <a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># The results are stored in</tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># path/to/site-packages/Bio/Restriction/Restriction_Dictionary.py</tt> </tt> <a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># the file contains two dictionary :</tt> </tt> <a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'rest_dict' which contains the data for the enzymes</tt> </tt> <a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and</tt> </tt> <a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'suppliers' which map the name of the suppliers to their abbreviation.</tt> </tt> <a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring">"""Convert a serie of Rebase files into a Restriction_Dictionary.py module.</tt> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring">The Rebase files are in the emboss format :</tt> </tt> <a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> emboss_e.### -> contains informations about the restriction sites.</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> emboss_r.### -> contains general informations about the enzymes.</tt> </tt> <a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> emboss_s.### -> contains informations about the suppliers.</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring">### is a 3 digit number. The first digit is the year and the two last the month.</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> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sre</tt> </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">os</tt> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">itertools</tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pprint</tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Method Bio.Sequencing.Phd._RecordConsumer.time()=Bio.Sequencing.Phd._RecordConsumer-class.html#time"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-0', 'time', 'link-0');">time</a></tt> </tt> <a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt> <a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">site</tt> </tt> <a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">shutil</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-1', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-2');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-3', 'Seq', 'link-2');">Seq</a></tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-5', 'Alphabet', 'link-5');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Module Bio.Alphabet.IUPAC=Bio.Alphabet.IUPAC-module.html"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-6', 'IUPAC', 'link-6');">IUPAC</a></tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt> <a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Package Bio.Restriction=Bio.Restriction-module.html,Module Bio.Restriction.Restriction=Bio.Restriction.Restriction-module.html"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-8', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-9', 'Restriction', 'link-8');">Restriction</a></tt> </tt> <a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-10" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-10', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-11', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-12', 'Restriction', 'link-8');">Restriction</a></tt> <tt class="py-keyword">import</tt> <tt id="link-13" class="py-name" targets="Class Bio.Restriction.Restriction.AbstractCut=Bio.Restriction.Restriction.AbstractCut-class.html"><a title="Bio.Restriction.Restriction.AbstractCut" class="py-name" href="#" onclick="return doclink('link-13', 'AbstractCut', 'link-13');">AbstractCut</a></tt><tt class="py-op">,</tt> <tt id="link-14" class="py-name" targets="Class Bio.Restriction.Restriction.RestrictionType=Bio.Restriction.Restriction.RestrictionType-class.html"><a title="Bio.Restriction.Restriction.RestrictionType" class="py-name" href="#" onclick="return doclink('link-14', 'RestrictionType', 'link-14');">RestrictionType</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Class Bio.Restriction.Restriction.NoCut=Bio.Restriction.Restriction.NoCut-class.html"><a title="Bio.Restriction.Restriction.NoCut" class="py-name" href="#" onclick="return doclink('link-15', 'NoCut', 'link-15');">NoCut</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Class Bio.Restriction.Restriction.OneCut=Bio.Restriction.Restriction.OneCut-class.html"><a title="Bio.Restriction.Restriction.OneCut" class="py-name" href="#" onclick="return doclink('link-16', 'OneCut', 'link-16');">OneCut</a></tt><tt class="py-op">,</tt>\ </tt> <a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Class Bio.Restriction.Restriction.TwoCuts=Bio.Restriction.Restriction.TwoCuts-class.html"><a title="Bio.Restriction.Restriction.TwoCuts" class="py-name" href="#" onclick="return doclink('link-17', 'TwoCuts', 'link-17');">TwoCuts</a></tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name" targets="Class Bio.Restriction.Restriction.Meth_Dep=Bio.Restriction.Restriction.Meth_Dep-class.html"><a title="Bio.Restriction.Restriction.Meth_Dep" class="py-name" href="#" onclick="return doclink('link-18', 'Meth_Dep', 'link-18');">Meth_Dep</a></tt><tt class="py-op">,</tt> <tt id="link-19" class="py-name" targets="Class Bio.Restriction.Restriction.Meth_Undep=Bio.Restriction.Restriction.Meth_Undep-class.html"><a title="Bio.Restriction.Restriction.Meth_Undep" class="py-name" href="#" onclick="return doclink('link-19', 'Meth_Undep', 'link-19');">Meth_Undep</a></tt><tt class="py-op">,</tt> <tt id="link-20" class="py-name" targets="Class Bio.Restriction.Restriction.Palindromic=Bio.Restriction.Restriction.Palindromic-class.html"><a title="Bio.Restriction.Restriction.Palindromic" class="py-name" href="#" onclick="return doclink('link-20', 'Palindromic', 'link-20');">Palindromic</a></tt><tt class="py-op">,</tt> <tt id="link-21" class="py-name" targets="Class Bio.Restriction.Restriction.NonPalindromic=Bio.Restriction.Restriction.NonPalindromic-class.html"><a title="Bio.Restriction.Restriction.NonPalindromic" class="py-name" href="#" onclick="return doclink('link-21', 'NonPalindromic', 'link-21');">NonPalindromic</a></tt><tt class="py-op">,</tt> <tt id="link-22" class="py-name" targets="Class Bio.Restriction.Restriction.Unknown=Bio.Restriction.Restriction.Unknown-class.html"><a title="Bio.Restriction.Restriction.Unknown" class="py-name" href="#" onclick="return doclink('link-22', 'Unknown', 'link-22');">Unknown</a></tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name" targets="Class Bio.Restriction.Restriction.Blunt=Bio.Restriction.Restriction.Blunt-class.html"><a title="Bio.Restriction.Restriction.Blunt" class="py-name" href="#" onclick="return doclink('link-23', 'Blunt', 'link-23');">Blunt</a></tt><tt class="py-op">,</tt>\ </tt> <a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt id="link-24" class="py-name" targets="Class Bio.Restriction.Restriction.Ov5=Bio.Restriction.Restriction.Ov5-class.html"><a title="Bio.Restriction.Restriction.Ov5" class="py-name" href="#" onclick="return doclink('link-24', 'Ov5', 'link-24');">Ov5</a></tt><tt class="py-op">,</tt> <tt id="link-25" class="py-name" targets="Class Bio.Restriction.Restriction.Ov3=Bio.Restriction.Restriction.Ov3-class.html"><a title="Bio.Restriction.Restriction.Ov3" class="py-name" href="#" onclick="return doclink('link-25', 'Ov3', 'link-25');">Ov3</a></tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name" targets="Class Bio.Restriction.Restriction.NotDefined=Bio.Restriction.Restriction.NotDefined-class.html"><a title="Bio.Restriction.Restriction.NotDefined" class="py-name" href="#" onclick="return doclink('link-26', 'NotDefined', 'link-26');">NotDefined</a></tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name" targets="Class Bio.Restriction.Restriction.Defined=Bio.Restriction.Restriction.Defined-class.html"><a title="Bio.Restriction.Restriction.Defined" class="py-name" href="#" onclick="return doclink('link-27', 'Defined', 'link-27');">Defined</a></tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name" targets="Class Bio.Restriction.Restriction.Ambiguous=Bio.Restriction.Restriction.Ambiguous-class.html"><a title="Bio.Restriction.Restriction.Ambiguous" class="py-name" href="#" onclick="return doclink('link-28', 'Ambiguous', 'link-28');">Ambiguous</a></tt><tt class="py-op">,</tt> <tt id="link-29" class="py-name" targets="Class Bio.Restriction.Restriction.Commercially_available=Bio.Restriction.Restriction.Commercially_available-class.html"><a title="Bio.Restriction.Restriction.Commercially_available" class="py-name" href="#" onclick="return doclink('link-29', 'Commercially_available', 'link-29');">Commercially_available</a></tt><tt class="py-op">,</tt> <tt id="link-30" class="py-name" targets="Class Bio.Restriction.Restriction.Not_available=Bio.Restriction.Restriction.Not_available-class.html"><a title="Bio.Restriction.Restriction.Not_available" class="py-name" href="#" onclick="return doclink('link-30', 'Not_available', 'link-30');">Not_available</a></tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-31" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-31', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-32', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name" targets="Module Bio.Restriction.RanaConfig=Bio.Restriction.RanaConfig-module.html"><a title="Bio.Restriction.RanaConfig" class="py-name" href="#" onclick="return doclink('link-33', 'RanaConfig', 'link-33');">RanaConfig</a></tt> <tt class="py-keyword">as</tt> <tt id="link-34" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-34', 'config', 'link-34');">config</a></tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-35" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-35', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-36', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Package Bio.Restriction._Update=Bio.Restriction._Update-module.html"><a title="Bio.Restriction._Update" class="py-name" href="#" onclick="return doclink('link-37', '_Update', 'link-37');">_Update</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Class Bio.DocSQL.Update=Bio.DocSQL.Update-class.html,Module Bio.Restriction._Update.Update=Bio.Restriction._Update.Update-module.html"><a title="Bio.DocSQL.Update Bio.Restriction._Update.Update" class="py-name" href="#" onclick="return doclink('link-38', 'Update', 'link-38');">Update</a></tt> <tt class="py-keyword">import</tt> <tt id="link-39" class="py-name" targets="Class Bio.Restriction._Update.Update.RebaseUpdate=Bio.Restriction._Update.Update.RebaseUpdate-class.html"><a title="Bio.Restriction._Update.Update.RebaseUpdate" class="py-name" href="#" onclick="return doclink('link-39', 'RebaseUpdate', 'link-39');">RebaseUpdate</a></tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-40" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-40', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-41', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-42', 'Restriction', 'link-8');">Restriction</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt> <a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-43" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-43', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-44', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt class="py-name">DNAUtils</tt> <tt class="py-keyword">import</tt> <tt class="py-name">antiparallel</tt> </tt> <a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt> <a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt id="link-45" class="py-name" targets="Variable Bio.Restriction.Restriction.DNA=Bio.Restriction.Restriction-module.html#DNA,Variable Bio.Restriction._Update.RestrictionCompiler.DNA=Bio.Restriction._Update.RestrictionCompiler-module.html#DNA"><a title="Bio.Restriction.Restriction.DNA Bio.Restriction._Update.RestrictionCompiler.DNA" class="py-name" href="#" onclick="return doclink('link-45', 'DNA', 'link-45');">DNA</a></tt><tt class="py-op">=</tt><tt id="link-46" class="py-name"><a title="Bio.Seq Bio.Seq.Seq Martel.Expression.Seq Martel.Seq" class="py-name" href="#" onclick="return doclink('link-46', 'Seq', 'link-2');">Seq</a></tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt id="link-47" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.dna_alphabet=Bio.Restriction._Update.RestrictionCompiler-module.html#dna_alphabet"><a title="Bio.Restriction._Update.RestrictionCompiler.dna_alphabet" class="py-name" href="#" onclick="return doclink('link-47', 'dna_alphabet', 'link-47');">dna_alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'A'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'G'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-string">'R'</tt><tt class="py-op">:</tt><tt class="py-string">'AG'</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">:</tt><tt class="py-string">'CT'</tt><tt class="py-op">,</tt> <tt class="py-string">'W'</tt><tt class="py-op">:</tt><tt class="py-string">'AT'</tt><tt class="py-op">,</tt> <tt class="py-string">'S'</tt><tt class="py-op">:</tt><tt class="py-string">'CG'</tt><tt class="py-op">,</tt> <tt class="py-string">'M'</tt><tt class="py-op">:</tt><tt class="py-string">'AC'</tt><tt class="py-op">,</tt> <tt class="py-string">'K'</tt><tt class="py-op">:</tt><tt class="py-string">'GT'</tt><tt class="py-op">,</tt> </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-string">'H'</tt><tt class="py-op">:</tt><tt class="py-string">'ACT'</tt><tt class="py-op">,</tt> <tt class="py-string">'B'</tt><tt class="py-op">:</tt><tt class="py-string">'CGT'</tt><tt class="py-op">,</tt> <tt class="py-string">'V'</tt><tt class="py-op">:</tt><tt class="py-string">'ACG'</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">:</tt><tt class="py-string">'AGT'</tt><tt class="py-op">,</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-string">'N'</tt><tt class="py-op">:</tt><tt class="py-string">'ACGT'</tt><tt class="py-op">,</tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-string">'a'</tt><tt class="py-op">:</tt> <tt class="py-string">'a'</tt><tt class="py-op">,</tt> <tt class="py-string">'c'</tt><tt class="py-op">:</tt> <tt class="py-string">'c'</tt><tt class="py-op">,</tt> <tt class="py-string">'g'</tt><tt class="py-op">:</tt> <tt class="py-string">'g'</tt><tt class="py-op">,</tt> <tt class="py-string">'t'</tt><tt class="py-op">:</tt> <tt class="py-string">'t'</tt><tt class="py-op">,</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-string">'r'</tt><tt class="py-op">:</tt><tt class="py-string">'ag'</tt><tt class="py-op">,</tt> <tt class="py-string">'y'</tt><tt class="py-op">:</tt><tt class="py-string">'ct'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">:</tt><tt class="py-string">'at'</tt><tt class="py-op">,</tt> <tt class="py-string">'s'</tt><tt class="py-op">:</tt><tt class="py-string">'cg'</tt><tt class="py-op">,</tt> <tt class="py-string">'m'</tt><tt class="py-op">:</tt><tt class="py-string">'ac'</tt><tt class="py-op">,</tt> <tt class="py-string">'k'</tt><tt class="py-op">:</tt><tt class="py-string">'gt'</tt><tt class="py-op">,</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-string">'h'</tt><tt class="py-op">:</tt><tt class="py-string">'act'</tt><tt class="py-op">,</tt> <tt class="py-string">'b'</tt><tt class="py-op">:</tt><tt class="py-string">'cgt'</tt><tt class="py-op">,</tt> <tt class="py-string">'v'</tt><tt class="py-op">:</tt><tt class="py-string">'acg'</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">:</tt><tt class="py-string">'agt'</tt><tt class="py-op">,</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-string">'n'</tt><tt class="py-op">:</tt><tt class="py-string">'acgt'</tt><tt class="py-op">}</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt id="link-48" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.complement_alphabet=Bio.Restriction._Update.RestrictionCompiler-module.html#complement_alphabet"><a title="Bio.Restriction._Update.RestrictionCompiler.complement_alphabet" class="py-name" href="#" onclick="return doclink('link-48', 'complement_alphabet', 'link-48');">complement_alphabet</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'A'</tt><tt class="py-op">:</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">:</tt><tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'G'</tt><tt class="py-op">:</tt><tt class="py-string">'C'</tt><tt class="py-op">,</tt><tt class="py-string">'R'</tt><tt class="py-op">:</tt><tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">:</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-string">'W'</tt><tt class="py-op">:</tt><tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'S'</tt><tt class="py-op">:</tt><tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'M'</tt><tt class="py-op">:</tt><tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'K'</tt><tt class="py-op">:</tt><tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'H'</tt><tt class="py-op">:</tt><tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">:</tt><tt class="py-string">'H'</tt><tt class="py-op">,</tt> </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-string">'B'</tt><tt class="py-op">:</tt><tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'V'</tt><tt class="py-op">:</tt><tt class="py-string">'B'</tt><tt class="py-op">,</tt> <tt class="py-string">'N'</tt><tt class="py-op">:</tt><tt class="py-string">'N'</tt><tt class="py-op">,</tt><tt class="py-string">'a'</tt><tt class="py-op">:</tt><tt class="py-string">'t'</tt><tt class="py-op">,</tt> <tt class="py-string">'c'</tt><tt class="py-op">:</tt><tt class="py-string">'g'</tt><tt class="py-op">,</tt> <tt class="py-string">'g'</tt><tt class="py-op">:</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-string">'t'</tt><tt class="py-op">:</tt><tt class="py-string">'a'</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">:</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt> <tt class="py-string">'y'</tt><tt class="py-op">:</tt><tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">:</tt><tt class="py-string">'w'</tt><tt class="py-op">,</tt> <tt class="py-string">'s'</tt><tt class="py-op">:</tt><tt class="py-string">'s'</tt><tt class="py-op">,</tt><tt class="py-string">'m'</tt><tt class="py-op">:</tt><tt class="py-string">'k'</tt><tt class="py-op">,</tt> </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-string">'k'</tt><tt class="py-op">:</tt><tt class="py-string">'m'</tt><tt class="py-op">,</tt> <tt class="py-string">'h'</tt><tt class="py-op">:</tt><tt class="py-string">'d'</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">:</tt><tt class="py-string">'h'</tt><tt class="py-op">,</tt> <tt class="py-string">'b'</tt><tt class="py-op">:</tt><tt class="py-string">'v'</tt><tt class="py-op">,</tt> <tt class="py-string">'v'</tt><tt class="py-op">:</tt><tt class="py-string">'b'</tt><tt class="py-op">,</tt> <tt class="py-string">'n'</tt><tt class="py-op">:</tt><tt class="py-string">'n'</tt><tt class="py-op">}</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt id="link-49" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.enzymedict=Bio.Restriction._Update.RestrictionCompiler-module.html#enzymedict"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-49', 'enzymedict', 'link-49');">enzymedict</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 id="link-50" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.suppliersdict=Bio.Restriction._Update.RestrictionCompiler-module.html#suppliersdict"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-50', 'suppliersdict', 'link-50');">suppliersdict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt id="link-51" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.classdict=Bio.Restriction._Update.RestrictionCompiler-module.html#classdict"><a title="Bio.Restriction._Update.RestrictionCompiler.classdict" class="py-name" href="#" onclick="return doclink('link-51', 'classdict', 'link-51');">classdict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt id="link-52" class="py-name" targets="Variable Bio.Restriction.Restriction_Dictionary.typedict=Bio.Restriction.Restriction_Dictionary-module.html#typedict,Variable Bio.Restriction._Update.RestrictionCompiler.typedict=Bio.Restriction._Update.RestrictionCompiler-module.html#typedict"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-52', 'typedict', 'link-52');">typedict</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> </tt> <a name="OverhangError"></a><div id="OverhangError-def"><a name="L84"></a><tt class="py-lineno"> 84</tt> <a class="py-toggle" href="#" id="OverhangError-toggle" onclick="return toggle('OverhangError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.OverhangError-class.html">OverhangError</a><tt class="py-op">(</tt><tt class="py-base-class">ValueError</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="OverhangError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="OverhangError-expanded"><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-docstring">"""Exception for dealing with overhang."""</tt> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> </div><a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt> <a name="BaseExpand"></a><div id="BaseExpand-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="BaseExpand-toggle" onclick="return toggle('BaseExpand');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler-module.html#BaseExpand">BaseExpand</a><tt class="py-op">(</tt><tt class="py-param">base</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="BaseExpand-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BaseExpand-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""BaseExpand(base) -> string.</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> given a degenerated base, returns its meaning in IUPAC alphabet.</tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> i.e:</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"> b= 'A' -> 'A'</tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> b= 'N' -> 'ACGT'</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> etc..."""</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">base</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="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.dna_alphabet" class="py-name" href="#" onclick="return doclink('link-53', 'dna_alphabet', 'link-47');">dna_alphabet</a></tt><tt class="py-op">[</tt><tt class="py-name">base</tt><tt class="py-op">]</tt> </tt> </div><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt> <a name="regex"></a><div id="regex-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="regex-toggle" onclick="return toggle('regex');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler-module.html#regex">regex</a><tt class="py-op">(</tt><tt class="py-param">site</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="regex-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="regex-expanded"><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-docstring">"""regex(site) -> string.</tt> </tt> <a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Construct a regular expression from a DNA sequence.</tt> </tt> <a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> i.e. :</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> site = 'ABCGN' -> 'A[CGT]CG.'"""</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">reg_ex</tt> <tt class="py-op">=</tt> <tt class="py-name">site</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-name">reg_ex</tt> <tt class="py-op">:</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'a'</tt><tt class="py-op">,</tt> <tt class="py-string">'c'</tt><tt class="py-op">,</tt> <tt class="py-string">'g'</tt><tt class="py-op">,</tt> <tt class="py-string">'t'</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'n'</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">reg_ex</tt> <tt class="py-op">=</tt> <tt class="py-string">'.'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">reg_ex</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-54', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'N'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-name">reg_ex</tt> <tt class="py-op">=</tt> <tt class="py-string">'.'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">reg_ex</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-55', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'n'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'B'</tt><tt class="py-op">,</tt> <tt class="py-string">'V'</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-name">expand</tt> <tt class="py-op">=</tt> <tt class="py-string">'['</tt><tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-56" class="py-name" targets="Function Bio.Restriction._Update.RestrictionCompiler.BaseExpand()=Bio.Restriction._Update.RestrictionCompiler-module.html#BaseExpand"><a title="Bio.Restriction._Update.RestrictionCompiler.BaseExpand" class="py-name" href="#" onclick="return doclink('link-56', 'BaseExpand', 'link-56');">BaseExpand</a></tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-string">']'</tt> </tt> <a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">reg_ex</tt> <tt class="py-op">=</tt> <tt class="py-name">expand</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">reg_ex</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-57', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">base</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-keyword">return</tt> <tt class="py-name">reg_ex</tt> </tt> </div><a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt> <a name="Antiparallel"></a><div id="Antiparallel-def"><a name="L118"></a><tt class="py-lineno">118</tt> <a class="py-toggle" href="#" id="Antiparallel-toggle" onclick="return toggle('Antiparallel');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler-module.html#Antiparallel">Antiparallel</a><tt class="py-op">(</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="Antiparallel-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Antiparallel-expanded"><a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-docstring">"""Antiparallel(sequence) -> string.</tt> </tt> <a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> returns a string which represents the reverse complementary strand of</tt> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> a DNA sequence."""</tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">antiparallel</tt><tt class="py-op">(</tt><tt id="link-58" 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-58', 'sequence', 'link-58');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring Bio.EUtils.POM.ElementNode.tostring Bio.Prosite.Pattern.Prosite.tostring Bio.Seq.MutableSeq.tostring Bio.Seq.Seq.tostring BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-59', 'tostring', 'link-59');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> </div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt> <a name="is_palindrom"></a><div id="is_palindrom-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="is_palindrom-toggle" onclick="return toggle('is_palindrom');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler-module.html#is_palindrom">is_palindrom</a><tt class="py-op">(</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="is_palindrom-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="is_palindrom-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-docstring">"""is_palindrom(sequence) -> bool.</tt> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> True is the sequence is a palindrom.</tt> </tt> <a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> sequence is a DNA object."""</tt> </tt> <a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-60" 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-60', 'sequence', 'link-58');">sequence</a></tt> <tt class="py-op">==</tt> <tt id="link-61" class="py-name"><a title="Bio.Restriction.Restriction.DNA Bio.Restriction._Update.RestrictionCompiler.DNA" class="py-name" href="#" onclick="return doclink('link-61', 'DNA', 'link-45');">DNA</a></tt><tt class="py-op">(</tt><tt id="link-62" class="py-name" targets="Function Bio.Restriction._Update.RestrictionCompiler.Antiparallel()=Bio.Restriction._Update.RestrictionCompiler-module.html#Antiparallel"><a title="Bio.Restriction._Update.RestrictionCompiler.Antiparallel" class="py-name" href="#" onclick="return doclink('link-62', 'Antiparallel', 'link-62');">Antiparallel</a></tt><tt class="py-op">(</tt><tt id="link-63" 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-63', 'sequence', 'link-58');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> </div><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> </tt> <a name="LocalTime"></a><div id="LocalTime-def"><a name="L132"></a><tt class="py-lineno">132</tt> <a class="py-toggle" href="#" id="LocalTime-toggle" onclick="return toggle('LocalTime');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler-module.html#LocalTime">LocalTime</a><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="LocalTime-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="LocalTime-expanded"><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-docstring">"""LocalTime() -> string.</tt> </tt> <a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> LocalTime calculate the extension for emboss file for the current year and</tt> </tt> <a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> month."""</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-64', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt class="py-name">gmtime</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 id="link-65" class="py-name" targets="Method Bio.Medline._RecordConsumer.year()=Bio.Medline._RecordConsumer-class.html#year"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-65', 'year', 'link-65');">year</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">tm_year</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-name">month</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">tm_mon</tt><tt class="py-op">)</tt> </tt> <a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">month</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-op">:</tt> <tt class="py-name">month</tt> <tt class="py-op">=</tt> <tt class="py-string">'0'</tt><tt class="py-op">+</tt><tt class="py-name">month</tt> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-66" class="py-name"><a title="Bio.Medline._RecordConsumer.year" class="py-name" href="#" onclick="return doclink('link-66', 'year', 'link-65');">year</a></tt><tt class="py-op">+</tt><tt class="py-name">month</tt> </tt> </div><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> </tt> <a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> </tt> <a name="newenzyme"></a><div id="newenzyme-def"><a name="L144"></a><tt class="py-lineno">144</tt> <a class="py-toggle" href="#" id="newenzyme-toggle" onclick="return toggle('newenzyme');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html">newenzyme</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="newenzyme-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="newenzyme-expanded"><a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-docstring">"""construct the attributes of the enzyme corresponding to 'name'."""</tt> </tt> <a name="newenzyme.__init__"></a><div id="newenzyme.__init__-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="newenzyme.__init__-toggle" onclick="return toggle('newenzyme.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="newenzyme.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="newenzyme.__init__-expanded"><a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">opt_temp</tt> <tt class="py-op">=</tt> <tt class="py-number">37</tt> </tt> <a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">inact_temp</tt> <tt class="py-op">=</tt> <tt class="py-number">65</tt> </tt> <a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">substrat</tt> <tt class="py-op">=</tt> <tt class="py-string">'DNA'</tt> </tt> <a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">target</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-67', 'enzymedict', 'link-49');">enzymedict</a></tt><tt class="py-op">[</tt><tt id="link-68" 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-68', 'name', 'link-68');">name</a></tt><tt class="py-op">]</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">site</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.Affy.CelFile.CelRecord.size()=Bio.Affy.CelFile.CelRecord-class.html#size,Variable Bio.Alphabet.Alphabet.size=Bio.Alphabet.Alphabet-class.html#size,Variable Bio.Alphabet.Reduced.HPModel.size=Bio.Alphabet.Reduced.HPModel-class.html#size,Variable Bio.Alphabet.Reduced.Murphy10.size=Bio.Alphabet.Reduced.Murphy10-class.html#size,Variable Bio.Alphabet.Reduced.Murphy15.size=Bio.Alphabet.Reduced.Murphy15-class.html#size,Variable Bio.Alphabet.Reduced.Murphy4.size=Bio.Alphabet.Reduced.Murphy4-class.html#size,Variable Bio.Alphabet.Reduced.Murphy8.size=Bio.Alphabet.Reduced.Murphy8-class.html#size,Variable Bio.Alphabet.Reduced.PC5.size=Bio.Alphabet.Reduced.PC5-class.html#size,Variable Bio.Alphabet.SingleLetterAlphabet.size=Bio.Alphabet.SingleLetterAlphabet-class.html#size,Variable Bio.Alphabet.ThreeLetterProtein.size=Bio.Alphabet.ThreeLetterProtein-class.html#size,Method Bio.GenBank._FeatureConsumer.size()=Bio.GenBank._FeatureConsumer-class.html#size,Method Bio.GenBank._RecordConsumer.size()=Bio.GenBank._RecordConsumer-class.html#size,Variable Bio.expressions.genbank.size=Bio.expressions.genbank-module.html#size"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-69', 'size', 'link-69');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">suppl</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">freq</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">11</tt><tt class="py-op">]</tt> </tt> <a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">13</tt><tt class="py-op">]</tt> </tt> <a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">14</tt><tt class="py-op">]</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Is the site palindromic?</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Important for the way the DNA is search for the site.</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Palindromic sites needs to be looked for only over 1 strand.</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Non Palindromic needs to be search for on the reverse complement</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># as well.</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">10</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Palindromic'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt> <a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'NonPalindromic'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Number of cut the enzyme produce.</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 0 => unknown, the enzyme has not been fully characterised.</tt> </tt> <a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 2 => 1 cut, (because one cut is realised by cutting 2 strands</tt> </tt> <a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 4 => 2 cuts, same logic.</tt> </tt> <a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># A little bit confusing but it is the way EMBOSS/Rebase works.</tt> </tt> <a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># => undefined enzymes, nothing to be done.</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'NoCut'</tt><tt class="py-op">,</tt><tt class="py-string">'Unknown'</tt><tt class="py-op">,</tt> <tt class="py-string">'NotDefined'</tt><tt class="py-op">)</tt> </tt> <a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst3</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd5</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd3</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we will need to calculate the overhang.</tt> </tt> <a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt> <tt class="py-op">:</tt> </tt> <a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'OneCut'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt> <a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst3</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt> <a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd5</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd3</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'TwoCuts'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt> <a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst3</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd5</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd3</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> </tt> <a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now, prepare the overhangs which will be added to the DNA </tt> </tt> <a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># after the cut.</tt> </tt> <a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Undefined enzymes will not be allowed to catalyse,</tt> </tt> <a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># they are not available commercially anyway.</tt> </tt> <a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># I assumed that if an enzyme cut twice the overhang will be of</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the same kind. The only exception is HaeIV. I do not deal</tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># with that at the moment (ie I don't include it,</tt> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># need to be fixed).</tt> </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># They generally cut outside their recognition site and</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># therefore the overhang is undetermined and dependent of</tt> </tt> <a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the DNA sequence upon which the enzyme act.</tt> </tt> <a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">target</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="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># rebase field for blunt: blunt == 1, other == 0.</tt> </tt> <a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The enzyme is blunt. No overhang.</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Blunt'</tt><tt class="py-op">,</tt> <tt class="py-string">'Defined'</tt><tt class="py-op">)</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># => overhang is sequence dependent</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt> <a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' overhang, ambiguous site (outside recognition site</tt> </tt> <a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># or site containing ambiguous bases (N, W, R,...)</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Ov3'</tt><tt class="py-op">,</tt> <tt class="py-string">'Ambiguous'</tt><tt class="py-op">)</tt> </tt> <a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt> <a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' overhang, ambiguous site (outside recognition site</tt> </tt> <a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># or site containing ambiguous bases (N, W, R,...)</tt> </tt> <a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Ov5'</tt><tt class="py-op">,</tt> <tt class="py-string">'Ambiguous'</tt><tt class="py-op">)</tt> </tt> <a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># cls.ovhg is a string => overhang is constant</tt> </tt> <a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst3</tt> <tt class="py-op">+</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-70', 'size', 'link-69');">size</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt> <a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Ov5'</tt><tt class="py-op">,</tt> <tt class="py-string">'Defined'</tt><tt class="py-op">)</tt> </tt> <a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt><tt class="py-op">)</tt> </tt> <a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Ov3'</tt><tt class="py-op">,</tt> <tt class="py-string">'Defined'</tt><tt class="py-op">)</tt> </tt> <a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt> <tt class="py-op">=</tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">ovhg</tt><tt class="py-op">)</tt> </tt> <a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Next class : sensibility to methylation.</tt> </tt> <a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Set by EmbossMixer from emboss_r.txt file</tt> </tt> <a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Not really methylation dependent at the moment, stands rather for</tt> </tt> <a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 'is the site methylable?'.</tt> </tt> <a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Proper methylation sensibility has yet to be implemented.</tt> </tt> <a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># But the class is there for further development.</tt> </tt> <a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Meth_Dep'</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt> </tt> <a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">compsite</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">12</tt><tt class="py-op">]</tt> </tt> <a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Meth_Undep'</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt> <a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">compsite</tt> <tt class="py-op">=</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">12</tt><tt class="py-op">]</tt> </tt> <a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Next class will allow to select enzymes in function of their</tt> </tt> <a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># suppliers. Not essential but can be useful.</tt> </tt> <a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">suppl</tt> <tt class="py-op">:</tt> </tt> <a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Commercially_available'</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt> </tt> <a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'Not_available'</tt><tt class="py-op">,</tt> <tt class="py-op">)</tt> </tt> <a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> <tt class="py-op">+=</tt> <tt class="py-op">(</tt><tt class="py-string">'AbstractCut'</tt><tt class="py-op">,</tt> <tt class="py-string">'RestrictionType'</tt><tt class="py-op">)</tt> </tt> <a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-71', 'name', 'link-68');">name</a></tt> </tt> <a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">__bases__</tt> <tt class="py-op">=</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> </tt> <a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">charac</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst5</tt><tt class="py-op">,</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">fst3</tt><tt class="py-op">,</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd5</tt><tt class="py-op">,</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">scd3</tt><tt class="py-op">,</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">site</tt><tt class="py-op">)</tt> </tt> <a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">target</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">and</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">suppl</tt> <tt class="py-op">:</tt> </tt> <a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">supp</tt> <tt class="py-op">=</tt> <tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-72" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-72', 'suppliersdict', 'link-50');">suppliersdict</a></tt><tt class="py-op">[</tt><tt id="link-73" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-73', 's', 'link-73');">s</a></tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-74" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-74', 's', 'link-73');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">suppl</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'WARNING : It seems that %s is both commercially available\</tt> </tt> <a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-string"> \n\tand its characteristics are unknown. \</tt> </tt> <a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-string"> \n\tThis seems counter-intuitive.\</tt> </tt> <a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-string"> \n\tThere is certainly an error either in ranacompiler or\</tt> </tt> <a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-string"> \n\tin this REBASE release.\</tt> </tt> <a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-string"> \n\tThe supplier is : %s.'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-75" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-75', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">supp</tt><tt class="py-op">)</tt> </tt> <a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div></div><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt> <a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt> <a name="TypeCompiler"></a><div id="TypeCompiler-def"><a name="L286"></a><tt class="py-lineno">286</tt> <a class="py-toggle" href="#" id="TypeCompiler-toggle" onclick="return toggle('TypeCompiler');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html">TypeCompiler</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="TypeCompiler-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TypeCompiler-expanded"><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt> <a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-docstring">"""Build the different types possible for Restriction Enzymes"""</tt> </tt> <a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt> <a name="TypeCompiler.__init__"></a><div id="TypeCompiler.__init__-def"><a name="L290"></a><tt class="py-lineno">290</tt> <a class="py-toggle" href="#" id="TypeCompiler.__init__-toggle" onclick="return toggle('TypeCompiler.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-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="TypeCompiler.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TypeCompiler.__init__-expanded"><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-docstring">"""TypeCompiler() -> new TypeCompiler instance."""</tt> </tt> <a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> </div><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt> <a name="TypeCompiler.buildtype"></a><div id="TypeCompiler.buildtype-def"><a name="L294"></a><tt class="py-lineno">294</tt> <a class="py-toggle" href="#" id="TypeCompiler.buildtype-toggle" onclick="return toggle('TypeCompiler.buildtype');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html#buildtype">buildtype</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="TypeCompiler.buildtype-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="TypeCompiler.buildtype-expanded"><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-docstring">"""TC.buildtype() -> generator.</tt> </tt> <a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> build the new types that will be needed for constructing the</tt> </tt> <a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> restriction enzymes."""</tt> </tt> <a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-name">baT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.Restriction.Restriction.AbstractCut" class="py-name" href="#" onclick="return doclink('link-76', 'AbstractCut', 'link-13');">AbstractCut</a></tt><tt class="py-op">,</tt> <tt id="link-77" class="py-name"><a title="Bio.Restriction.Restriction.RestrictionType" class="py-name" href="#" onclick="return doclink('link-77', 'RestrictionType', 'link-14');">RestrictionType</a></tt><tt class="py-op">)</tt> </tt> <a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-name">cuT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-78" class="py-name"><a title="Bio.Restriction.Restriction.NoCut" class="py-name" href="#" onclick="return doclink('link-78', 'NoCut', 'link-15');">NoCut</a></tt><tt class="py-op">,</tt> <tt id="link-79" class="py-name"><a title="Bio.Restriction.Restriction.OneCut" class="py-name" href="#" onclick="return doclink('link-79', 'OneCut', 'link-16');">OneCut</a></tt><tt class="py-op">,</tt> <tt id="link-80" class="py-name"><a title="Bio.Restriction.Restriction.TwoCuts" class="py-name" href="#" onclick="return doclink('link-80', 'TwoCuts', 'link-17');">TwoCuts</a></tt><tt class="py-op">)</tt> </tt> <a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-name">meT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-81" class="py-name"><a title="Bio.Restriction.Restriction.Meth_Dep" class="py-name" href="#" onclick="return doclink('link-81', 'Meth_Dep', 'link-18');">Meth_Dep</a></tt><tt class="py-op">,</tt> <tt id="link-82" class="py-name"><a title="Bio.Restriction.Restriction.Meth_Undep" class="py-name" href="#" onclick="return doclink('link-82', 'Meth_Undep', 'link-19');">Meth_Undep</a></tt><tt class="py-op">)</tt> </tt> <a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-name">paT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.Restriction.Restriction.Palindromic" class="py-name" href="#" onclick="return doclink('link-83', 'Palindromic', 'link-20');">Palindromic</a></tt><tt class="py-op">,</tt> <tt id="link-84" class="py-name"><a title="Bio.Restriction.Restriction.NonPalindromic" class="py-name" href="#" onclick="return doclink('link-84', 'NonPalindromic', 'link-21');">NonPalindromic</a></tt><tt class="py-op">)</tt> </tt> <a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">ovT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-85" class="py-name"><a title="Bio.Restriction.Restriction.Unknown" class="py-name" href="#" onclick="return doclink('link-85', 'Unknown', 'link-22');">Unknown</a></tt><tt class="py-op">,</tt> <tt id="link-86" class="py-name"><a title="Bio.Restriction.Restriction.Blunt" class="py-name" href="#" onclick="return doclink('link-86', 'Blunt', 'link-23');">Blunt</a></tt><tt class="py-op">,</tt> <tt id="link-87" class="py-name"><a title="Bio.Restriction.Restriction.Ov5" class="py-name" href="#" onclick="return doclink('link-87', 'Ov5', 'link-24');">Ov5</a></tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name"><a title="Bio.Restriction.Restriction.Ov3" class="py-name" href="#" onclick="return doclink('link-88', 'Ov3', 'link-25');">Ov3</a></tt><tt class="py-op">)</tt> </tt> <a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">deT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-89" class="py-name"><a title="Bio.Restriction.Restriction.NotDefined" class="py-name" href="#" onclick="return doclink('link-89', 'NotDefined', 'link-26');">NotDefined</a></tt><tt class="py-op">,</tt> <tt id="link-90" class="py-name"><a title="Bio.Restriction.Restriction.Defined" class="py-name" href="#" onclick="return doclink('link-90', 'Defined', 'link-27');">Defined</a></tt><tt class="py-op">,</tt> <tt id="link-91" class="py-name"><a title="Bio.Restriction.Restriction.Ambiguous" class="py-name" href="#" onclick="return doclink('link-91', 'Ambiguous', 'link-28');">Ambiguous</a></tt><tt class="py-op">)</tt> </tt> <a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">coT</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-92" class="py-name"><a title="Bio.Restriction.Restriction.Commercially_available" class="py-name" href="#" onclick="return doclink('link-92', 'Commercially_available', 'link-29');">Commercially_available</a></tt><tt class="py-op">,</tt> <tt id="link-93" class="py-name"><a title="Bio.Restriction.Restriction.Not_available" class="py-name" href="#" onclick="return doclink('link-93', 'Not_available', 'link-30');">Not_available</a></tt><tt class="py-op">)</tt> </tt> <a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-name">All</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">baT</tt><tt class="py-op">,</tt> <tt class="py-name">cuT</tt><tt class="py-op">,</tt> <tt class="py-name">meT</tt><tt class="py-op">,</tt> <tt class="py-name">paT</tt><tt class="py-op">,</tt> <tt class="py-name">ovT</tt><tt class="py-op">,</tt> <tt class="py-name">deT</tt><tt class="py-op">,</tt> <tt class="py-name">coT</tt><tt class="py-op">)</tt> </tt> <a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now build the types. Only the most obvious are left out.</tt> </tt> <a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Modified even the most obvious are not so obvious.</tt> </tt> <a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># emboss_*.403 AspCNI is unknown and commercially available.</tt> </tt> <a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># So now do not remove the most obvious.</tt> </tt> <a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">types</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt><tt class="py-name">c</tt><tt class="py-op">,</tt><tt class="py-name">o</tt><tt class="py-op">,</tt><tt id="link-94" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-94', 'd', 'link-94');">d</a></tt><tt class="py-op">,</tt><tt class="py-name">m</tt><tt class="py-op">,</tt><tt class="py-name">co</tt><tt class="py-op">,</tt><tt class="py-name">baT</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">baT</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">paT</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cuT</tt> <tt class="py-keyword">for</tt> <tt class="py-name">o</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ovT</tt> </tt> <a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-95" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-95', 'd', 'link-94');">d</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">deT</tt> <tt class="py-keyword">for</tt> <tt class="py-name">m</tt> <tt class="py-keyword">in</tt> <tt class="py-name">meT</tt> <tt class="py-keyword">for</tt> <tt class="py-name">co</tt> <tt class="py-keyword">in</tt> <tt class="py-name">coT</tt><tt class="py-op">]</tt> </tt> <a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ty</tt> <tt class="py-keyword">in</tt> <tt class="py-name">types</tt> <tt class="py-op">:</tt> </tt> <a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">dct</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ty</tt> <tt class="py-op">:</tt> </tt> <a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">dct</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-96', 'update', 'link-96');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">)</tt> </tt> <a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># here we need to customize the dictionary.</tt> </tt> <a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># i.e. types deriving from OneCut have always scd5 and scd3</tt> </tt> <a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># equal to None. No need therefore to store that in a specific</tt> </tt> <a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># enzyme of this type. but it then need to be in the type.</tt> </tt> <a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'results'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'substrat'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">'DNA'</tt> </tt> <a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'dna'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt id="link-97" class="py-name"><a title="Bio.Restriction.Restriction.NoCut" class="py-name" href="#" onclick="return doclink('link-97', 'NoCut', 'link-15');">NoCut</a></tt> <tt class="py-op">:</tt> </tt> <a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">dct</tt><tt class="py-op">.</tt><tt id="link-98" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-98', 'update', 'link-96');">update</a></tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt class="py-string">'fst5'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">'fst3'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt> <a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-string">'scd5'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">'scd3'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt> <a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-string">'ovhg'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">'ovhgseq'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt> <a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">t</tt> <tt class="py-op">==</tt> <tt id="link-99" class="py-name"><a title="Bio.Restriction.Restriction.OneCut" class="py-name" href="#" onclick="return doclink('link-99', 'OneCut', 'link-16');">OneCut</a></tt> <tt class="py-op">:</tt> </tt> <a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">dct</tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-100', 'update', 'link-96');">update</a></tt><tt class="py-op">(</tt><tt class="py-op">{</tt><tt class="py-string">'scd5'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">'scd3'</tt><tt class="py-op">:</tt><tt class="py-name">None</tt><tt class="py-op">}</tt><tt class="py-op">)</tt> </tt> <a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">class</tt> <tt class="py-def-name">klass</tt><tt class="py-op">(</tt><tt class="py-base-class">type</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">__new__</tt><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-101" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type Bio.GenBank.LocationParser.Symbol.type Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-101', 'type', 'link-101');">type</a></tt><tt class="py-op">.</tt><tt class="py-name">__new__</tt><tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">,</tt> <tt class="py-string">'type%i'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">ty</tt><tt class="py-op">,</tt><tt class="py-name">dct</tt><tt class="py-op">)</tt> </tt> </div><a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">__init__</tt><tt class="py-op">(</tt><tt class="py-param">cls</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-name">super</tt><tt class="py-op">(</tt><tt class="py-name">klass</tt><tt class="py-op">,</tt> <tt class="py-name">cls</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__()=Bio.Blast.NCBIStandalone._PSIBlastConsumer-class.html#__init__,Method Bio.Blast.NCBIWWW.BlastParser.__init__()=Bio.Blast.NCBIWWW.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML.BlastParser.__init__()=Bio.Blast.NCBIXML.BlastParser-class.html#__init__,Method Bio.Blast.NCBIXML._XMLparser.__init__()=Bio.Blast.NCBIXML._XMLparser-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableEntry.__init__()=Bio.Blast.ParseBlastTable.BlastTableEntry-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableReader.__init__()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#__init__,Method Bio.Blast.ParseBlastTable.BlastTableRec.__init__()=Bio.Blast.ParseBlastTable.BlastTableRec-class.html#__init__,Method Bio.Blast.Record.Alignment.__init__()=Bio.Blast.Record.Alignment-class.html#__init__,Method Bio.Blast.Record.Blast.__init__()=Bio.Blast.Record.Blast-class.html#__init__,Method Bio.Blast.Record.DatabaseReport.__init__()=Bio.Blast.Record.DatabaseReport-class.html#__init__,Method Bio.Blast.Record.Description.__init__()=Bio.Blast.Record.Description-class.html#__init__,Method Bio.Blast.Record.HSP.__init__()=Bio.Blast.Record.HSP-class.html#__init__,Method Bio.Blast.Record.Header.__init__()=Bio.Blast.Record.Header-class.html#__init__,Method Bio.Blast.Record.MultipleAlignment.__init__()=Bio.Blast.Record.MultipleAlignment-class.html#__init__,Method Bio.Blast.Record.PSIBlast.__init__()=Bio.Blast.Record.PSIBlast-class.html#__init__,Method Bio.Blast.Record.Parameters.__init__()=Bio.Blast.Record.Parameters-class.html#__init__,Method Bio.Blast.Record.Round.__init__()=Bio.Blast.Record.Round-class.html#__init__,Method Bio.CAPS.CAPSMap.__init__()=Bio.CAPS.CAPSMap-class.html#__init__,Method Bio.CAPS.DifferentialCutsite.__init__()=Bio.CAPS.DifferentialCutsite-class.html#__init__,Method Bio.CDD.Iterator.__init__()=Bio.CDD.Iterator-class.html#__init__,Method Bio.CDD.Record.Record.__init__()=Bio.CDD.Record.Record-class.html#__init__,Method Bio.CDD.RecordParser.__init__()=Bio.CDD.RecordParser-class.html#__init__,Method Bio.CDD._RecordConsumer.__init__()=Bio.CDD._RecordConsumer-class.html#__init__,Method Bio.CDD._Scanner.__init__()=Bio.CDD._Scanner-class.html#__init__,Method Bio.Clustalw.ClustalAlignment.__init__()=Bio.Clustalw.ClustalAlignment-class.html#__init__,Method Bio.Clustalw.MultipleAlignCL.__init__()=Bio.Clustalw.MultipleAlignCL-class.html#__init__,Method Bio.Cluster.DataFile.__init__()=Bio.Cluster.DataFile-class.html#__init__,Method Bio.Cluster.Record.__init__()=Bio.Cluster.Record-class.html#__init__,Method Bio.Compass.Iterator.__init__()=Bio.Compass.Iterator-class.html#__init__,Method Bio.Compass.Record.__init__()=Bio.Compass.Record-class.html#__init__,Method Bio.Compass.RecordParser.__init__()=Bio.Compass.RecordParser-class.html#__init__,Method Bio.Compass._Consumer.__init__()=Bio.Compass._Consumer-class.html#__init__,Method Bio.Crystal.Chain.__init__()=Bio.Crystal.Chain-class.html#__init__,Method Bio.Crystal.Crystal.__init__()=Bio.Crystal.Crystal-class.html#__init__,Method Bio.Crystal.CrystalError.__init__()=Bio.Crystal.CrystalError-class.html#__init__,Method Bio.Crystal.Error.__init__()=Bio.Crystal.Error-class.html#__init__,Method Bio.Crystal.Hetero.__init__()=Bio.Crystal.Hetero-class.html#__init__,Method Bio.DBXRef.DBXRef.__init__()=Bio.DBXRef.DBXRef-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousCodonTable.__init__()=Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__init__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__init__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__init__,Method Bio.Data.CodonTable.CodonTable.__init__()=Bio.Data.CodonTable.CodonTable-class.html#__init__,Method Bio.Data.CodonTable.NCBICodonTable.__init__()=Bio.Data.CodonTable.NCBICodonTable-class.html#__init__,Method Bio.Decode.DecodeParser.__init__()=Bio.Decode.DecodeParser-class.html#__init__,Method Bio.Decode.DecodeScanner.__init__()=Bio.Decode.DecodeScanner-class.html#__init__,Method Bio.Decode.Float.__init__()=Bio.Decode.Float-class.html#__init__,Method Bio.Decode.Function.__init__()=Bio.Decode.Function-class.html#__init__,Method Bio.Decode.FunctionCall.__init__()=Bio.Decode.FunctionCall-class.html#__init__,Method Bio.Decode.FunctionCallChain.__init__()=Bio.Decode.FunctionCallChain-class.html#__init__,Method Bio.Decode.FunctionName.__init__()=Bio.Decode.FunctionName-class.html#__init__,Method Bio.Decode.Integer.__init__()=Bio.Decode.Integer-class.html#__init__,Method Bio.Decode.String.__init__()=Bio.Decode.String-class.html#__init__,Method Bio.Decode.Token.__init__()=Bio.Decode.Token-class.html#__init__,Method Bio.Decode.ValueToken.__init__()=Bio.Decode.ValueToken-class.html#__init__,Method Bio.DocSQL.Create.__init__()=Bio.DocSQL.Create-class.html#__init__,Method Bio.DocSQL.Insert.__init__()=Bio.DocSQL.Insert-class.html#__init__,Method Bio.DocSQL.IterationCursor.__init__()=Bio.DocSQL.IterationCursor-class.html#__init__,Method Bio.DocSQL.Query.__init__()=Bio.DocSQL.Query-class.html#__init__,Method Bio.DocSQL.QueryAll.__init__()=Bio.DocSQL.QueryAll-class.html#__init__,Method Bio.DocSQL.QueryGeneric.__init__()=Bio.DocSQL.QueryGeneric-class.html#__init__,Method Bio.DocSQL.QueryRow.__init__()=Bio.DocSQL.QueryRow-class.html#__init__,Method Bio.DocSQL.QuerySingle.__init__()=Bio.DocSQL.QuerySingle-class.html#__init__,Method Bio.ECell.ECellError.__init__()=Bio.ECell.ECellError-class.html#__init__,Method Bio.ECell.Error.__init__()=Bio.ECell.Error-class.html#__init__,Method Bio.ECell.Iterator.__init__()=Bio.ECell.Iterator-class.html#__init__,Method Bio.ECell.Record.Record.__init__()=Bio.ECell.Record.Record-class.html#__init__,Method Bio.ECell.RecordParser.__init__()=Bio.ECell.RecordParser-class.html#__init__,Method Bio.ECell._RecordConsumer.__init__()=Bio.ECell._RecordConsumer-class.html#__init__,Method Bio.ECell._Scanner.__init__()=Bio.ECell._Scanner-class.html#__init__,Method Bio.EUtils.Config.DatabaseInfo.__init__()=Bio.EUtils.Config.DatabaseInfo-class.html#__init__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsClient.__init__()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#__init__,Method Bio.EUtils.DBIdsClient.DBIdsLookup.__init__()=Bio.EUtils.DBIdsClient.DBIdsLookup-class.html#__init__,Method Bio.EUtils.Datatypes.BinaryOp.__init__()=Bio.EUtils.Datatypes.BinaryOp-class.html#__init__,Method Bio.EUtils.Datatypes.CheckLinkSet.__init__()=Bio.EUtils.Datatypes.CheckLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.DBIds.__init__()=Bio.EUtils.Datatypes.DBIds-class.html#__init__,Method Bio.EUtils.Datatypes.Date.__init__()=Bio.EUtils.Datatypes.Date-class.html#__init__,Method Bio.EUtils.Datatypes.DateRange.__init__()=Bio.EUtils.Datatypes.DateRange-class.html#__init__,Method Bio.EUtils.Datatypes.EUtilsSearchError.__init__()=Bio.EUtils.Datatypes.EUtilsSearchError-class.html#__init__,Method Bio.EUtils.Datatypes.IdCheck.__init__()=Bio.EUtils.Datatypes.IdCheck-class.html#__init__,Method Bio.EUtils.Datatypes.IdUrlSet.__init__()=Bio.EUtils.Datatypes.IdUrlSet-class.html#__init__,Method Bio.EUtils.Datatypes.Link.__init__()=Bio.EUtils.Datatypes.Link-class.html#__init__,Method Bio.EUtils.Datatypes.LinkSetDb.__init__()=Bio.EUtils.Datatypes.LinkSetDb-class.html#__init__,Method Bio.EUtils.Datatypes.LinksLinkSet.__init__()=Bio.EUtils.Datatypes.LinksLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.NeighborLinkSet.__init__()=Bio.EUtils.Datatypes.NeighborLinkSet-class.html#__init__,Method Bio.EUtils.Datatypes.ObjUrl.__init__()=Bio.EUtils.Datatypes.ObjUrl-class.html#__init__,Method Bio.EUtils.Datatypes.PostResult.__init__()=Bio.EUtils.Datatypes.PostResult-class.html#__init__,Method Bio.EUtils.Datatypes.Problem.__init__()=Bio.EUtils.Datatypes.Problem-class.html#__init__,Method Bio.EUtils.Datatypes.Provider.__init__()=Bio.EUtils.Datatypes.Provider-class.html#__init__,Method Bio.EUtils.Datatypes.Range.__init__()=Bio.EUtils.Datatypes.Range-class.html#__init__,Method Bio.EUtils.Datatypes.SearchResult.__init__()=Bio.EUtils.Datatypes.SearchResult-class.html#__init__,Method Bio.EUtils.Datatypes.Summary.__init__()=Bio.EUtils.Datatypes.Summary-class.html#__init__,Method Bio.EUtils.Datatypes.Term.__init__()=Bio.EUtils.Datatypes.Term-class.html#__init__,Method Bio.EUtils.Datatypes.WithinNDays.__init__()=Bio.EUtils.Datatypes.WithinNDays-class.html#__init__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryClient.__init__()=Bio.EUtils.HistoryClient.HistoryClient-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryCookie.__init__()=Bio.EUtils.HistoryClient.HistoryCookie-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryLookup.__init__()=Bio.EUtils.HistoryClient.HistoryLookup-class.html#__init__,Method Bio.EUtils.HistoryClient.HistoryRecord.__init__()=Bio.EUtils.HistoryClient.HistoryRecord-class.html#__init__,Method Bio.EUtils.MultiDict.OrderedMultiDict.__init__()=Bio.EUtils.MultiDict.OrderedMultiDict-class.html#__init__,Method Bio.EUtils.MultiDict.UnorderedMultiDict.__init__()=Bio.EUtils.MultiDict.UnorderedMultiDict-class.html#__init__,Method Bio.EUtils.POM.Comment.__init__()=Bio.EUtils.POM.Comment-class.html#__init__,Method Bio.EUtils.POM.ContentModel.__init__()=Bio.EUtils.POM.ContentModel-class.html#__init__,Method Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__()=Bio.EUtils.POM.DTDConsumerForSourceGeneration-class.html#__init__,Method Bio.EUtils.POM.ElementNode.__init__()=Bio.EUtils.POM.ElementNode-class.html#__init__,Method Bio.EUtils.POM.IndentedText.__init__()=Bio.EUtils.POM.IndentedText-class.html#__init__,Method Bio.EUtils.POM.ObjectParserHandler.__init__()=Bio.EUtils.POM.ObjectParserHandler-class.html#__init__,Method Bio.EUtils.POM.POMDocument.__init__()=Bio.EUtils.POM.POMDocument-class.html#__init__,Method Bio.EUtils.POM.XMLAttribute.__init__()=Bio.EUtils.POM.XMLAttribute-class.html#__init__,Method Bio.EUtils.POM._ContentModelGenerator.__init__()=Bio.EUtils.POM._ContentModelGenerator-class.html#__init__,Method Bio.EUtils.ReseekFile.ReseekFile.__init__()=Bio.EUtils.ReseekFile.ReseekFile-class.html#__init__,Method Bio.EUtils.ThinClient.ThinClient.__init__()=Bio.EUtils.ThinClient.ThinClient-class.html#__init__,Method Bio.EUtils.parse.UsePOMParser.__init__()=Bio.EUtils.parse.UsePOMParser-class.html#__init__,Method Bio.EUtils.sourcegen.ClassHolder.__init__()=Bio.EUtils.sourcegen.ClassHolder-class.html#__init__,Method Bio.EUtils.sourcegen.FunctionHolder.__init__()=Bio.EUtils.sourcegen.FunctionHolder-class.html#__init__,Method Bio.EUtils.sourcegen.MethodHolder.__init__()=Bio.EUtils.sourcegen.MethodHolder-class.html#__init__,Method Bio.EUtils.sourcegen.SourceFile.__init__()=Bio.EUtils.sourcegen.SourceFile-class.html#__init__,Method Bio.EUtils.sourcegen.SourceGen.__init__()=Bio.EUtils.sourcegen.SourceGen-class.html#__init__,Method Bio.Emboss.Applications.EConsenseCommandline.__init__()=Bio.Emboss.Applications.EConsenseCommandline-class.html#__init__,Method Bio.Emboss.Applications.EInvertedCommandline.__init__()=Bio.Emboss.Applications.EInvertedCommandline-class.html#__init__,Method Bio.Emboss.Applications.ENeighborCommandline.__init__()=Bio.Emboss.Applications.ENeighborCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtDistCommandline.__init__()=Bio.Emboss.Applications.EProtDistCommandline-class.html#__init__,Method Bio.Emboss.Applications.EProtParsCommandline.__init__()=Bio.Emboss.Applications.EProtParsCommandline-class.html#__init__,Method Bio.Emboss.Applications.ESeqBootCommandline.__init__()=Bio.Emboss.Applications.ESeqBootCommandline-class.html#__init__,Method Bio.Emboss.Applications.ETandemCommandline.__init__()=Bio.Emboss.Applications.ETandemCommandline-class.html#__init__,Method Bio.Emboss.Applications.Est2GenomeCommandline.__init__()=Bio.Emboss.Applications.Est2GenomeCommandline-class.html#__init__,Method Bio.Emboss.Applications.FuzznucCommandline.__init__()=Bio.Emboss.Applications.FuzznucCommandline-class.html#__init__,Method Bio.Emboss.Applications.PalindromeCommandline.__init__()=Bio.Emboss.Applications.PalindromeCommandline-class.html#__init__,Method Bio.Emboss.Applications.Primer3Commandline.__init__()=Bio.Emboss.Applications.Primer3Commandline-class.html#__init__,Method Bio.Emboss.Applications.PrimerSearchCommandline.__init__()=Bio.Emboss.Applications.PrimerSearchCommandline-class.html#__init__,Method Bio.Emboss.Applications.TranalignCommandline.__init__()=Bio.Emboss.Applications.TranalignCommandline-class.html#__init__,Method Bio.Emboss.Applications.WaterCommandline.__init__()=Bio.Emboss.Applications.WaterCommandline-class.html#__init__,Method Bio.Emboss.Primer.Primer3Parser.__init__()=Bio.Emboss.Primer.Primer3Parser-class.html#__init__,Method Bio.Emboss.Primer.Primer3Primers.__init__()=Bio.Emboss.Primer.Primer3Primers-class.html#__init__,Method Bio.Emboss.Primer.Primer3Record.__init__()=Bio.Emboss.Primer.Primer3Record-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchAmplifier.__init__()=Bio.Emboss.Primer.PrimerSearchAmplifier-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchInputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchInputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__()=Bio.Emboss.Primer.PrimerSearchOutputRecord-class.html#__init__,Method Bio.Emboss.Primer.PrimerSearchParser.__init__()=Bio.Emboss.Primer.PrimerSearchParser-class.html#__init__,Method Bio.Emboss.Primer._Primer3RecordConsumer.__init__()=Bio.Emboss.Primer._Primer3RecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._Primer3Scanner.__init__()=Bio.Emboss.Primer._Primer3Scanner-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__()=Bio.Emboss.Primer._PrimerSearchRecordConsumer-class.html#__init__,Method Bio.Emboss.Primer._PrimerSearchScanner.__init__()=Bio.Emboss.Primer._PrimerSearchScanner-class.html#__init__,Method Bio.Entrez.Parser.DataHandler.__init__()=Bio.Entrez.Parser.DataHandler-class.html#__init__,Method Bio.Entrez.Parser.StructureElement.__init__()=Bio.Entrez.Parser.StructureElement-class.html#__init__,Method Bio.Enzyme.DataRecord.__init__()=Bio.Enzyme.DataRecord-class.html#__init__,Method Bio.Enzyme.EnzymeRecord.__init__()=Bio.Enzyme.EnzymeRecord-class.html#__init__,Method Bio.Enzyme.Iterator.__init__()=Bio.Enzyme.Iterator-class.html#__init__,Method Bio.Enzyme.RecordParser.__init__()=Bio.Enzyme.RecordParser-class.html#__init__,Method Bio.Enzyme._RecordConsumer.__init__()=Bio.Enzyme._RecordConsumer-class.html#__init__,Method Bio.FSSP.FSSPAlignDict.__init__()=Bio.FSSP.FSSPAlignDict-class.html#__init__,Method Bio.FSSP.FSSPAlignRec.__init__()=Bio.FSSP.FSSPAlignRec-class.html#__init__,Method Bio.FSSP.FSSPHeader.__init__()=Bio.FSSP.FSSPHeader-class.html#__init__,Method Bio.FSSP.FSSPSumRec.__init__()=Bio.FSSP.FSSPSumRec-class.html#__init__,Method Bio.FSSP.FSSPTools.FSSPMultAlign.__init__()=Bio.FSSP.FSSPTools.FSSPMultAlign-class.html#__init__,Method Bio.FSSP.PosAlign.__init__()=Bio.FSSP.PosAlign-class.html#__init__,Method Bio.FSSP.fssp_rec.fff_rec.__init__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__init__,Method Bio.Fasta.FastaAlign.FastaAlignment.__init__()=Bio.Fasta.FastaAlign.FastaAlignment-class.html#__init__,Method Bio.Fasta.Iterator.__init__()=Bio.Fasta.Iterator-class.html#__init__,Method Bio.Fasta.Record.__init__()=Bio.Fasta.Record-class.html#__init__,Method Bio.Fasta.RecordParser.__init__()=Bio.Fasta.RecordParser-class.html#__init__,Method Bio.Fasta.SequenceParser.__init__()=Bio.Fasta.SequenceParser-class.html#__init__,Method Bio.File.SGMLHandle.__init__()=Bio.File.SGMLHandle-class.html#__init__,Method Bio.File.SGMLStripper.MyParser.__init__()=Bio.File.SGMLStripper.MyParser-class.html#__init__,Method Bio.File.SGMLStripper.__init__()=Bio.File.SGMLStripper-class.html#__init__,Method Bio.File.UndoHandle.__init__()=Bio.File.UndoHandle-class.html#__init__,Method Bio.FilteredReader.FilteredReader.__init__()=Bio.FilteredReader.FilteredReader-class.html#__init__,Method Bio.GA.Crossover.General.SafeFitnessCrossover.__init__()=Bio.GA.Crossover.General.SafeFitnessCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover-class.html#__init__,Method Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__()=Bio.GA.Crossover.GeneralPoint.InterleaveCrossover-class.html#__init__,Method Bio.GA.Crossover.Point.SinglePointCrossover.__init__()=Bio.GA.Crossover.Point.SinglePointCrossover-class.html#__init__,Method Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__()=Bio.GA.Crossover.TwoPoint.TwoPointCrossover-class.html#__init__,Method Bio.GA.Crossover.Uniform.UniformCrossover.__init__()=Bio.GA.Crossover.Uniform.UniformCrossover-class.html#__init__,Method Bio.GA.Evolver.GenerationEvolver.__init__()=Bio.GA.Evolver.GenerationEvolver-class.html#__init__,Method Bio.GA.Evolver.SteadyStateEvolver.__init__()=Bio.GA.Evolver.SteadyStateEvolver-class.html#__init__,Method Bio.GA.Mutation.General.SafeFitnessMutation.__init__()=Bio.GA.Mutation.General.SafeFitnessMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.ConversionMutation.__init__()=Bio.GA.Mutation.Simple.ConversionMutation-class.html#__init__,Method Bio.GA.Mutation.Simple.SinglePositionMutation.__init__()=Bio.GA.Mutation.Simple.SinglePositionMutation-class.html#__init__,Method Bio.GA.Organism.Organism.__init__()=Bio.GA.Organism.Organism-class.html#__init__,Method Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__()=Bio.GA.Repair.Stabilizing.AmbiguousRepair-class.html#__init__,Method Bio.GA.Selection.Abstract.AbstractSelection.__init__()=Bio.GA.Selection.Abstract.AbstractSelection-class.html#__init__,Method Bio.GA.Selection.Diversity.DiversitySelection.__init__()=Bio.GA.Selection.Diversity.DiversitySelection-class.html#__init__,Method Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__()=Bio.GA.Selection.RouletteWheel.RouletteWheelSelection-class.html#__init__,Method Bio.GA.Selection.Tournament.TournamentSelection.__init__()=Bio.GA.Selection.Tournament.TournamentSelection-class.html#__init__,Method Bio.GFF.Connection.__init__()=Bio.GFF.Connection-class.html#__init__,Method Bio.GFF.Feature.__init__()=Bio.GFF.Feature-class.html#__init__,Method Bio.GFF.FeatureAggregate.__init__()=Bio.GFF.FeatureAggregate-class.html#__init__,Method Bio.GFF.FeatureQuery.__init__()=Bio.GFF.FeatureQuery-class.html#__init__,Method Bio.GFF.FeatureQueryRow.__init__()=Bio.GFF.FeatureQueryRow-class.html#__init__,Method Bio.GFF.GenericTools.ArgsParser.__init__()=Bio.GFF.GenericTools.ArgsParser-class.html#__init__,Method Bio.GFF.GenericTools.Surrogate.__init__()=Bio.GFF.GenericTools.Surrogate-class.html#__init__,Method Bio.GFF.GenericTools.TempFile.__init__()=Bio.GFF.GenericTools.TempFile-class.html#__init__,Method Bio.GFF.RetrieveSeqname.__init__()=Bio.GFF.RetrieveSeqname-class.html#__init__,Method Bio.GFF.Segment.__init__()=Bio.GFF.Segment-class.html#__init__,Method Bio.GFF.easy.FeatureDict.__init__()=Bio.GFF.easy.FeatureDict-class.html#__init__,Method Bio.GFF.easy.Location.__init__()=Bio.GFF.easy.Location-class.html#__init__,Method Bio.GFF.easy.LocationFromCoords.__init__()=Bio.GFF.easy.LocationFromCoords-class.html#__init__,Method Bio.GFF.easy.LocationFromString.__init__()=Bio.GFF.easy.LocationFromString-class.html#__init__,Method Bio.GFF.easy.LocationJoin.__init__()=Bio.GFF.easy.LocationJoin-class.html#__init__,Method Bio.GenBank.FeatureParser.__init__()=Bio.GenBank.FeatureParser-class.html#__init__,Method Bio.GenBank.Iterator.__init__()=Bio.GenBank.Iterator-class.html#__init__,Method Bio.GenBank.LocationParser.AbsoluteLocation.__init__()=Bio.GenBank.LocationParser.AbsoluteLocation-class.html#__init__,Method Bio.GenBank.LocationParser.Between.__init__()=Bio.GenBank.LocationParser.Between-class.html#__init__,Method Bio.GenBank.LocationParser.FeatureName.__init__()=Bio.GenBank.LocationParser.FeatureName-class.html#__init__,Method Bio.GenBank.LocationParser.Function.__init__()=Bio.GenBank.LocationParser.Function-class.html#__init__,Method Bio.GenBank.LocationParser.HighBound.__init__()=Bio.GenBank.LocationParser.HighBound-class.html#__init__,Method Bio.GenBank.LocationParser.Integer.__init__()=Bio.GenBank.LocationParser.Integer-class.html#__init__,Method Bio.GenBank.LocationParser.LocationParser.__init__()=Bio.GenBank.LocationParser.LocationParser-class.html#__init__,Method Bio.GenBank.LocationParser.LocationScanner.__init__()=Bio.GenBank.LocationParser.LocationScanner-class.html#__init__,Method Bio.GenBank.LocationParser.LowBound.__init__()=Bio.GenBank.LocationParser.LowBound-class.html#__init__,Method Bio.GenBank.LocationParser.Path.__init__()=Bio.GenBank.LocationParser.Path-class.html#__init__,Method Bio.GenBank.LocationParser.Range.__init__()=Bio.GenBank.LocationParser.Range-class.html#__init__,Method Bio.GenBank.LocationParser.Symbol.__init__()=Bio.GenBank.LocationParser.Symbol-class.html#__init__,Method Bio.GenBank.LocationParser.Token.__init__()=Bio.GenBank.LocationParser.Token-class.html#__init__,Method Bio.GenBank.LocationParser.TwoBound.__init__()=Bio.GenBank.LocationParser.TwoBound-class.html#__init__,Method Bio.GenBank.NCBIDictionary.__init__()=Bio.GenBank.NCBIDictionary-class.html#__init__,Method Bio.GenBank.Record.Feature.__init__()=Bio.GenBank.Record.Feature-class.html#__init__,Method Bio.GenBank.Record.Qualifier.__init__()=Bio.GenBank.Record.Qualifier-class.html#__init__,Method Bio.GenBank.Record.Record.__init__()=Bio.GenBank.Record.Record-class.html#__init__,Method Bio.GenBank.Record.Reference.__init__()=Bio.GenBank.Record.Reference-class.html#__init__,Method Bio.GenBank.RecordParser.__init__()=Bio.GenBank.RecordParser-class.html#__init__,Method Bio.GenBank.Scanner.InsdcScanner.__init__()=Bio.GenBank.Scanner.InsdcScanner-class.html#__init__,Method Bio.GenBank._BaseGenBankConsumer.__init__()=Bio.GenBank._BaseGenBankConsumer-class.html#__init__,Method Bio.GenBank._FeatureConsumer.__init__()=Bio.GenBank._FeatureConsumer-class.html#__init__,Method Bio.GenBank._RecordConsumer.__init__()=Bio.GenBank._RecordConsumer-class.html#__init__,Method Bio.GenBank.utils.FeatureValueCleaner.__init__()=Bio.GenBank.utils.FeatureValueCleaner-class.html#__init__,Method Bio.Geo.Record.Record.__init__()=Bio.Geo.Record.Record-class.html#__init__,Method Bio.Gobase.Dictionary.__init__()=Bio.Gobase.Dictionary-class.html#__init__,Method Bio.Gobase.GeneRecord.__init__()=Bio.Gobase.GeneRecord-class.html#__init__,Method Bio.Gobase.Iterator.__init__()=Bio.Gobase.Iterator-class.html#__init__,Method Bio.Gobase.ProteinRecord.__init__()=Bio.Gobase.ProteinRecord-class.html#__init__,Method Bio.Gobase.Record.__init__()=Bio.Gobase.Record-class.html#__init__,Method Bio.Gobase.RecordParser.__init__()=Bio.Gobase.RecordParser-class.html#__init__,Method Bio.Gobase.SequenceRecord.__init__()=Bio.Gobase.SequenceRecord-class.html#__init__,Method Bio.Gobase._RecordConsumer.__init__()=Bio.Gobase._RecordConsumer-class.html#__init__,Method Bio.Graphics.BasicChromosome.Chromosome.__init__()=Bio.Graphics.BasicChromosome.Chromosome-class.html#__init__,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome.Organism.__init__()=Bio.Graphics.BasicChromosome.Organism-class.html#__init__,Method Bio.Graphics.BasicChromosome.TelomereSegment.__init__()=Bio.Graphics.BasicChromosome.TelomereSegment-class.html#__init__,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#__init__,Method Bio.Graphics.Comparative.ComparativeScatterPlot.__init__()=Bio.Graphics.Comparative.ComparativeScatterPlot-class.html#__init__,Method Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__()=Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#__init__,Method Bio.Graphics.Distribution.BarChartDistribution.__init__()=Bio.Graphics.Distribution.BarChartDistribution-class.html#__init__,Method Bio.Graphics.Distribution.DistributionPage.__init__()=Bio.Graphics.Distribution.DistributionPage-class.html#__init__,Method Bio.Graphics.Distribution.LineDistribution.__init__()=Bio.Graphics.Distribution.LineDistribution-class.html#__init__,Method Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.AbstractDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.LogDPAlgorithms-class.html#__init__,Method Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__()=Bio.HMM.DynamicProgramming.ScaledDPAlgorithms-class.html#__init__,Method Bio.HMM.MarkovModel.HiddenMarkovModel.__init__()=Bio.HMM.MarkovModel.HiddenMarkovModel-class.html#__init__,Method Bio.HMM.MarkovModel.MarkovModelBuilder.__init__()=Bio.HMM.MarkovModel.MarkovModelBuilder-class.html#__init__,Method Bio.HMM.Trainer.AbstractTrainer.__init__()=Bio.HMM.Trainer.AbstractTrainer-class.html#__init__,Method Bio.HMM.Trainer.BaumWelchTrainer.__init__()=Bio.HMM.Trainer.BaumWelchTrainer-class.html#__init__,Method Bio.HMM.Trainer.KnownStateTrainer.__init__()=Bio.HMM.Trainer.KnownStateTrainer-class.html#__init__,Method Bio.HMM.Trainer.TrainingSequence.__init__()=Bio.HMM.Trainer.TrainingSequence-class.html#__init__,Method Bio.HotRand.HotCache.__init__()=Bio.HotRand.HotCache-class.html#__init__,Method Bio.HotRand.HotRandom.__init__()=Bio.HotRand.HotRandom-class.html#__init__,Method Bio.Index._InMemoryIndex.__init__()=Bio.Index._InMemoryIndex-class.html#__init__,Method Bio.Index._ShelveIndex.__init__()=Bio.Index._ShelveIndex-class.html#__init__,Method Bio.IntelliGenetics.IntelliGeneticsReader.__init__()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#__init__,Method Bio.IntelliGenetics.Iterator.__init__()=Bio.IntelliGenetics.Iterator-class.html#__init__,Method Bio.IntelliGenetics.Record.Record.__init__()=Bio.IntelliGenetics.Record.Record-class.html#__init__,Method Bio.IntelliGenetics.RecordParser.__init__()=Bio.IntelliGenetics.RecordParser-class.html#__init__,Method Bio.IntelliGenetics._RecordConsumer.__init__()=Bio.IntelliGenetics._RecordConsumer-class.html#__init__,Method Bio.IntelliGenetics._Scanner.__init__()=Bio.IntelliGenetics._Scanner-class.html#__init__,Method Bio.KDTree.CKDTree.KDTree.__init__()=Bio.KDTree.CKDTree.KDTree-class.html#__init__,Method Bio.KDTree.CKDTree.KDTreePtr.__init__()=Bio.KDTree.CKDTree.KDTreePtr-class.html#__init__,Method Bio.KDTree.KDTree.KDTree.__init__()=Bio.KDTree.KDTree.KDTree-class.html#__init__,Method Bio.KEGG.Compound.Record.__init__()=Bio.KEGG.Compound.Record-class.html#__init__,Method Bio.KEGG.Enzyme.Record.__init__()=Bio.KEGG.Enzyme.Record-class.html#__init__,Method Bio.LocusLink.Iterator.__init__()=Bio.LocusLink.Iterator-class.html#__init__,Method Bio.LocusLink.Record.__init__()=Bio.LocusLink.Record-class.html#__init__,Method Bio.LocusLink.RecordParser.__init__()=Bio.LocusLink.RecordParser-class.html#__init__,Method Bio.LocusLink._RecordConsumer.__init__()=Bio.LocusLink._RecordConsumer-class.html#__init__,Method Bio.LocusLink._Scanner.__init__()=Bio.LocusLink._Scanner-class.html#__init__,Method Bio.LocusLink.web_parse.Record.__init__()=Bio.LocusLink.web_parse.Record-class.html#__init__,Method Bio.LocusLink.web_parse.Token.__init__()=Bio.LocusLink.web_parse.Token-class.html#__init__,Method Bio.LocusLink.web_parse.Url.__init__()=Bio.LocusLink.web_parse.Url-class.html#__init__,Method Bio.LogisticRegression.LogisticRegression.__init__()=Bio.LogisticRegression.LogisticRegression-class.html#__init__,Method Bio.MEME.Motif.Instance.__init__()=Bio.MEME.Motif.Instance-class.html#__init__,Method Bio.MEME.Motif.MEMEMotif.__init__()=Bio.MEME.Motif.MEMEMotif-class.html#__init__,Method Bio.MEME.Motif.Motif.__init__()=Bio.MEME.Motif.Motif-class.html#__init__,Method Bio.MEME.Parser.MASTParser.__init__()=Bio.MEME.Parser.MASTParser-class.html#__init__,Method Bio.MEME.Parser.MASTRecord.__init__()=Bio.MEME.Parser.MASTRecord-class.html#__init__,Method Bio.MEME.Parser.MEMEParser.__init__()=Bio.MEME.Parser.MEMEParser-class.html#__init__,Method Bio.MEME.Parser.MEMERecord.__init__()=Bio.MEME.Parser.MEMERecord-class.html#__init__,Method Bio.MEME.Parser._MASTConsumer.__init__()=Bio.MEME.Parser._MASTConsumer-class.html#__init__,Method Bio.MEME.Parser._MEMEConsumer.__init__()=Bio.MEME.Parser._MEMEConsumer-class.html#__init__,Method Bio.MarkovModel.MarkovModel.__init__()=Bio.MarkovModel.MarkovModel-class.html#__init__,Method Bio.MaxEntropy.MaxEntropy.__init__()=Bio.MaxEntropy.MaxEntropy-class.html#__init__,Method Bio.Medline.Iterator.__init__()=Bio.Medline.Iterator-class.html#__init__,Method Bio.Medline.Record.__init__()=Bio.Medline.Record-class.html#__init__,Method Bio.Medline.RecordParser.__init__()=Bio.Medline.RecordParser-class.html#__init__,Method Bio.Medline._RecordConsumer.__init__()=Bio.Medline._RecordConsumer-class.html#__init__,Method Bio.MetaTool.Iterator.__init__()=Bio.MetaTool.Iterator-class.html#__init__,Method Bio.MetaTool.Record.Metabolite.__init__()=Bio.MetaTool.Record.Metabolite-class.html#__init__,Method Bio.MetaTool.Record.MetaboliteRole.__init__()=Bio.MetaTool.Record.MetaboliteRole-class.html#__init__,Method Bio.MetaTool.Record.PathwayTransform.__init__()=Bio.MetaTool.Record.PathwayTransform-class.html#__init__,Method Bio.MetaTool.Record.Record.__init__()=Bio.MetaTool.Record.Record-class.html#__init__,Method Bio.MetaTool.RecordParser.__init__()=Bio.MetaTool.RecordParser-class.html#__init__,Method Bio.MetaTool._RecordConsumer.__init__()=Bio.MetaTool._RecordConsumer-class.html#__init__,Method Bio.MetaTool._Scanner.__init__()=Bio.MetaTool._Scanner-class.html#__init__,Method Bio.Mindy.BaseDB.OpenDB.__init__()=Bio.Mindy.BaseDB.OpenDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__init__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.BaseFlatDB.__init__()=Bio.Mindy.FlatDB.BaseFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.BisectFile.__init__()=Bio.Mindy.FlatDB.BisectFile-class.html#__init__,Method Bio.Mindy.FlatDB.DiskFlatDB.__init__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__init__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__init__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.PrimaryTable.__init__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__init__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__init__,Method Bio.Mindy.FlatDB.SecondaryTable.__init__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__init__,Method Bio.Mindy.Location.Location.__init__()=Bio.Mindy.Location.Location-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__()=Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.FunctionIndexer-class.html#__init__,Method Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__()=Bio.Mindy.SimpleSeqRecord.SimpleIndexer-class.html#__init__,Method Bio.Mindy.XPath.GrabXPathNodes.__init__()=Bio.Mindy.XPath.GrabXPathNodes-class.html#__init__,Method Bio.NBRF.Iterator.__init__()=Bio.NBRF.Iterator-class.html#__init__,Method Bio.NBRF.Record.Record.__init__()=Bio.NBRF.Record.Record-class.html#__init__,Method Bio.NBRF.RecordParser.__init__()=Bio.NBRF.RecordParser-class.html#__init__,Method Bio.NBRF._RecordConsumer.__init__()=Bio.NBRF._RecordConsumer-class.html#__init__,Method Bio.NBRF._Scanner.__init__()=Bio.NBRF._Scanner-class.html#__init__,Method Bio.NMR.xpktools.Peaklist.__init__()=Bio.NMR.xpktools.Peaklist-class.html#__init__,Method Bio.NMR.xpktools.XpkEntry.__init__()=Bio.NMR.xpktools.XpkEntry-class.html#__init__,Method Bio.NaiveBayes.NaiveBayes.__init__()=Bio.NaiveBayes.NaiveBayes-class.html#__init__,Method Bio.Ndb.Record.__init__()=Bio.Ndb.Record-class.html#__init__,Method Bio.NetCatch.ExtractUrls.__init__()=Bio.NetCatch.ExtractUrls-class.html#__init__,Method Bio.NetCatch.NetCatch.__init__()=Bio.NetCatch.NetCatch-class.html#__init__,Method Bio.NetCatch.Url.__init__()=Bio.NetCatch.Url-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#__init__,Method Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__()=Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#__init__,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__()=Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__()=Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.Schema.__init__()=Bio.NeuralNetwork.Gene.Schema.Schema-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFactory-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__()=Bio.NeuralNetwork.Gene.Schema.SimpleFinisher-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureCoder-class.html#__init__,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#__init__,Method Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__()=Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop-class.html#__init__,Method Bio.NeuralNetwork.Training.ExampleManager.__init__()=Bio.NeuralNetwork.Training.ExampleManager-class.html#__init__,Method Bio.NeuralNetwork.Training.TrainingExample.__init__()=Bio.NeuralNetwork.Training.TrainingExample-class.html#__init__,Method Bio.Nexus.Nexus.Block.__init__()=Bio.Nexus.Nexus.Block-class.html#__init__,Method Bio.Nexus.Nexus.CharBuffer.__init__()=Bio.Nexus.Nexus.CharBuffer-class.html#__init__,Method Bio.Nexus.Nexus.Commandline.__init__()=Bio.Nexus.Nexus.Commandline-class.html#__init__,Method Bio.Nexus.Nexus.Nexus.__init__()=Bio.Nexus.Nexus.Nexus-class.html#__init__,Method Bio.Nexus.Nexus.StepMatrix.__init__()=Bio.Nexus.Nexus.StepMatrix-class.html#__init__,Method Bio.Nexus.Nodes.Chain.__init__()=Bio.Nexus.Nodes.Chain-class.html#__init__,Method Bio.Nexus.Nodes.Node.__init__()=Bio.Nexus.Nodes.Node-class.html#__init__,Method Bio.Nexus.Trees.NodeData.__init__()=Bio.Nexus.Trees.NodeData-class.html#__init__,Method Bio.Nexus.Trees.Tree.__init__()=Bio.Nexus.Trees.Tree-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__init__,Method Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__()=Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap-class.html#__init__,Method Bio.PDB.Atom.Atom.__init__()=Bio.PDB.Atom.Atom-class.html#__init__,Method Bio.PDB.Atom.DisorderedAtom.__init__()=Bio.PDB.Atom.DisorderedAtom-class.html#__init__,Method Bio.PDB.Chain.Chain.__init__()=Bio.PDB.Chain.Chain-class.html#__init__,Method Bio.PDB.DSSP'.DSSP.__init__()=Bio.PDB.DSSP%27.DSSP-class.html#__init__,Method Bio.PDB.Dice.ChainSelector.__init__()=Bio.PDB.Dice.ChainSelector-class.html#__init__,Method Bio.PDB.Entity.DisorderedEntityWrapper.__init__()=Bio.PDB.Entity.DisorderedEntityWrapper-class.html#__init__,Method Bio.PDB.Entity.Entity.__init__()=Bio.PDB.Entity.Entity-class.html#__init__,Method Bio.PDB.FragmentMapper'.Fragment.__init__()=Bio.PDB.FragmentMapper%27.Fragment-class.html#__init__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__init__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__init__,Method Bio.PDB.HSExposure.ExposureCN.__init__()=Bio.PDB.HSExposure.ExposureCN-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCA.__init__()=Bio.PDB.HSExposure.HSExposureCA-class.html#__init__,Method Bio.PDB.HSExposure.HSExposureCB.__init__()=Bio.PDB.HSExposure.HSExposureCB-class.html#__init__,Method Bio.PDB.HSExposure._AbstractHSExposure.__init__()=Bio.PDB.HSExposure._AbstractHSExposure-class.html#__init__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__init__,Method Bio.PDB.Model.Model.__init__()=Bio.PDB.Model.Model-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS.__init__()=Bio.PDB.NACCESS.NACCESS-class.html#__init__,Method Bio.PDB.NACCESS.NACCESS_atomic.__init__()=Bio.PDB.NACCESS.NACCESS_atomic-class.html#__init__,Method Bio.PDB.NeighborSearch.NeighborSearch.__init__()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#__init__,Method Bio.PDB.PDBIO'.PDBIO.__init__()=Bio.PDB.PDBIO%27.PDBIO-class.html#__init__,Method Bio.PDB.PDBList'.PDBList.__init__()=Bio.PDB.PDBList%27.PDBList-class.html#__init__,Method Bio.PDB.PDBParser'.PDBParser.__init__()=Bio.PDB.PDBParser%27.PDBParser-class.html#__init__,Method Bio.PDB.PSEA.PSEA.__init__()=Bio.PDB.PSEA.PSEA-class.html#__init__,Method Bio.PDB.Polypeptide.CaPPBuilder.__init__()=Bio.PDB.Polypeptide.CaPPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide.PPBuilder.__init__()=Bio.PDB.Polypeptide.PPBuilder-class.html#__init__,Method Bio.PDB.Polypeptide._PPBuilder.__init__()=Bio.PDB.Polypeptide._PPBuilder-class.html#__init__,Method Bio.PDB.Residue.DisorderedResidue.__init__()=Bio.PDB.Residue.DisorderedResidue-class.html#__init__,Method Bio.PDB.Residue.Residue.__init__()=Bio.PDB.Residue.Residue-class.html#__init__,Method Bio.PDB.ResidueDepth'.ResidueDepth.__init__()=Bio.PDB.ResidueDepth%27.ResidueDepth-class.html#__init__,Method Bio.PDB.Structure.Structure.__init__()=Bio.PDB.Structure.Structure-class.html#__init__,Method Bio.PDB.StructureAlignment'.StructureAlignment.__init__()=Bio.PDB.StructureAlignment%27.StructureAlignment-class.html#__init__,Method Bio.PDB.StructureBuilder.StructureBuilder.__init__()=Bio.PDB.StructureBuilder.StructureBuilder-class.html#__init__,Method Bio.PDB.Superimposer'.Superimposer.__init__()=Bio.PDB.Superimposer%27.Superimposer-class.html#__init__,Method Bio.PDB.Vector'.Vector.__init__()=Bio.PDB.Vector%27.Vector-class.html#__init__,Method Bio.ParserSupport.EventGenerator.__init__()=Bio.ParserSupport.EventGenerator-class.html#__init__,Method Bio.ParserSupport.SGMLStrippingConsumer.__init__()=Bio.ParserSupport.SGMLStrippingConsumer-class.html#__init__,Method Bio.ParserSupport.TaggingConsumer.__init__()=Bio.ParserSupport.TaggingConsumer-class.html#__init__,Method Bio.Parsers.spark.GenericASTBuilder.__init__()=Bio.Parsers.spark.GenericASTBuilder-class.html#__init__,Method Bio.Parsers.spark.GenericASTMatcher.__init__()=Bio.Parsers.spark.GenericASTMatcher-class.html#__init__,Method Bio.Parsers.spark.GenericASTTraversal.__init__()=Bio.Parsers.spark.GenericASTTraversal-class.html#__init__,Method Bio.Parsers.spark.GenericParser.__init__()=Bio.Parsers.spark.GenericParser-class.html#__init__,Method Bio.Parsers.spark.GenericScanner.__init__()=Bio.Parsers.spark.GenericScanner-class.html#__init__,Method Bio.Pathway.Network.__init__()=Bio.Pathway.Network-class.html#__init__,Method Bio.Pathway.Reaction.__init__()=Bio.Pathway.Reaction-class.html#__init__,Method Bio.Pathway.Rep.Graph.Graph.__init__()=Bio.Pathway.Rep.Graph.Graph-class.html#__init__,Method Bio.Pathway.Rep.HashSet.HashSet.__init__()=Bio.Pathway.Rep.HashSet.HashSet-class.html#__init__,Method Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__()=Bio.Pathway.Rep.MultiGraph.MultiGraph-class.html#__init__,Method Bio.Pathway.System.__init__()=Bio.Pathway.System-class.html#__init__,Method Bio.PopGen.Async.Async.__init__()=Bio.PopGen.Async.Async-class.html#__init__,Method Bio.PopGen.Async.DirectoryRetriever.__init__()=Bio.PopGen.Async.DirectoryRetriever-class.html#__init__,Method Bio.PopGen.Async.FileRetriever.__init__()=Bio.PopGen.Async.FileRetriever-class.html#__init__,Method Bio.PopGen.Async.Local.Local.__init__()=Bio.PopGen.Async.Local.Local-class.html#__init__,Method Bio.PopGen.FDist.Async.FDistAsync.__init__()=Bio.PopGen.FDist.Async.FDistAsync-class.html#__init__,Method Bio.PopGen.FDist.Async.SplitFDist.__init__()=Bio.PopGen.FDist.Async.SplitFDist-class.html#__init__,Method Bio.PopGen.FDist.Controller.FDistController.__init__()=Bio.PopGen.FDist.Controller.FDistController-class.html#__init__,Method Bio.PopGen.FDist.Record.__init__()=Bio.PopGen.FDist.Record-class.html#__init__,Method Bio.PopGen.FDist.RecordParser.__init__()=Bio.PopGen.FDist.RecordParser-class.html#__init__,Method Bio.PopGen.FDist._RecordConsumer.__init__()=Bio.PopGen.FDist._RecordConsumer-class.html#__init__,Method Bio.PopGen.GenePop.Record.__init__()=Bio.PopGen.GenePop.Record-class.html#__init__,Method Bio.PopGen.GenePop.RecordParser.__init__()=Bio.PopGen.GenePop.RecordParser-class.html#__init__,Method Bio.PopGen.GenePop._RecordConsumer.__init__()=Bio.PopGen.GenePop._RecordConsumer-class.html#__init__,Method Bio.PopGen.SimCoal.Async.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Async.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__()=Bio.PopGen.SimCoal.Cache.SimCoalCache-class.html#__init__,Method Bio.PopGen.SimCoal.Controller.SimCoalController.__init__()=Bio.PopGen.SimCoal.Controller.SimCoalController-class.html#__init__,Method Bio.PropertyManager.PropertyManager.__init__()=Bio.PropertyManager.PropertyManager-class.html#__init__,Method Bio.Prosite.Dictionary.__init__()=Bio.Prosite.Dictionary-class.html#__init__,Method Bio.Prosite.ExPASyDictionary.__init__()=Bio.Prosite.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Iterator.__init__()=Bio.Prosite.Iterator-class.html#__init__,Method Bio.Prosite.Pattern.Prosite.__init__()=Bio.Prosite.Pattern.Prosite-class.html#__init__,Method Bio.Prosite.Pattern.PrositeMatch.__init__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__init__,Method Bio.Prosite.Pattern.PrositeTerm.__init__()=Bio.Prosite.Pattern.PrositeTerm-class.html#__init__,Method Bio.Prosite.PatternHit.__init__()=Bio.Prosite.PatternHit-class.html#__init__,Method Bio.Prosite.Prodoc.Dictionary.__init__()=Bio.Prosite.Prodoc.Dictionary-class.html#__init__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__init__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__init__,Method Bio.Prosite.Prodoc.Iterator.__init__()=Bio.Prosite.Prodoc.Iterator-class.html#__init__,Method Bio.Prosite.Prodoc.Record.__init__()=Bio.Prosite.Prodoc.Record-class.html#__init__,Method Bio.Prosite.Prodoc.RecordParser.__init__()=Bio.Prosite.Prodoc.RecordParser-class.html#__init__,Method Bio.Prosite.Prodoc.Reference.__init__()=Bio.Prosite.Prodoc.Reference-class.html#__init__,Method Bio.Prosite.Prodoc._RecordConsumer.__init__()=Bio.Prosite.Prodoc._RecordConsumer-class.html#__init__,Method Bio.Prosite.Record.__init__()=Bio.Prosite.Record-class.html#__init__,Method Bio.Prosite.RecordParser.__init__()=Bio.Prosite.RecordParser-class.html#__init__,Method Bio.Prosite._RecordConsumer.__init__()=Bio.Prosite._RecordConsumer-class.html#__init__,Method Bio.PubMed.Dictionary.__init__()=Bio.PubMed.Dictionary-class.html#__init__,Method Bio.Rebase.Dictionary.__init__()=Bio.Rebase.Dictionary-class.html#__init__,Method Bio.Rebase.Iterator.__init__()=Bio.Rebase.Iterator-class.html#__init__,Method Bio.Rebase.Record.__init__()=Bio.Rebase.Record-class.html#__init__,Method Bio.Rebase.RecordParser.__init__()=Bio.Rebase.RecordParser-class.html#__init__,Method Bio.Rebase._RecordConsumer.__init__()=Bio.Rebase._RecordConsumer-class.html#__init__,Method Bio.Restriction.PrintFormat.PrintFormat.__init__()=Bio.Restriction.PrintFormat.PrintFormat-class.html#__init__,Method Bio.Restriction.Restriction.Analysis.__init__()=Bio.Restriction.Restriction.Analysis-class.html#__init__,Method Bio.Restriction.Restriction.FormattedSeq.__init__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionBatch.__init__()=Bio.Restriction.Restriction.RestrictionBatch-class.html#__init__,Method Bio.Restriction.Restriction.RestrictionType.__init__()=Bio.Restriction.Restriction.RestrictionType-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__()=Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html#__init__,Method Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__()=Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html#__init__,Method Bio.Restriction._Update.Update.ConnectionError.__init__()=Bio.Restriction._Update.Update.ConnectionError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpNameError.__init__()=Bio.Restriction._Update.Update.FtpNameError-class.html#__init__,Method Bio.Restriction._Update.Update.FtpPasswordError.__init__()=Bio.Restriction._Update.Update.FtpPasswordError-class.html#__init__,Method Bio.Restriction._Update.Update.RebaseUpdate.__init__()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#__init__,Method Bio.SCOP.Astral.__init__()=Bio.SCOP.Astral-class.html#__init__,Method Bio.SCOP.Cla.Index.__init__()=Bio.SCOP.Cla.Index-class.html#__init__,Method Bio.SCOP.Cla.Iterator.__init__()=Bio.SCOP.Cla.Iterator-class.html#__init__,Method Bio.SCOP.Cla.Parser.__init__()=Bio.SCOP.Cla.Parser-class.html#__init__,Method Bio.SCOP.Cla.Record.__init__()=Bio.SCOP.Cla.Record-class.html#__init__,Method Bio.SCOP.Des.Iterator.__init__()=Bio.SCOP.Des.Iterator-class.html#__init__,Method Bio.SCOP.Des.Parser.__init__()=Bio.SCOP.Des.Parser-class.html#__init__,Method Bio.SCOP.Des.Record.__init__()=Bio.SCOP.Des.Record-class.html#__init__,Method Bio.SCOP.Dom.Iterator.__init__()=Bio.SCOP.Dom.Iterator-class.html#__init__,Method Bio.SCOP.Dom.Record.__init__()=Bio.SCOP.Dom.Record-class.html#__init__,Method Bio.SCOP.Domain.__init__()=Bio.SCOP.Domain-class.html#__init__,Method Bio.SCOP.FileIndex.FileIndex.__init__()=Bio.SCOP.FileIndex.FileIndex-class.html#__init__,Method Bio.SCOP.FileIndex.defaultdict.__init__()=Bio.SCOP.FileIndex.defaultdict-class.html#__init__,Method Bio.SCOP.Hie.Iterator.__init__()=Bio.SCOP.Hie.Iterator-class.html#__init__,Method Bio.SCOP.Hie.Parser.__init__()=Bio.SCOP.Hie.Parser-class.html#__init__,Method Bio.SCOP.Hie.Record.__init__()=Bio.SCOP.Hie.Record-class.html#__init__,Method Bio.SCOP.Node.__init__()=Bio.SCOP.Node-class.html#__init__,Method Bio.SCOP.Raf.Iterator.__init__()=Bio.SCOP.Raf.Iterator-class.html#__init__,Method Bio.SCOP.Raf.Parser.__init__()=Bio.SCOP.Raf.Parser-class.html#__init__,Method Bio.SCOP.Raf.Res.__init__()=Bio.SCOP.Raf.Res-class.html#__init__,Method Bio.SCOP.Raf.SeqMap.__init__()=Bio.SCOP.Raf.SeqMap-class.html#__init__,Method Bio.SCOP.Raf.SeqMapIndex.__init__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__init__,Method Bio.SCOP.Residues'.Residues.__init__()=Bio.SCOP.Residues%27.Residues-class.html#__init__,Method Bio.SCOP.Scop.__init__()=Bio.SCOP.Scop-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__()=Bio.SGMLExtractor.SGMLExtractor.LocalParser-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractor.__init__()=Bio.SGMLExtractor.SGMLExtractor-class.html#__init__,Method Bio.SGMLExtractor.SGMLExtractorHandle.__init__()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#__init__,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#__init__,Method Bio.Saf.Iterator.__init__()=Bio.Saf.Iterator-class.html#__init__,Method Bio.Saf.Record.Record.__init__()=Bio.Saf.Record.Record-class.html#__init__,Method Bio.Saf.RecordParser.__init__()=Bio.Saf.RecordParser-class.html#__init__,Method Bio.Saf._RecordConsumer.__init__()=Bio.Saf._RecordConsumer-class.html#__init__,Method Bio.Saf._Scanner.__init__()=Bio.Saf._Scanner-class.html#__init__,Method Bio.Search.Algorithm.__init__()=Bio.Search.Algorithm-class.html#__init__,Method Bio.Search.Database.__init__()=Bio.Search.Database-class.html#__init__,Method Bio.Search.HSP.__init__()=Bio.Search.HSP-class.html#__init__,Method Bio.Search.HSPSeq.__init__()=Bio.Search.HSPSeq-class.html#__init__,Method Bio.Search.Hit.__init__()=Bio.Search.Hit-class.html#__init__,Method Bio.Search.HomologySeq.__init__()=Bio.Search.HomologySeq-class.html#__init__,Method Bio.Search.Query.__init__()=Bio.Search.Query-class.html#__init__,Method Bio.Search.Search.__init__()=Bio.Search.Search-class.html#__init__,Method Bio.Search.TableInfo.__init__()=Bio.Search.TableInfo-class.html#__init__,Method Bio.Search._SeqLength.__init__()=Bio.Search._SeqLength-class.html#__init__,Method Bio.Seq.MutableSeq.__init__()=Bio.Seq.MutableSeq-class.html#__init__,Method Bio.Seq.Seq.__init__()=Bio.Seq.Seq-class.html#__init__,Method Bio.SeqFeature.AbstractPosition.__init__()=Bio.SeqFeature.AbstractPosition-class.html#__init__,Method Bio.SeqFeature.AfterPosition.__init__()=Bio.SeqFeature.AfterPosition-class.html#__init__,Method Bio.SeqFeature.BeforePosition.__init__()=Bio.SeqFeature.BeforePosition-class.html#__init__,Method Bio.SeqFeature.BetweenPosition.__init__()=Bio.SeqFeature.BetweenPosition-class.html#__init__,Method Bio.SeqFeature.ExactPosition.__init__()=Bio.SeqFeature.ExactPosition-class.html#__init__,Method Bio.SeqFeature.FeatureLocation.__init__()=Bio.SeqFeature.FeatureLocation-class.html#__init__,Method Bio.SeqFeature.OneOfPosition.__init__()=Bio.SeqFeature.OneOfPosition-class.html#__init__,Method Bio.SeqFeature.PositionGap.__init__()=Bio.SeqFeature.PositionGap-class.html#__init__,Method Bio.SeqFeature.Reference.__init__()=Bio.SeqFeature.Reference-class.html#__init__,Method Bio.SeqFeature.SeqFeature.__init__()=Bio.SeqFeature.SeqFeature-class.html#__init__,Method Bio.SeqFeature.WithinPosition.__init__()=Bio.SeqFeature.WithinPosition-class.html#__init__,Method Bio.SeqIO.ClustalIO.ClustalWriter.__init__()=Bio.SeqIO.ClustalIO.ClustalWriter-class.html#__init__,Method Bio.SeqIO.FastaIO.FastaWriter.__init__()=Bio.SeqIO.FastaIO.FastaWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceIterator.__init__()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#__init__,Method Bio.SeqIO.Interfaces.SequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequenceWriter-class.html#__init__,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#__init__,Method Bio.SeqIO.PhylipIO.PhylipWriter.__init__()=Bio.SeqIO.PhylipIO.PhylipWriter-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__init__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__init__,Method Bio.SeqIO.StockholmIO.StockholmWriter.__init__()=Bio.SeqIO.StockholmIO.StockholmWriter-class.html#__init__,Method Bio.SeqRecord.SeqRecord.__init__()=Bio.SeqRecord.SeqRecord-class.html#__init__,Method Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__()=Bio.SeqUtils.CodonUsage.CodonAdaptationIndex-class.html#__init__,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#__init__,Method Bio.SeqUtils.MissingTable.__init__()=Bio.SeqUtils.MissingTable-class.html#__init__,Method Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__()=Bio.SeqUtils.ProtParam.ProteinAnalysis-class.html#__init__,Method Bio.Sequencing.Ace.ACEFileRecord.__init__()=Bio.Sequencing.Ace.ACEFileRecord-class.html#__init__,Method Bio.Sequencing.Ace.ACEParser.__init__()=Bio.Sequencing.Ace.ACEParser-class.html#__init__,Method Bio.Sequencing.Ace.Contig.__init__()=Bio.Sequencing.Ace.Contig-class.html#__init__,Method Bio.Sequencing.Ace.Iterator.__init__()=Bio.Sequencing.Ace.Iterator-class.html#__init__,Method Bio.Sequencing.Ace.Reads.__init__()=Bio.Sequencing.Ace.Reads-class.html#__init__,Method Bio.Sequencing.Ace.RecordParser.__init__()=Bio.Sequencing.Ace.RecordParser-class.html#__init__,Method Bio.Sequencing.Ace._RecordConsumer.__init__()=Bio.Sequencing.Ace._RecordConsumer-class.html#__init__,Method Bio.Sequencing.Ace.af.__init__()=Bio.Sequencing.Ace.af-class.html#__init__,Method Bio.Sequencing.Ace.bs.__init__()=Bio.Sequencing.Ace.bs-class.html#__init__,Method Bio.Sequencing.Ace.ct.__init__()=Bio.Sequencing.Ace.ct-class.html#__init__,Method Bio.Sequencing.Ace.ds.__init__()=Bio.Sequencing.Ace.ds-class.html#__init__,Method Bio.Sequencing.Ace.qa.__init__()=Bio.Sequencing.Ace.qa-class.html#__init__,Method Bio.Sequencing.Ace.rd.__init__()=Bio.Sequencing.Ace.rd-class.html#__init__,Method Bio.Sequencing.Ace.rt.__init__()=Bio.Sequencing.Ace.rt-class.html#__init__,Method Bio.Sequencing.Ace.wa.__init__()=Bio.Sequencing.Ace.wa-class.html#__init__,Method Bio.Sequencing.Ace.wr.__init__()=Bio.Sequencing.Ace.wr-class.html#__init__,Method Bio.Sequencing.Phd.Iterator.__init__()=Bio.Sequencing.Phd.Iterator-class.html#__init__,Method Bio.Sequencing.Phd.Record.__init__()=Bio.Sequencing.Phd.Record-class.html#__init__,Method Bio.Sequencing.Phd.RecordParser.__init__()=Bio.Sequencing.Phd.RecordParser-class.html#__init__,Method Bio.Sequencing.Phd._RecordConsumer.__init__()=Bio.Sequencing.Phd._RecordConsumer-class.html#__init__,Method Bio.Std.StdTerm.__init__()=Bio.Std.StdTerm-class.html#__init__,Method Bio.StdHandler.ConvertDispatchHandler.__init__()=Bio.StdHandler.ConvertDispatchHandler-class.html#__init__,Method Bio.StdHandler.ConvertHandler.__init__()=Bio.StdHandler.ConvertHandler-class.html#__init__,Method Bio.StdHandler.Feature.__init__()=Bio.StdHandler.Feature-class.html#__init__,Method Bio.StdHandler.Handle_dbxref.__init__()=Bio.StdHandler.Handle_dbxref-class.html#__init__,Method Bio.StdHandler.Handle_feature_location.__init__()=Bio.StdHandler.Handle_feature_location-class.html#__init__,Method Bio.StdHandler.Handle_feature_qualifier.__init__()=Bio.StdHandler.Handle_feature_qualifier-class.html#__init__,Method Bio.StdHandler.Handle_features.__init__()=Bio.StdHandler.Handle_features-class.html#__init__,Method Bio.StdHandler.Handle_hsp.__init__()=Bio.StdHandler.Handle_hsp-class.html#__init__,Method Bio.StdHandler.RecognizeHandler.__init__()=Bio.StdHandler.RecognizeHandler-class.html#__init__,Method Bio.SubsMat.FreqTable.FreqTable.__init__()=Bio.SubsMat.FreqTable.FreqTable-class.html#__init__,Method Bio.SubsMat.SeqMat.__init__()=Bio.SubsMat.SeqMat-class.html#__init__,Method Bio.SwissProt.KeyWList.ListParser.__init__()=Bio.SwissProt.KeyWList.ListParser-class.html#__init__,Method Bio.SwissProt.KeyWList.Record.__init__()=Bio.SwissProt.KeyWList.Record-class.html#__init__,Method Bio.SwissProt.KeyWList._ListConsumer.__init__()=Bio.SwissProt.KeyWList._ListConsumer-class.html#__init__,Method Bio.SwissProt.KeyWList._Scanner.__init__()=Bio.SwissProt.KeyWList._Scanner-class.html#__init__,Method Bio.SwissProt.SProt.Dictionary.__init__()=Bio.SwissProt.SProt.Dictionary-class.html#__init__,Method Bio.SwissProt.SProt.ExPASyDictionary.__init__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__init__,Method Bio.SwissProt.SProt.Iterator.__init__()=Bio.SwissProt.SProt.Iterator-class.html#__init__,Method Bio.SwissProt.SProt.Record.__init__()=Bio.SwissProt.SProt.Record-class.html#__init__,Method Bio.SwissProt.SProt.RecordParser.__init__()=Bio.SwissProt.SProt.RecordParser-class.html#__init__,Method Bio.SwissProt.SProt.Reference.__init__()=Bio.SwissProt.SProt.Reference-class.html#__init__,Method Bio.SwissProt.SProt.SequenceParser.__init__()=Bio.SwissProt.SProt.SequenceParser-class.html#__init__,Method Bio.SwissProt.SProt._RecordConsumer.__init__()=Bio.SwissProt.SProt._RecordConsumer-class.html#__init__,Method Bio.SwissProt.SProt._SequenceConsumer.__init__()=Bio.SwissProt.SProt._SequenceConsumer-class.html#__init__,Method Bio.Transcribe.Transcribe.__init__()=Bio.Transcribe.Transcribe-class.html#__init__,Method Bio.Translate.Translator.__init__()=Bio.Translate.Translator-class.html#__init__,Method Bio.UniGene.Iterator.__init__()=Bio.UniGene.Iterator-class.html#__init__,Method Bio.UniGene.RecordParser.__init__()=Bio.UniGene.RecordParser-class.html#__init__,Method Bio.UniGene.UnigeneProtsimRecord.__init__()=Bio.UniGene.UnigeneProtsimRecord-class.html#__init__,Method Bio.UniGene.UnigeneRecord.__init__()=Bio.UniGene.UnigeneRecord-class.html#__init__,Method Bio.UniGene.UnigeneSTSRecord.__init__()=Bio.UniGene.UnigeneSTSRecord-class.html#__init__,Method Bio.UniGene.UnigeneSequenceRecord.__init__()=Bio.UniGene.UnigeneSequenceRecord-class.html#__init__,Method Bio.UniGene._RecordConsumer.__init__()=Bio.UniGene._RecordConsumer-class.html#__init__,Method Bio.WWW.RequestLimiter.__init__()=Bio.WWW.RequestLimiter-class.html#__init__,Method Bio.Wise.dnal.Statistics.__init__()=Bio.Wise.dnal.Statistics-class.html#__init__,Method Bio.Wise.psw.AlignmentColumn.__init__()=Bio.Wise.psw.AlignmentColumn-class.html#__init__,Method Bio.Wise.psw.ColumnUnit.__init__()=Bio.Wise.psw.ColumnUnit-class.html#__init__,Method Bio.Writer.Writer.__init__()=Bio.Writer.Writer-class.html#__init__,Method Bio.biblio.Biblio.__init__()=Bio.biblio.Biblio-class.html#__init__,Method Bio.biblio.BiblioCollection.__init__()=Bio.biblio.BiblioCollection-class.html#__init__,Method Bio.builders.Search.search.BuildSearch.__init__()=Bio.builders.Search.search.BuildSearch-class.html#__init__,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#__init__,Method Bio.config.DBRegistry.BioCorbaDB.__init__()=Bio.config.DBRegistry.BioCorbaDB-class.html#__init__,Method Bio.config.DBRegistry.BioSQLDB.__init__()=Bio.config.DBRegistry.BioSQLDB-class.html#__init__,Method Bio.config.DBRegistry.CGIDB.__init__()=Bio.config.DBRegistry.CGIDB-class.html#__init__,Method Bio.config.DBRegistry.DBGroup.__init__()=Bio.config.DBRegistry.DBGroup-class.html#__init__,Method Bio.config.DBRegistry.DBObject.__init__()=Bio.config.DBRegistry.DBObject-class.html#__init__,Method Bio.config.DBRegistry.DBRegistry.__init__()=Bio.config.DBRegistry.DBRegistry-class.html#__init__,Method Bio.config.DBRegistry.EUtilsDB.__init__()=Bio.config.DBRegistry.EUtilsDB-class.html#__init__,Method Bio.config.DBRegistry.IndexedFileDB.__init__()=Bio.config.DBRegistry.IndexedFileDB-class.html#__init__,Method Bio.config.FormatRegistry.FormatGroup.__init__()=Bio.config.FormatRegistry.FormatGroup-class.html#__init__,Method Bio.config.FormatRegistry.FormatObject.__init__()=Bio.config.FormatRegistry.FormatObject-class.html#__init__,Method Bio.config.FormatRegistry.FormatRegistry.__init__()=Bio.config.FormatRegistry.FormatRegistry-class.html#__init__,Method Bio.config.Registry.RegisterableGroup.__init__()=Bio.config.Registry.RegisterableGroup-class.html#__init__,Method Bio.config.Registry.RegisterableObject.__init__()=Bio.config.Registry.RegisterableObject-class.html#__init__,Method Bio.config.Registry.Registry.__init__()=Bio.config.Registry.Registry-class.html#__init__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__init__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__init__,Method Bio.config._stanzaformat.Stanza.__init__()=Bio.config._stanzaformat.Stanza-class.html#__init__,Method Bio.config._stanzaformat.StanzaFormat.__init__()=Bio.config._stanzaformat.StanzaFormat-class.html#__init__,Method Bio.config._support.make_cached_expression.__init__()=Bio.config._support.make_cached_expression-class.html#__init__,Method Bio.config._support.make_rate_limited_function.__init__()=Bio.config._support.make_rate_limited_function-class.html#__init__,Method Bio.kNN.kNN.__init__()=Bio.kNN.kNN-class.html#__init__,Method Bio.pairwise2.affine_penalty.__init__()=Bio.pairwise2.affine_penalty-class.html#__init__,Method Bio.pairwise2.dictionary_match.__init__()=Bio.pairwise2.dictionary_match-class.html#__init__,Method Bio.pairwise2.identity_match.__init__()=Bio.pairwise2.identity_match-class.html#__init__,Method Bio.writers.SeqRecord.embl.WriteEmbl.__init__()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#__init__,Method Bio.writers.SeqRecord.fasta.WriteFasta.__init__()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#__init__,Method BioSQL.BioSeq.DBSeq.__init__()=BioSQL.BioSeq.DBSeq-class.html#__init__,Method BioSQL.BioSeq.DBSeqRecord.__init__()=BioSQL.BioSeq.DBSeqRecord-class.html#__init__,Method BioSQL.BioSeqDatabase.Adaptor.__init__()=BioSQL.BioSeqDatabase.Adaptor-class.html#__init__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__init__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__init__,Method BioSQL.BioSeqDatabase.DBServer.__init__()=BioSQL.BioSeqDatabase.DBServer-class.html#__init__,Method BioSQL.DBUtils.Generic_dbutils.__init__()=BioSQL.DBUtils.Generic_dbutils-class.html#__init__,Method BioSQL.Loader.DatabaseLoader.__init__()=BioSQL.Loader.DatabaseLoader-class.html#__init__,Method BioSQL.Loader.DatabaseRemover.__init__()=BioSQL.Loader.DatabaseRemover-class.html#__init__,Method Martel.Dispatch.Callback.__init__()=Martel.Dispatch.Callback-class.html#__init__,Method Martel.Dispatch.DispatchHandler.__init__()=Martel.Dispatch.DispatchHandler-class.html#__init__,Method Martel.Dispatch.Dispatcher.__init__()=Martel.Dispatch.Dispatcher-class.html#__init__,Method Martel.Dispatch.Multicall.__init__()=Martel.Dispatch.Multicall-class.html#__init__,Method Martel.Dispatch.RemapEnd.__init__()=Martel.Dispatch.RemapEnd-class.html#__init__,Method Martel.Dispatch.RemapStart.__init__()=Martel.Dispatch.RemapStart-class.html#__init__,Method Martel.Expression.Alt.__init__()=Martel.Expression.Alt-class.html#__init__,Method Martel.Expression.Any.__init__()=Martel.Expression.Any-class.html#__init__,Method Martel.Expression.Assert.__init__()=Martel.Expression.Assert-class.html#__init__,Method Martel.Expression.Debug.__init__()=Martel.Expression.Debug-class.html#__init__,Method Martel.Expression.FastFeature.__init__()=Martel.Expression.FastFeature-class.html#__init__,Method Martel.Expression.Group.__init__()=Martel.Expression.Group-class.html#__init__,Method Martel.Expression.GroupRef.__init__()=Martel.Expression.GroupRef-class.html#__init__,Method Martel.Expression.HeaderFooter.__init__()=Martel.Expression.HeaderFooter-class.html#__init__,Method Martel.Expression.Literal.__init__()=Martel.Expression.Literal-class.html#__init__,Method Martel.Expression.MaxRepeat.__init__()=Martel.Expression.MaxRepeat-class.html#__init__,Method Martel.Expression.NullOp.__init__()=Martel.Expression.NullOp-class.html#__init__,Method Martel.Expression.ParseRecords.__init__()=Martel.Expression.ParseRecords-class.html#__init__,Method Martel.Expression.PassThrough.__init__()=Martel.Expression.PassThrough-class.html#__init__,Method Martel.Expression.Seq.__init__()=Martel.Expression.Seq-class.html#__init__,Method Martel.Expression.Str.__init__()=Martel.Expression.Str-class.html#__init__,Method Martel.Generate.CheckAssert.__init__()=Martel.Generate.CheckAssert-class.html#__init__,Method Martel.Generate.CheckAssertNot.__init__()=Martel.Generate.CheckAssertNot-class.html#__init__,Method Martel.Generate.CheckGroupRef.__init__()=Martel.Generate.CheckGroupRef-class.html#__init__,Method Martel.Generate.GeneratorState.__init__()=Martel.Generate.GeneratorState-class.html#__init__,Method Martel.Generate.HandleRepeatCount.__init__()=Martel.Generate.HandleRepeatCount-class.html#__init__,Method Martel.Generate.SetGroupValue.__init__()=Martel.Generate.SetGroupValue-class.html#__init__,Method Martel.Generate._call_call.__init__()=Martel.Generate._call_call-class.html#__init__,Method Martel.Generate._call_calltag.__init__()=Martel.Generate._call_calltag-class.html#__init__,Method Martel.Generate.print_debug.__init__()=Martel.Generate.print_debug-class.html#__init__,Method Martel.Generate.print_info.__init__()=Martel.Generate.print_info-class.html#__init__,Method Martel.IterParser.IterHeaderFooter.__init__()=Martel.IterParser.IterHeaderFooter-class.html#__init__,Method Martel.IterParser.IterRecords.__init__()=Martel.IterParser.IterRecords-class.html#__init__,Method Martel.Iterator.EventStream.__init__()=Martel.Iterator.EventStream-class.html#__init__,Method Martel.Iterator.HeaderFooterEventStream.__init__()=Martel.Iterator.HeaderFooterEventStream-class.html#__init__,Method Martel.Iterator.Iterate.__init__()=Martel.Iterator.Iterate-class.html#__init__,Method Martel.Iterator.Iterator.__init__()=Martel.Iterator.Iterator-class.html#__init__,Method Martel.Iterator.IteratorHeaderFooter.__init__()=Martel.Iterator.IteratorHeaderFooter-class.html#__init__,Method Martel.Iterator.IteratorRecords.__init__()=Martel.Iterator.IteratorRecords-class.html#__init__,Method Martel.Iterator.RecordEventStream.__init__()=Martel.Iterator.RecordEventStream-class.html#__init__,Method Martel.Iterator.StoreEvents.__init__()=Martel.Iterator.StoreEvents-class.html#__init__,Method Martel.LAX.ElementInfo.__init__()=Martel.LAX.ElementInfo-class.html#__init__,Method Martel.LAX.LAX.__init__()=Martel.LAX.LAX-class.html#__init__,Method Martel.Parser.HeaderFooterParser.__init__()=Martel.Parser.HeaderFooterParser-class.html#__init__,Method Martel.Parser.Parser.__init__()=Martel.Parser.Parser-class.html#__init__,Method Martel.Parser.ParserIncompleteException.__init__()=Martel.Parser.ParserIncompleteException-class.html#__init__,Method Martel.Parser.ParserPositionException.__init__()=Martel.Parser.ParserPositionException-class.html#__init__,Method Martel.Parser.RecordParser.__init__()=Martel.Parser.RecordParser-class.html#__init__,Method Martel.RecordReader.CountLines.__init__()=Martel.RecordReader.CountLines-class.html#__init__,Method Martel.RecordReader.EndsWith.__init__()=Martel.RecordReader.EndsWith-class.html#__init__,Method Martel.RecordReader.Everything.__init__()=Martel.RecordReader.Everything-class.html#__init__,Method Martel.RecordReader.Nothing.__init__()=Martel.RecordReader.Nothing-class.html#__init__,Method Martel.RecordReader.RecordReader.__init__()=Martel.RecordReader.RecordReader-class.html#__init__,Method Martel.RecordReader.StartsWith.__init__()=Martel.RecordReader.StartsWith-class.html#__init__,Method Martel.RecordReader.Until.__init__()=Martel.RecordReader.Until-class.html#__init__,Method Martel.convert_re.GroupNames.__init__()=Martel.convert_re.GroupNames-class.html#__init__,Method Martel.msre_parse.Pattern.__init__()=Martel.msre_parse.Pattern-class.html#__init__,Method Martel.msre_parse.SubPattern.__init__()=Martel.msre_parse.SubPattern-class.html#__init__,Method Martel.msre_parse.Tokenizer.__init__()=Martel.msre_parse.Tokenizer-class.html#__init__,Method Martel.test.support.CheckGood.__init__()=Martel.test.support.CheckGood-class.html#__init__,Method Martel.test.support.Dump.__init__()=Martel.test.support.Dump-class.html#__init__,Method Martel.test.support.Storage.__init__()=Martel.test.support.Storage-class.html#__init__,Method Martel.test.test_Parser.CountErrors.__init__()=Martel.test.test_Parser.CountErrors-class.html#__init__,Method Martel.test.test_Parser.CountRecords.__init__()=Martel.test.test_Parser.CountRecords-class.html#__init__,Method Martel.test.test_delimiter.CatchFields.__init__()=Martel.test.test_delimiter.CatchFields-class.html#__init__,Method Martel.test.test_optimize.GetErrorPos.__init__()=Martel.test.test_optimize.GetErrorPos-class.html#__init__"><a title="Bio.Affy.CelFile.CelConsumer.__init__ Bio.Affy.CelFile.CelParser.__init__ Bio.Affy.CelFile.CelRecord.__init__ Bio.Ais.Immune.__init__ Bio.Ais.Lymphocyte.__init__ Bio.Align.AlignInfo.PSSM.__init__ Bio.Align.AlignInfo.SummaryInfo.__init__ Bio.Align.FormatConvert.FormatConverter.__init__ Bio.Align.Generic.Alignment.__init__ Bio.AlignAce.Applications.AlignAceCommandline.__init__ Bio.AlignAce.Applications.CompareAceCommandline.__init__ Bio.AlignAce.Motif.Motif.__init__ Bio.AlignAce.Parser.AlignAceConsumer.__init__ Bio.AlignAce.Parser.AlignAceParser.__init__ Bio.AlignAce.Parser.CompareAceConsumer.__init__ Bio.AlignAce.Parser.CompareAceParser.__init__ Bio.AlignIO.Interfaces.AlignmentIterator.__init__ Bio.AlignIO.Interfaces.AlignmentWriter.__init__ Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__ Bio.Alphabet.AlphabetEncoder.__init__ Bio.Alphabet.Gapped.__init__ Bio.Alphabet.HasStopCodon.__init__ Bio.Application.AbstractCommandline.__init__ Bio.Application.ApplicationResult.__init__ Bio.Application._AbstractParameter.__init__ Bio.Blast.Applications.BlastallCommandline.__init__ Bio.Blast.Applications.FastacmdCommandline.__init__ Bio.Blast.NCBIStandalone.BlastErrorParser.__init__ Bio.Blast.NCBIStandalone.BlastParser.__init__ Bio.Blast.NCBIStandalone.Iterator.__init__ Bio.Blast.NCBIStandalone.PSIBlastParser.__init__ Bio.Blast.NCBIStandalone._BlastConsumer.__init__ Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__ Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__ Bio.Blast.NCBIWWW.BlastParser.__init__ Bio.Blast.NCBIXML.BlastParser.__init__ Bio.Blast.NCBIXML._XMLparser.__init__ Bio.Blast.ParseBlastTable.BlastTableEntry.__init__ Bio.Blast.ParseBlastTable.BlastTableReader.__init__ Bio.Blast.ParseBlastTable.BlastTableRec.__init__ Bio.Blast.Record.Alignment.__init__ Bio.Blast.Record.Blast.__init__ Bio.Blast.Record.DatabaseReport.__init__ Bio.Blast.Record.Description.__init__ Bio.Blast.Record.HSP.__init__ Bio.Blast.Record.Header.__init__ Bio.Blast.Record.MultipleAlignment.__init__ Bio.Blast.Record.PSIBlast.__init__ Bio.Blast.Record.Parameters.__init__ Bio.Blast.Record.Round.__init__ Bio.CAPS.CAPSMap.__init__ Bio.CAPS.DifferentialCutsite.__init__ Bio.CDD.Iterator.__init__ Bio.CDD.Record.Record.__init__ Bio.CDD.RecordParser.__init__ Bio.CDD._RecordConsumer.__init__ Bio.CDD._Scanner.__init__ Bio.Clustalw.ClustalAlignment.__init__ Bio.Clustalw.MultipleAlignCL.__init__ Bio.Cluster.DataFile.__init__ Bio.Cluster.Record.__init__ Bio.Compass.Iterator.__init__ Bio.Compass.Record.__init__ Bio.Compass.RecordParser.__init__ Bio.Compass._Consumer.__init__ Bio.Crystal.Chain.__init__ Bio.Crystal.Crystal.__init__ Bio.Crystal.CrystalError.__init__ Bio.Crystal.Error.__init__ Bio.Crystal.Hetero.__init__ Bio.DBXRef.DBXRef.__init__ Bio.Data.CodonTable.AmbiguousCodonTable.__init__ Bio.Data.CodonTable.AmbiguousForwardTable.__init__ Bio.Data.CodonTable.CodonTable.__init__ Bio.Data.CodonTable.NCBICodonTable.__init__ Bio.Decode.DecodeParser.__init__ Bio.Decode.DecodeScanner.__init__ Bio.Decode.Float.__init__ Bio.Decode.Function.__init__ Bio.Decode.FunctionCall.__init__ Bio.Decode.FunctionCallChain.__init__ Bio.Decode.FunctionName.__init__ Bio.Decode.Integer.__init__ Bio.Decode.String.__init__ Bio.Decode.Token.__init__ Bio.Decode.ValueToken.__init__ Bio.DocSQL.Create.__init__ Bio.DocSQL.Insert.__init__ Bio.DocSQL.IterationCursor.__init__ Bio.DocSQL.Query.__init__ Bio.DocSQL.QueryAll.__init__ Bio.DocSQL.QueryGeneric.__init__ Bio.DocSQL.QueryRow.__init__ Bio.DocSQL.QuerySingle.__init__ Bio.ECell.ECellError.__init__ Bio.ECell.Error.__init__ Bio.ECell.Iterator.__init__ Bio.ECell.Record.Record.__init__ Bio.ECell.RecordParser.__init__ Bio.ECell._RecordConsumer.__init__ Bio.ECell._Scanner.__init__ Bio.EUtils.Config.DatabaseInfo.__init__ Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__ Bio.EUtils.DBIdsClient.DBIdsClient.__init__ Bio.EUtils.DBIdsClient.DBIdsLookup.__init__ Bio.EUtils.Datatypes.BinaryOp.__init__ Bio.EUtils.Datatypes.CheckLinkSet.__init__ Bio.EUtils.Datatypes.DBIds.__init__ Bio.EUtils.Datatypes.Date.__init__ Bio.EUtils.Datatypes.DateRange.__init__ Bio.EUtils.Datatypes.EUtilsSearchError.__init__ Bio.EUtils.Datatypes.IdCheck.__init__ Bio.EUtils.Datatypes.IdUrlSet.__init__ Bio.EUtils.Datatypes.Link.__init__ Bio.EUtils.Datatypes.LinkSetDb.__init__ Bio.EUtils.Datatypes.LinksLinkSet.__init__ Bio.EUtils.Datatypes.NeighborLinkSet.__init__ Bio.EUtils.Datatypes.ObjUrl.__init__ Bio.EUtils.Datatypes.PostResult.__init__ Bio.EUtils.Datatypes.Problem.__init__ Bio.EUtils.Datatypes.Provider.__init__ Bio.EUtils.Datatypes.Range.__init__ Bio.EUtils.Datatypes.SearchResult.__init__ Bio.EUtils.Datatypes.Summary.__init__ Bio.EUtils.Datatypes.Term.__init__ Bio.EUtils.Datatypes.WithinNDays.__init__ Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__ Bio.EUtils.HistoryClient.HistoryClient.__init__ Bio.EUtils.HistoryClient.HistoryCookie.__init__ Bio.EUtils.HistoryClient.HistoryLookup.__init__ Bio.EUtils.HistoryClient.HistoryRecord.__init__ Bio.EUtils.MultiDict.OrderedMultiDict.__init__ Bio.EUtils.MultiDict.UnorderedMultiDict.__init__ Bio.EUtils.POM.Comment.__init__ Bio.EUtils.POM.ContentModel.__init__ Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__ Bio.EUtils.POM.ElementNode.__init__ Bio.EUtils.POM.IndentedText.__init__ Bio.EUtils.POM.ObjectParserHandler.__init__ Bio.EUtils.POM.POMDocument.__init__ Bio.EUtils.POM.XMLAttribute.__init__ Bio.EUtils.POM._ContentModelGenerator.__init__ Bio.EUtils.ReseekFile.ReseekFile.__init__ Bio.EUtils.ThinClient.ThinClient.__init__ Bio.EUtils.parse.UsePOMParser.__init__ Bio.EUtils.sourcegen.ClassHolder.__init__ Bio.EUtils.sourcegen.FunctionHolder.__init__ Bio.EUtils.sourcegen.MethodHolder.__init__ Bio.EUtils.sourcegen.SourceFile.__init__ Bio.EUtils.sourcegen.SourceGen.__init__ Bio.Emboss.Applications.EConsenseCommandline.__init__ Bio.Emboss.Applications.EInvertedCommandline.__init__ Bio.Emboss.Applications.ENeighborCommandline.__init__ Bio.Emboss.Applications.EProtDistCommandline.__init__ Bio.Emboss.Applications.EProtParsCommandline.__init__ Bio.Emboss.Applications.ESeqBootCommandline.__init__ Bio.Emboss.Applications.ETandemCommandline.__init__ Bio.Emboss.Applications.Est2GenomeCommandline.__init__ Bio.Emboss.Applications.FuzznucCommandline.__init__ Bio.Emboss.Applications.PalindromeCommandline.__init__ Bio.Emboss.Applications.Primer3Commandline.__init__ Bio.Emboss.Applications.PrimerSearchCommandline.__init__ Bio.Emboss.Applications.TranalignCommandline.__init__ Bio.Emboss.Applications.WaterCommandline.__init__ Bio.Emboss.Primer.Primer3Parser.__init__ Bio.Emboss.Primer.Primer3Primers.__init__ Bio.Emboss.Primer.Primer3Record.__init__ Bio.Emboss.Primer.PrimerSearchAmplifier.__init__ Bio.Emboss.Primer.PrimerSearchInputRecord.__init__ Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__ Bio.Emboss.Primer.PrimerSearchParser.__init__ Bio.Emboss.Primer._Primer3RecordConsumer.__init__ Bio.Emboss.Primer._Primer3Scanner.__init__ Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__ Bio.Emboss.Primer._PrimerSearchScanner.__init__ Bio.Entrez.Parser.DataHandler.__init__ Bio.Entrez.Parser.StructureElement.__init__ Bio.Enzyme.DataRecord.__init__ Bio.Enzyme.EnzymeRecord.__init__ Bio.Enzyme.Iterator.__init__ Bio.Enzyme.RecordParser.__init__ Bio.Enzyme._RecordConsumer.__init__ Bio.FSSP.FSSPAlignDict.__init__ Bio.FSSP.FSSPAlignRec.__init__ Bio.FSSP.FSSPHeader.__init__ Bio.FSSP.FSSPSumRec.__init__ Bio.FSSP.FSSPTools.FSSPMultAlign.__init__ Bio.FSSP.PosAlign.__init__ Bio.FSSP.fssp_rec.fff_rec.__init__ Bio.Fasta.FastaAlign.FastaAlignment.__init__ Bio.Fasta.Iterator.__init__ Bio.Fasta.Record.__init__ Bio.Fasta.RecordParser.__init__ Bio.Fasta.SequenceParser.__init__ Bio.File.SGMLHandle.__init__ Bio.File.SGMLStripper.MyParser.__init__ Bio.File.SGMLStripper.__init__ Bio.File.UndoHandle.__init__ Bio.FilteredReader.FilteredReader.__init__ Bio.GA.Crossover.General.SafeFitnessCrossover.__init__ Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__ Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__ Bio.GA.Crossover.Point.SinglePointCrossover.__init__ Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__ Bio.GA.Crossover.Uniform.UniformCrossover.__init__ Bio.GA.Evolver.GenerationEvolver.__init__ Bio.GA.Evolver.SteadyStateEvolver.__init__ Bio.GA.Mutation.General.SafeFitnessMutation.__init__ Bio.GA.Mutation.Simple.ConversionMutation.__init__ Bio.GA.Mutation.Simple.SinglePositionMutation.__init__ Bio.GA.Organism.Organism.__init__ Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__ Bio.GA.Selection.Abstract.AbstractSelection.__init__ Bio.GA.Selection.Diversity.DiversitySelection.__init__ Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__ Bio.GA.Selection.Tournament.TournamentSelection.__init__ Bio.GFF.Connection.__init__ Bio.GFF.Feature.__init__ Bio.GFF.FeatureAggregate.__init__ Bio.GFF.FeatureQuery.__init__ Bio.GFF.FeatureQueryRow.__init__ Bio.GFF.GenericTools.ArgsParser.__init__ Bio.GFF.GenericTools.Surrogate.__init__ Bio.GFF.GenericTools.TempFile.__init__ Bio.GFF.RetrieveSeqname.__init__ Bio.GFF.Segment.__init__ Bio.GFF.easy.FeatureDict.__init__ Bio.GFF.easy.Location.__init__ Bio.GFF.easy.LocationFromCoords.__init__ Bio.GFF.easy.LocationFromString.__init__ Bio.GFF.easy.LocationJoin.__init__ Bio.GenBank.FeatureParser.__init__ Bio.GenBank.Iterator.__init__ Bio.GenBank.LocationParser.AbsoluteLocation.__init__ Bio.GenBank.LocationParser.Between.__init__ Bio.GenBank.LocationParser.FeatureName.__init__ Bio.GenBank.LocationParser.Function.__init__ Bio.GenBank.LocationParser.HighBound.__init__ Bio.GenBank.LocationParser.Integer.__init__ Bio.GenBank.LocationParser.LocationParser.__init__ Bio.GenBank.LocationParser.LocationScanner.__init__ Bio.GenBank.LocationParser.LowBound.__init__ Bio.GenBank.LocationParser.Path.__init__ Bio.GenBank.LocationParser.Range.__init__ Bio.GenBank.LocationParser.Symbol.__init__ Bio.GenBank.LocationParser.Token.__init__ Bio.GenBank.LocationParser.TwoBound.__init__ Bio.GenBank.NCBIDictionary.__init__ Bio.GenBank.Record.Feature.__init__ Bio.GenBank.Record.Qualifier.__init__ Bio.GenBank.Record.Record.__init__ Bio.GenBank.Record.Reference.__init__ Bio.GenBank.RecordParser.__init__ Bio.GenBank.Scanner.InsdcScanner.__init__ Bio.GenBank._BaseGenBankConsumer.__init__ Bio.GenBank._FeatureConsumer.__init__ Bio.GenBank._RecordConsumer.__init__ Bio.GenBank.utils.FeatureValueCleaner.__init__ Bio.Geo.Record.Record.__init__ Bio.Gobase.Dictionary.__init__ Bio.Gobase.GeneRecord.__init__ Bio.Gobase.Iterator.__init__ Bio.Gobase.ProteinRecord.__init__ Bio.Gobase.Record.__init__ Bio.Gobase.RecordParser.__init__ Bio.Gobase.SequenceRecord.__init__ Bio.Gobase._RecordConsumer.__init__ Bio.Graphics.BasicChromosome.Chromosome.__init__ Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__ Bio.Graphics.BasicChromosome.Organism.__init__ Bio.Graphics.BasicChromosome.TelomereSegment.__init__ Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__ Bio.Graphics.Comparative.ComparativeScatterPlot.__init__ Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__ Bio.Graphics.Distribution.BarChartDistribution.__init__ Bio.Graphics.Distribution.DistributionPage.__init__ Bio.Graphics.Distribution.LineDistribution.__init__ Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__ Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__ Bio.HMM.MarkovModel.HiddenMarkovModel.__init__ Bio.HMM.MarkovModel.MarkovModelBuilder.__init__ Bio.HMM.Trainer.AbstractTrainer.__init__ Bio.HMM.Trainer.BaumWelchTrainer.__init__ Bio.HMM.Trainer.KnownStateTrainer.__init__ Bio.HMM.Trainer.TrainingSequence.__init__ Bio.HotRand.HotCache.__init__ Bio.HotRand.HotRandom.__init__ Bio.Index._InMemoryIndex.__init__ Bio.Index._ShelveIndex.__init__ Bio.IntelliGenetics.IntelliGeneticsReader.__init__ Bio.IntelliGenetics.Iterator.__init__ Bio.IntelliGenetics.Record.Record.__init__ Bio.IntelliGenetics.RecordParser.__init__ Bio.IntelliGenetics._RecordConsumer.__init__ Bio.IntelliGenetics._Scanner.__init__ Bio.KDTree.CKDTree.KDTree.__init__ Bio.KDTree.CKDTree.KDTreePtr.__init__ Bio.KDTree.KDTree.KDTree.__init__ Bio.KEGG.Compound.Record.__init__ Bio.KEGG.Enzyme.Record.__init__ Bio.LocusLink.Iterator.__init__ Bio.LocusLink.Record.__init__ Bio.LocusLink.RecordParser.__init__ Bio.LocusLink._RecordConsumer.__init__ Bio.LocusLink._Scanner.__init__ Bio.LocusLink.web_parse.Record.__init__ Bio.LocusLink.web_parse.Token.__init__ Bio.LocusLink.web_parse.Url.__init__ Bio.LogisticRegression.LogisticRegression.__init__ Bio.MEME.Motif.Instance.__init__ Bio.MEME.Motif.MEMEMotif.__init__ Bio.MEME.Motif.Motif.__init__ Bio.MEME.Parser.MASTParser.__init__ Bio.MEME.Parser.MASTRecord.__init__ Bio.MEME.Parser.MEMEParser.__init__ Bio.MEME.Parser.MEMERecord.__init__ Bio.MEME.Parser._MASTConsumer.__init__ Bio.MEME.Parser._MEMEConsumer.__init__ Bio.MarkovModel.MarkovModel.__init__ Bio.MaxEntropy.MaxEntropy.__init__ Bio.Medline.Iterator.__init__ Bio.Medline.Record.__init__ Bio.Medline.RecordParser.__init__ Bio.Medline._RecordConsumer.__init__ Bio.MetaTool.Iterator.__init__ Bio.MetaTool.Record.Metabolite.__init__ Bio.MetaTool.Record.MetaboliteRole.__init__ Bio.MetaTool.Record.PathwayTransform.__init__ Bio.MetaTool.Record.Record.__init__ Bio.MetaTool.RecordParser.__init__ Bio.MetaTool._RecordConsumer.__init__ Bio.MetaTool._Scanner.__init__ Bio.Mindy.BaseDB.OpenDB.__init__ Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__ Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__ Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__ Bio.Mindy.FlatDB.BaseFlatDB.__init__ Bio.Mindy.FlatDB.BisectFile.__init__ Bio.Mindy.FlatDB.DiskFlatDB.__init__ Bio.Mindy.FlatDB.MemoryFlatDB.__init__ Bio.Mindy.FlatDB.PrimaryNamespace.__init__ Bio.Mindy.FlatDB.PrimaryTable.__init__ Bio.Mindy.FlatDB.SecondaryNamespace.__init__ Bio.Mindy.FlatDB.SecondaryTable.__init__ Bio.Mindy.Location.Location.__init__ Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__ Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__ Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__ Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__ Bio.Mindy.XPath.GrabXPathNodes.__init__ Bio.NBRF.Iterator.__init__ Bio.NBRF.Record.Record.__init__ Bio.NBRF.RecordParser.__init__ Bio.NBRF._RecordConsumer.__init__ Bio.NBRF._Scanner.__init__ Bio.NMR.xpktools.Peaklist.__init__ Bio.NMR.xpktools.XpkEntry.__init__ Bio.NaiveBayes.NaiveBayes.__init__ Bio.Ndb.Record.__init__ Bio.NetCatch.ExtractUrls.__init__ Bio.NetCatch.NetCatch.__init__ Bio.NetCatch.Url.__init__ Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__ Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__ Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__ Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__ Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__ Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__ Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__ Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__ Bio.NeuralNetwork.Gene.Schema.Schema.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__ Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__ Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__ Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__ Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__ Bio.NeuralNetwork.Training.ExampleManager.__init__ Bio.NeuralNetwork.Training.TrainingExample.__init__ Bio.Nexus.Nexus.Block.__init__ Bio.Nexus.Nexus.CharBuffer.__init__ Bio.Nexus.Nexus.Commandline.__init__ Bio.Nexus.Nexus.Nexus.__init__ Bio.Nexus.Nexus.StepMatrix.__init__ Bio.Nexus.Nodes.Chain.__init__ Bio.Nexus.Nodes.Node.__init__ Bio.Nexus.Trees.NodeData.__init__ Bio.Nexus.Trees.Tree.__init__ Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__ Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__ Bio.PDB.Atom.Atom.__init__ Bio.PDB.Atom.DisorderedAtom.__init__ Bio.PDB.Chain.Chain.__init__ Bio.PDB.DSSP'.DSSP.__init__ Bio.PDB.Dice.ChainSelector.__init__ Bio.PDB.Entity.DisorderedEntityWrapper.__init__ Bio.PDB.Entity.Entity.__init__ Bio.PDB.FragmentMapper'.Fragment.__init__ Bio.PDB.FragmentMapper'.FragmentMapper.__init__ Bio.PDB.HSExposure.ExposureCN.__init__ Bio.PDB.HSExposure.HSExposureCA.__init__ Bio.PDB.HSExposure.HSExposureCB.__init__ Bio.PDB.HSExposure._AbstractHSExposure.__init__ Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__ Bio.PDB.Model.Model.__init__ Bio.PDB.NACCESS.NACCESS.__init__ Bio.PDB.NACCESS.NACCESS_atomic.__init__ Bio.PDB.NeighborSearch.NeighborSearch.__init__ Bio.PDB.PDBIO'.PDBIO.__init__ Bio.PDB.PDBList'.PDBList.__init__ Bio.PDB.PDBParser'.PDBParser.__init__ Bio.PDB.PSEA.PSEA.__init__ Bio.PDB.Polypeptide.CaPPBuilder.__init__ Bio.PDB.Polypeptide.PPBuilder.__init__ Bio.PDB.Polypeptide._PPBuilder.__init__ Bio.PDB.Residue.DisorderedResidue.__init__ Bio.PDB.Residue.Residue.__init__ Bio.PDB.ResidueDepth'.ResidueDepth.__init__ Bio.PDB.Structure.Structure.__init__ Bio.PDB.StructureAlignment'.StructureAlignment.__init__ Bio.PDB.StructureBuilder.StructureBuilder.__init__ Bio.PDB.Superimposer'.Superimposer.__init__ Bio.PDB.Vector'.Vector.__init__ Bio.ParserSupport.EventGenerator.__init__ Bio.ParserSupport.SGMLStrippingConsumer.__init__ Bio.ParserSupport.TaggingConsumer.__init__ Bio.Parsers.spark.GenericASTBuilder.__init__ Bio.Parsers.spark.GenericASTMatcher.__init__ Bio.Parsers.spark.GenericASTTraversal.__init__ Bio.Parsers.spark.GenericParser.__init__ Bio.Parsers.spark.GenericScanner.__init__ Bio.Pathway.Network.__init__ Bio.Pathway.Reaction.__init__ Bio.Pathway.Rep.Graph.Graph.__init__ Bio.Pathway.Rep.HashSet.HashSet.__init__ Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__ Bio.Pathway.System.__init__ Bio.PopGen.Async.Async.__init__ Bio.PopGen.Async.DirectoryRetriever.__init__ Bio.PopGen.Async.FileRetriever.__init__ Bio.PopGen.Async.Local.Local.__init__ Bio.PopGen.FDist.Async.FDistAsync.__init__ Bio.PopGen.FDist.Async.SplitFDist.__init__ Bio.PopGen.FDist.Controller.FDistController.__init__ Bio.PopGen.FDist.Record.__init__ Bio.PopGen.FDist.RecordParser.__init__ Bio.PopGen.FDist._RecordConsumer.__init__ Bio.PopGen.GenePop.Record.__init__ Bio.PopGen.GenePop.RecordParser.__init__ Bio.PopGen.GenePop._RecordConsumer.__init__ Bio.PopGen.SimCoal.Async.SimCoalCache.__init__ Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__ Bio.PopGen.SimCoal.Controller.SimCoalController.__init__ Bio.PropertyManager.PropertyManager.__init__ Bio.Prosite.Dictionary.__init__ Bio.Prosite.ExPASyDictionary.__init__ Bio.Prosite.Iterator.__init__ Bio.Prosite.Pattern.Prosite.__init__ Bio.Prosite.Pattern.PrositeMatch.__init__ Bio.Prosite.Pattern.PrositeTerm.__init__ Bio.Prosite.PatternHit.__init__ Bio.Prosite.Prodoc.Dictionary.__init__ Bio.Prosite.Prodoc.ExPASyDictionary.__init__ Bio.Prosite.Prodoc.Iterator.__init__ Bio.Prosite.Prodoc.Record.__init__ Bio.Prosite.Prodoc.RecordParser.__init__ Bio.Prosite.Prodoc.Reference.__init__ Bio.Prosite.Prodoc._RecordConsumer.__init__ Bio.Prosite.Record.__init__ Bio.Prosite.RecordParser.__init__ Bio.Prosite._RecordConsumer.__init__ Bio.PubMed.Dictionary.__init__ Bio.Rebase.Dictionary.__init__ Bio.Rebase.Iterator.__init__ Bio.Rebase.Record.__init__ Bio.Rebase.RecordParser.__init__ Bio.Rebase._RecordConsumer.__init__ Bio.Restriction.PrintFormat.PrintFormat.__init__ Bio.Restriction.Restriction.Analysis.__init__ Bio.Restriction.Restriction.FormattedSeq.__init__ Bio.Restriction.Restriction.RestrictionBatch.__init__ Bio.Restriction.Restriction.RestrictionType.__init__ Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__ Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__ Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__ Bio.Restriction._Update.Update.ConnectionError.__init__ Bio.Restriction._Update.Update.FtpNameError.__init__ Bio.Restriction._Update.Update.FtpPasswordError.__init__ Bio.Restriction._Update.Update.RebaseUpdate.__init__ Bio.SCOP.Astral.__init__ Bio.SCOP.Cla.Index.__init__ Bio.SCOP.Cla.Iterator.__init__ Bio.SCOP.Cla.Parser.__init__ Bio.SCOP.Cla.Record.__init__ Bio.SCOP.Des.Iterator.__init__ Bio.SCOP.Des.Parser.__init__ Bio.SCOP.Des.Record.__init__ Bio.SCOP.Dom.Iterator.__init__ Bio.SCOP.Dom.Record.__init__ Bio.SCOP.Domain.__init__ Bio.SCOP.FileIndex.FileIndex.__init__ Bio.SCOP.FileIndex.defaultdict.__init__ Bio.SCOP.Hie.Iterator.__init__ Bio.SCOP.Hie.Parser.__init__ Bio.SCOP.Hie.Record.__init__ Bio.SCOP.Node.__init__ Bio.SCOP.Raf.Iterator.__init__ Bio.SCOP.Raf.Parser.__init__ Bio.SCOP.Raf.Res.__init__ Bio.SCOP.Raf.SeqMap.__init__ Bio.SCOP.Raf.SeqMapIndex.__init__ Bio.SCOP.Residues'.Residues.__init__ Bio.SCOP.Scop.__init__ Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__ Bio.SGMLExtractor.SGMLExtractor.__init__ Bio.SGMLExtractor.SGMLExtractorHandle.__init__ Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__ Bio.Saf.Iterator.__init__ Bio.Saf.Record.Record.__init__ Bio.Saf.RecordParser.__init__ Bio.Saf._RecordConsumer.__init__ Bio.Saf._Scanner.__init__ Bio.Search.Algorithm.__init__ Bio.Search.Database.__init__ Bio.Search.HSP.__init__ Bio.Search.HSPSeq.__init__ Bio.Search.Hit.__init__ Bio.Search.HomologySeq.__init__ Bio.Search.Query.__init__ Bio.Search.Search.__init__ Bio.Search.TableInfo.__init__ Bio.Search._SeqLength.__init__ Bio.Seq.MutableSeq.__init__ Bio.Seq.Seq.__init__ Bio.SeqFeature.AbstractPosition.__init__ Bio.SeqFeature.AfterPosition.__init__ Bio.SeqFeature.BeforePosition.__init__ Bio.SeqFeature.BetweenPosition.__init__ Bio.SeqFeature.ExactPosition.__init__ Bio.SeqFeature.FeatureLocation.__init__ Bio.SeqFeature.OneOfPosition.__init__ Bio.SeqFeature.PositionGap.__init__ Bio.SeqFeature.Reference.__init__ Bio.SeqFeature.SeqFeature.__init__ Bio.SeqFeature.WithinPosition.__init__ Bio.SeqIO.ClustalIO.ClustalWriter.__init__ Bio.SeqIO.FastaIO.FastaWriter.__init__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceIterator.__init__ Bio.SeqIO.Interfaces.SequenceWriter.__init__ Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__ Bio.SeqIO.PhylipIO.PhylipWriter.__init__ Bio.SeqIO.StockholmIO.StockholmIterator.__init__ Bio.SeqIO.StockholmIO.StockholmWriter.__init__ Bio.SeqRecord.SeqRecord.__init__ Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__ Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__ Bio.SeqUtils.MissingTable.__init__ Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__ Bio.Sequencing.Ace.ACEFileRecord.__init__ Bio.Sequencing.Ace.ACEParser.__init__ Bio.Sequencing.Ace.Contig.__init__ Bio.Sequencing.Ace.Iterator.__init__ Bio.Sequencing.Ace.Reads.__init__ Bio.Sequencing.Ace.RecordParser.__init__ Bio.Sequencing.Ace._RecordConsumer.__init__ Bio.Sequencing.Ace.af.__init__ Bio.Sequencing.Ace.bs.__init__ Bio.Sequencing.Ace.ct.__init__ Bio.Sequencing.Ace.ds.__init__ Bio.Sequencing.Ace.qa.__init__ Bio.Sequencing.Ace.rd.__init__ Bio.Sequencing.Ace.rt.__init__ Bio.Sequencing.Ace.wa.__init__ Bio.Sequencing.Ace.wr.__init__ Bio.Sequencing.Phd.Iterator.__init__ Bio.Sequencing.Phd.Record.__init__ Bio.Sequencing.Phd.RecordParser.__init__ Bio.Sequencing.Phd._RecordConsumer.__init__ Bio.Std.StdTerm.__init__ Bio.StdHandler.ConvertDispatchHandler.__init__ Bio.StdHandler.ConvertHandler.__init__ Bio.StdHandler.Feature.__init__ Bio.StdHandler.Handle_dbxref.__init__ Bio.StdHandler.Handle_feature_location.__init__ Bio.StdHandler.Handle_feature_qualifier.__init__ Bio.StdHandler.Handle_features.__init__ Bio.StdHandler.Handle_hsp.__init__ Bio.StdHandler.RecognizeHandler.__init__ Bio.SubsMat.FreqTable.FreqTable.__init__ Bio.SubsMat.SeqMat.__init__ Bio.SwissProt.KeyWList.ListParser.__init__ Bio.SwissProt.KeyWList.Record.__init__ Bio.SwissProt.KeyWList._ListConsumer.__init__ Bio.SwissProt.KeyWList._Scanner.__init__ Bio.SwissProt.SProt.Dictionary.__init__ Bio.SwissProt.SProt.ExPASyDictionary.__init__ Bio.SwissProt.SProt.Iterator.__init__ Bio.SwissProt.SProt.Record.__init__ Bio.SwissProt.SProt.RecordParser.__init__ Bio.SwissProt.SProt.Reference.__init__ Bio.SwissProt.SProt.SequenceParser.__init__ Bio.SwissProt.SProt._RecordConsumer.__init__ Bio.SwissProt.SProt._SequenceConsumer.__init__ Bio.Transcribe.Transcribe.__init__ Bio.Translate.Translator.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.WWW.RequestLimiter.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.Writer.Writer.__init__ Bio.biblio.Biblio.__init__ Bio.biblio.BiblioCollection.__init__ Bio.builders.Search.search.BuildSearch.__init__ Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__ Bio.config.DBRegistry.BioCorbaDB.__init__ Bio.config.DBRegistry.BioSQLDB.__init__ Bio.config.DBRegistry.CGIDB.__init__ Bio.config.DBRegistry.DBGroup.__init__ Bio.config.DBRegistry.DBObject.__init__ Bio.config.DBRegistry.DBRegistry.__init__ Bio.config.DBRegistry.EUtilsDB.__init__ Bio.config.DBRegistry.IndexedFileDB.__init__ Bio.config.FormatRegistry.FormatGroup.__init__ Bio.config.FormatRegistry.FormatObject.__init__ Bio.config.FormatRegistry.FormatRegistry.__init__ Bio.config.Registry.RegisterableGroup.__init__ Bio.config.Registry.RegisterableObject.__init__ Bio.config.Registry.Registry.__init__ Bio.config.SeqDBRegistry.SeqDBRegistry.__init__ Bio.config._stanzaformat.Stanza.__init__ Bio.config._stanzaformat.StanzaFormat.__init__ Bio.config._support.make_cached_expression.__init__ Bio.config._support.make_rate_limited_function.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ Bio.writers.SeqRecord.embl.WriteEmbl.__init__ Bio.writers.SeqRecord.fasta.WriteFasta.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__ Martel.Dispatch.Callback.__init__ Martel.Dispatch.DispatchHandler.__init__ Martel.Dispatch.Dispatcher.__init__ Martel.Dispatch.Multicall.__init__ Martel.Dispatch.RemapEnd.__init__ Martel.Dispatch.RemapStart.__init__ Martel.Expression.Alt.__init__ Martel.Expression.Any.__init__ Martel.Expression.Assert.__init__ Martel.Expression.Debug.__init__ Martel.Expression.FastFeature.__init__ Martel.Expression.Group.__init__ Martel.Expression.GroupRef.__init__ Martel.Expression.HeaderFooter.__init__ Martel.Expression.Literal.__init__ Martel.Expression.MaxRepeat.__init__ Martel.Expression.NullOp.__init__ Martel.Expression.ParseRecords.__init__ Martel.Expression.PassThrough.__init__ Martel.Expression.Seq.__init__ Martel.Expression.Str.__init__ Martel.Generate.CheckAssert.__init__ Martel.Generate.CheckAssertNot.__init__ Martel.Generate.CheckGroupRef.__init__ Martel.Generate.GeneratorState.__init__ Martel.Generate.HandleRepeatCount.__init__ Martel.Generate.SetGroupValue.__init__ Martel.Generate._call_call.__init__ Martel.Generate._call_calltag.__init__ Martel.Generate.print_debug.__init__ Martel.Generate.print_info.__init__ Martel.IterParser.IterHeaderFooter.__init__ Martel.IterParser.IterRecords.__init__ Martel.Iterator.EventStream.__init__ Martel.Iterator.HeaderFooterEventStream.__init__ Martel.Iterator.Iterate.__init__ Martel.Iterator.Iterator.__init__ Martel.Iterator.IteratorHeaderFooter.__init__ Martel.Iterator.IteratorRecords.__init__ Martel.Iterator.RecordEventStream.__init__ Martel.Iterator.StoreEvents.__init__ Martel.LAX.ElementInfo.__init__ Martel.LAX.LAX.__init__ Martel.Parser.HeaderFooterParser.__init__ Martel.Parser.Parser.__init__ Martel.Parser.ParserIncompleteException.__init__ Martel.Parser.ParserPositionException.__init__ Martel.Parser.RecordParser.__init__ Martel.RecordReader.CountLines.__init__ Martel.RecordReader.EndsWith.__init__ Martel.RecordReader.Everything.__init__ Martel.RecordReader.Nothing.__init__ Martel.RecordReader.RecordReader.__init__ Martel.RecordReader.StartsWith.__init__ Martel.RecordReader.Until.__init__ Martel.convert_re.GroupNames.__init__ Martel.msre_parse.Pattern.__init__ Martel.msre_parse.SubPattern.__init__ Martel.msre_parse.Tokenizer.__init__ Martel.test.support.CheckGood.__init__ Martel.test.support.Dump.__init__ Martel.test.support.Storage.__init__ Martel.test.test_Parser.CountErrors.__init__ Martel.test.test_Parser.CountRecords.__init__ Martel.test.test_delimiter.CatchFields.__init__ Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-102', '__init__', 'link-102');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-string">'type%i'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt><tt class="py-op">,</tt><tt class="py-name">ty</tt><tt class="py-op">,</tt><tt class="py-name">dct</tt><tt class="py-op">)</tt> </tt> </div></div><a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-name">klass</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-name">n</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt> </div></div><a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt> <a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt id="link-103" 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-103', 'start', 'link-103');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'\n\</tt> </tt> <a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-string">#!/usr/bin/env python\n\</tt> </tt> <a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-string">#\n\</tt> </tt> <a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-string"># Restriction Analysis Libraries.\n\</tt> </tt> <a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-string"># Copyright (C) 2004. Frederic Sohm.\n\</tt> </tt> <a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-string">#\n\</tt> </tt> <a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"><tt class="py-string"># This code is part of the Biopython distribution and governed by its\n\</tt> </tt> <a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-string"># license. Please see the LICENSE file that should have been included\n\</tt> </tt> <a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"><tt class="py-string"># as part of this package.\n\</tt> </tt> <a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"><tt class="py-string">#\n\</tt> </tt> <a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-string">#\n\</tt> </tt> <a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-string">rest_dict = \\\n'</tt> </tt> <a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder"></a><div id="DictionaryBuilder-def"><a name="L357"></a><tt class="py-lineno">357</tt> <a class="py-toggle" href="#" id="DictionaryBuilder-toggle" onclick="return toggle('DictionaryBuilder');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html">DictionaryBuilder</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="DictionaryBuilder-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DictionaryBuilder-expanded"><a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.__init__"></a><div id="DictionaryBuilder.__init__-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.__init__-toggle" onclick="return toggle('DictionaryBuilder.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">e_mail</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">,</tt> <tt class="py-param">ftp_proxy</tt><tt class="py-op">=</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="DictionaryBuilder.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.__init__-expanded"><a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-docstring">"""DictionaryBuilder([e_mail[, ftp_proxy]) -> DictionaryBuilder instance.</tt> </tt> <a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> If the emboss files used for the construction need to be updated this</tt> </tt> <a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> class will download them if the ftp connection is correctly set.</tt> </tt> <a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"> either in RanaConfig.py or given at run time.</tt> </tt> <a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt> <a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-docstring"> e_mail is the e-mail address used as password for the anonymous</tt> </tt> <a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-docstring"> ftp connection.</tt> </tt> <a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-docstring"> proxy is the ftp_proxy to use if any."""</tt> </tt> <a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rebase_pass</tt> <tt class="py-op">=</tt> <tt class="py-name">e_mail</tt> <tt class="py-keyword">or</tt> <tt id="link-104" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-104', 'config', 'link-34');">config</a></tt><tt class="py-op">.</tt><tt id="link-105" class="py-name" targets="Variable Bio.Restriction.RanaConfig.Rebase_password=Bio.Restriction.RanaConfig-module.html#Rebase_password"><a title="Bio.Restriction.RanaConfig.Rebase_password" class="py-name" href="#" onclick="return doclink('link-105', 'Rebase_password', 'link-105');">Rebase_password</a></tt> </tt> <a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">proxy</tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name" targets="Variable Bio.Restriction.RanaConfig.ftp_proxy=Bio.Restriction.RanaConfig-module.html#ftp_proxy"><a title="Bio.Restriction.RanaConfig.ftp_proxy" class="py-name" href="#" onclick="return doclink('link-106', 'ftp_proxy', 'link-106');">ftp_proxy</a></tt> <tt class="py-keyword">or</tt> <tt id="link-107" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-107', 'config', 'link-34');">config</a></tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.Restriction.RanaConfig.ftp_proxy" class="py-name" href="#" onclick="return doclink('link-108', 'ftp_proxy', 'link-106');">ftp_proxy</a></tt> </tt> </div><a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.build_dict"></a><div id="DictionaryBuilder.build_dict-def"><a name="L373"></a><tt class="py-lineno">373</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.build_dict-toggle" onclick="return toggle('DictionaryBuilder.build_dict');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#build_dict">build_dict</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="DictionaryBuilder.build_dict-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.build_dict-expanded"><a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-docstring">"""DB.build_dict() -> None.</tt> </tt> <a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-docstring"> Construct the dictionary and build the files containing the new</tt> </tt> <a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-docstring"> dictionaries."""</tt> </tt> <a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># first parse the emboss files.</tt> </tt> <a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">emboss_e</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_r</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_s</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-109" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.lastrebasefile()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#lastrebasefile"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.lastrebasefile" class="py-name" href="#" onclick="return doclink('link-109', 'lastrebasefile', 'link-109');">lastrebasefile</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the results will be stored into enzymedict.</tt> </tt> <a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.information_mixer()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#information_mixer"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.information_mixer" class="py-name" href="#" onclick="return doclink('link-110', 'information_mixer', 'link-110');">information_mixer</a></tt><tt class="py-op">(</tt><tt class="py-name">emboss_r</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_e</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_s</tt><tt class="py-op">)</tt> </tt> <a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">emboss_r</tt><tt class="py-op">.</tt><tt id="link-111" 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-111', 'close', 'link-111');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">emboss_e</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-112', 'close', 'link-111');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">emboss_s</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-113', 'close', 'link-111');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we build all the possible type </tt> </tt> <a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">tdct</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">klass</tt> <tt class="py-keyword">in</tt> <tt id="link-114" class="py-name" targets="Class Bio.Restriction._Update.RestrictionCompiler.TypeCompiler=Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html"><a title="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler" class="py-name" href="#" onclick="return doclink('link-114', 'TypeCompiler', 'link-114');">TypeCompiler</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.buildtype()=Bio.Restriction._Update.RestrictionCompiler.TypeCompiler-class.html#buildtype"><a title="Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.buildtype" class="py-name" href="#" onclick="return doclink('link-115', 'buildtype', 'link-115');">buildtype</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">exec</tt> <tt class="py-name">klass</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> <tt class="py-op">+</tt><tt class="py-string">'= klass'</tt> </tt> <a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-keyword">exec</tt> <tt class="py-string">"tdct['"</tt><tt class="py-op">+</tt><tt class="py-name">klass</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">+</tt><tt class="py-string">"'] = klass"</tt> </tt> <a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt> <a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now we build the enzymes from enzymedict</tt> </tt> <a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and store them in a dictionary.</tt> </tt> <a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The type we will need will also be stored.</tt> </tt> <a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-116" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-116', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-117" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-117', 'enzymedict', 'link-49');">enzymedict</a></tt> <tt class="py-op">:</tt> </tt> <a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the class attributes first:</tt> </tt> <a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">cls</tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name" targets="Class Bio.Restriction._Update.RestrictionCompiler.newenzyme=Bio.Restriction._Update.RestrictionCompiler.newenzyme-class.html"><a title="Bio.Restriction._Update.RestrictionCompiler.newenzyme" class="py-name" href="#" onclick="return doclink('link-118', 'newenzyme', 'link-118');">newenzyme</a></tt><tt class="py-op">(</tt><tt id="link-119" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-119', 'name', 'link-68');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now select the right type for the enzyme.</tt> </tt> <a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">bases</tt> <tt class="py-op">=</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">bases</tt> </tt> <a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">clsbases</tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">eval</tt><tt class="py-op">(</tt><tt id="link-120" 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-120', 'x', 'link-120');">x</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-121" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-121', 'x', 'link-120');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">bases</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">typestuff</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt><tt class="py-op">,</tt> <tt class="py-name">t</tt> <tt class="py-keyword">in</tt> <tt class="py-name">tdct</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># if the bases are the same. it is the right type.</tt> </tt> <a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># create the enzyme and remember the type</tt> </tt> <a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">__bases__</tt> <tt class="py-op">==</tt> <tt class="py-name">clsbases</tt> <tt class="py-op">:</tt> </tt> <a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-name">typestuff</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt> </tt> <a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">typename</tt> <tt class="py-op">=</tt> <tt class="py-name">t</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt> </tt> <a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># now we build the dictionaries.</tt> </tt> <a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dct</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">)</tt> </tt> <a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'bases'</tt><tt class="py-op">]</tt> </tt> <a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'__bases__'</tt><tt class="py-op">]</tt> </tt> <a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">dct</tt><tt class="py-op">[</tt><tt class="py-string">'__name__'</tt><tt class="py-op">]</tt><tt class="py-comment"># no need to keep that, it's already in the type.</tt> </tt> <a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt id="link-122" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.classdict" class="py-name" href="#" onclick="return doclink('link-122', 'classdict', 'link-51');">classdict</a></tt><tt class="py-op">[</tt><tt id="link-123" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-123', 'name', 'link-68');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">dct</tt> </tt> <a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> </tt> <a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-name">commonattr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'fst5'</tt><tt class="py-op">,</tt> <tt class="py-string">'fst3'</tt><tt class="py-op">,</tt> <tt class="py-string">'scd5'</tt><tt class="py-op">,</tt> <tt class="py-string">'scd3'</tt><tt class="py-op">,</tt> <tt class="py-string">'substrat'</tt><tt class="py-op">,</tt> </tt> <a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-string">'ovhg'</tt><tt class="py-op">,</tt> <tt class="py-string">'ovhgseq'</tt><tt class="py-op">,</tt><tt class="py-string">'results'</tt><tt class="py-op">,</tt> <tt class="py-string">'dna'</tt><tt class="py-op">]</tt> </tt> <a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">typename</tt> <tt class="py-keyword">in</tt> <tt id="link-124" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-124', 'typedict', 'link-52');">typedict</a></tt> <tt class="py-op">:</tt> </tt> <a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt id="link-125" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-125', 'typedict', 'link-52');">typedict</a></tt><tt class="py-op">[</tt><tt class="py-name">typename</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-126" 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-126', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-127', 'name', 'link-68');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">enzlst</tt><tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-name">tydct</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">typestuff</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">)</tt> </tt> <a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-name">tydct</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">k</tt><tt class="py-op">,</tt><tt id="link-128" class="py-name" targets="Variable Martel.Time.v=Martel.Time-module.html#v"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-128', 'v', 'link-128');">v</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">k</tt><tt class="py-op">,</tt><tt id="link-129" class="py-name"><a title="Martel.Time.v" class="py-name" href="#" onclick="return doclink('link-129', 'v', 'link-128');">v</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">tydct</tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt class="py-name">k</tt> <tt class="py-keyword">in</tt> <tt class="py-name">commonattr</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-name">enzlst</tt><tt class="py-op">.</tt><tt id="link-130" 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-130', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt id="link-131" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-131', 'name', 'link-68');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt id="link-132" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-132', 'typedict', 'link-52');">typedict</a></tt><tt class="py-op">[</tt><tt class="py-name">typename</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">bases</tt><tt class="py-op">,</tt> <tt class="py-name">enzlst</tt><tt class="py-op">)</tt> </tt> <a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt class="py-name">cls</tt><tt class="py-op">.</tt><tt class="py-name">__dict__</tt><tt class="py-op">[</tt><tt class="py-string">'suppl'</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">supplier</tt> <tt class="py-op">=</tt> <tt id="link-133" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-133', 'suppliersdict', 'link-50');">suppliersdict</a></tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt> </tt> <a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt id="link-134" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-134', 'suppliersdict', 'link-50');">suppliersdict</a></tt><tt class="py-op">[</tt><tt class="py-name">letter</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-135" 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-135', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt id="link-136" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-136', 'name', 'link-68');">name</a></tt><tt class="py-op">)</tt> </tt> <a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-137" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.classdict" class="py-name" href="#" onclick="return doclink('link-137', 'classdict', 'link-51');">classdict</a></tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt id="link-138" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-138', 'suppliersdict', 'link-50');">suppliersdict</a></tt> <tt class="py-keyword">or</tt> <tt class="py-keyword">not</tt> <tt id="link-139" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-139', 'typedict', 'link-52');">typedict</a></tt> <tt class="py-op">:</tt> </tt> <a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'One of the new dictionaries is empty.'</tt> </tt> <a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Check the integrity of the emboss file before continuing.'</tt> </tt> <a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Update aborted.'</tt> </tt> <a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># How many enzymes this time?</tt> </tt> <a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\nThe new database contains %i enzymes.\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-140" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.classdict" class="py-name" href="#" onclick="return doclink('link-140', 'classdict', 'link-51');">classdict</a></tt><tt class="py-op">)</tt> </tt> <a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the dictionaries are done. Build the file </tt> </tt> <a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#update = config.updatefolder</tt> </tt> <a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-141', 'update', 'link-96');">update</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-142" 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-142', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-143" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-143', 'update', 'link-96');">update</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Restriction_Dictionary.py'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">)</tt> </tt> <a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Writing the dictionary containing the new Restriction classes.\t'</tt><tt class="py-op">,</tt> </tt> <a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write Bio.AlignIO.write Bio.EUtils.sourcegen.SourceFile.write Bio.EUtils.sourcegen.SourceGen.write Bio.NeuralNetwork.Gene.Pattern.PatternIO.write Bio.SeqIO.write Bio.Writer.Writer.write Bio.writers.SeqRecord.embl.WriteEmbl.write Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-144', 'write', 'link-144');">write</a></tt><tt class="py-op">(</tt><tt id="link-145" 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-145', 'start', 'link-103');">start</a></tt><tt class="py-op">)</tt> </tt> <a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">pprint</tt><tt class="py-op">.</tt><tt class="py-name">PrettyPrinter</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">80</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">results</tt><tt class="py-op">)</tt> </tt> <a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">pprint</tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.classdict" class="py-name" href="#" onclick="return doclink('link-146', 'classdict', 'link-51');">classdict</a></tt><tt class="py-op">)</tt> </tt> <a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'OK.\n'</tt> </tt> <a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Writing the dictionary containing the suppliers datas.\t\t'</tt><tt class="py-op">,</tt> </tt> <a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write Bio.AlignIO.write Bio.EUtils.sourcegen.SourceFile.write Bio.EUtils.sourcegen.SourceGen.write Bio.NeuralNetwork.Gene.Pattern.PatternIO.write Bio.SeqIO.write Bio.Writer.Writer.write Bio.writers.SeqRecord.embl.WriteEmbl.write Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-147', 'write', 'link-144');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'suppliers = \\\n'</tt><tt class="py-op">)</tt> </tt> <a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">pprint</tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-148', 'suppliersdict', 'link-50');">suppliersdict</a></tt><tt class="py-op">)</tt> </tt> <a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'OK.\n'</tt> </tt> <a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Writing the dictionary containing the Restriction types.\t'</tt><tt class="py-op">,</tt> </tt> <a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.AlignAce.Motif.Motif.write Bio.AlignIO.write Bio.EUtils.sourcegen.SourceFile.write Bio.EUtils.sourcegen.SourceGen.write Bio.NeuralNetwork.Gene.Pattern.PatternIO.write Bio.SeqIO.write Bio.Writer.Writer.write Bio.writers.SeqRecord.embl.WriteEmbl.write Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-149', 'write', 'link-144');">write</a></tt><tt class="py-op">(</tt><tt class="py-string">'typedict = \\\n'</tt><tt class="py-op">)</tt> </tt> <a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">pprint</tt><tt class="py-op">(</tt><tt id="link-150" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary.typedict Bio.Restriction._Update.RestrictionCompiler.typedict" class="py-name" href="#" onclick="return doclink('link-150', 'typedict', 'link-52');">typedict</a></tt><tt class="py-op">)</tt> </tt> <a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'OK.\n'</tt> </tt> <a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-151', 'close', 'link-111');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div><a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.install_dict"></a><div id="DictionaryBuilder.install_dict-def"><a name="L477"></a><tt class="py-lineno">477</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.install_dict-toggle" onclick="return toggle('DictionaryBuilder.install_dict');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#install_dict">install_dict</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="DictionaryBuilder.install_dict-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.install_dict-expanded"><a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-docstring">"""DB.install_dict() -> None.</tt> </tt> <a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"> Install the newly created dictionary in the site-packages folder.</tt> </tt> <a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"><tt class="py-docstring"> May need super user privilege on some architectures."""</tt> </tt> <a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n '</tt> <tt class="py-op">+</tt><tt class="py-string">'*'</tt><tt class="py-op">*</tt><tt class="py-number">78</tt> <tt class="py-op">+</tt> <tt class="py-string">' \n'</tt> </tt> <a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n\t\tInstalling Restriction_Dictionary.py'</tt> </tt> <a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-152" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-152', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-153', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-154" class="py-name" targets="Module Bio.Restriction.Restriction_Dictionary=Bio.Restriction.Restriction_Dictionary-module.html"><a title="Bio.Restriction.Restriction_Dictionary" class="py-name" href="#" onclick="return doclink('link-154', 'Restriction_Dictionary', 'link-154');">Restriction_Dictionary</a></tt> <tt class="py-keyword">as</tt> <tt id="link-155" class="py-name" targets="Class Bio.Sequencing.Ace.rd=Bio.Sequencing.Ace.rd-class.html"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-155', 'rd', 'link-155');">rd</a></tt> </tt> <a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt> <tt class="py-op">:</tt> </tt> <a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"><tt class="py-string"> \n Unable to locate the previous Restriction_Dictionary.py module\</tt> </tt> <a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"><tt class="py-string"> \n Aborting installation.'</tt> </tt> <a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># first save the old file in Updates</tt> </tt> <a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">old</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-156', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-157', 'rd', 'link-155');">rd</a></tt><tt class="py-op">.</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-string">'Restriction_Dictionary.py'</tt><tt class="py-op">)</tt> </tt> <a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-comment">#update_folder = config.updatefolder</tt> </tt> <a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">update_folder</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-name">shutil</tt><tt class="py-op">.</tt><tt class="py-name">copyfile</tt><tt class="py-op">(</tt><tt class="py-name">old</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">update_folder</tt><tt class="py-op">,</tt> </tt> <a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-string">'Restriction_Dictionary.old'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now test and install.</tt> </tt> <a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">new</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">update_folder</tt><tt class="py-op">,</tt> <tt class="py-string">'Restriction_Dictionary.py'</tt><tt class="py-op">)</tt> </tt> <a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-name">execfile</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">)</tt> </tt> <a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"><tt class="py-string"> \n\tThe new file seems ok. Proceeding with the installation.'</tt> </tt> <a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">SyntaxError</tt> <tt class="py-op">:</tt> </tt> <a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-string"> \n The new dictionary file is corrupted. Aborting the installation.'</tt> </tt> <a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> <a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-name">shutil</tt><tt class="py-op">.</tt><tt class="py-name">copyfile</tt><tt class="py-op">(</tt><tt class="py-name">new</tt><tt class="py-op">,</tt> <tt class="py-name">old</tt><tt class="py-op">)</tt> </tt> <a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-string">'\n\t Everything ok. If you need it a version of the old\</tt> </tt> <a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-string"> \n\t dictionary have been saved in the Updates folder under\</tt> </tt> <a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-string"> \n\t the name Restriction_Dictionary.old.'</tt> </tt> <a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n '</tt> <tt class="py-op">+</tt><tt class="py-string">'*'</tt><tt class="py-op">*</tt><tt class="py-number">78</tt> <tt class="py-op">+</tt> <tt class="py-string">' \n'</tt> </tt> <a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IOError</tt> <tt class="py-op">:</tt> </tt> <a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n '</tt> <tt class="py-op">+</tt><tt class="py-string">'*'</tt><tt class="py-op">*</tt><tt class="py-number">78</tt> <tt class="py-op">+</tt> <tt class="py-string">' \n'</tt> </tt> <a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-string"> \n\t WARNING : Impossible to install the new dictionary.\</tt> </tt> <a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"><tt class="py-string"> \n\t Are you sure you have write permission to the folder :\n\</tt> </tt> <a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"><tt class="py-string"> \n\t %s ?\n\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-158" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-158', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-name">old</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.no_install()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#no_install"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.no_install" class="py-name" href="#" onclick="return doclink('link-159', 'no_install', 'link-159');">no_install</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div><a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.no_install"></a><div id="DictionaryBuilder.no_install-def"><a name="L528"></a><tt class="py-lineno">528</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.no_install-toggle" onclick="return toggle('DictionaryBuilder.no_install');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#no_install">no_install</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="DictionaryBuilder.no_install-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.no_install-expanded"><a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-docstring">"""BD.no_install() -> None.</tt> </tt> <a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"><tt class="py-docstring"> build the new dictionary but do not install the dictionary."""</tt> </tt> <a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n '</tt> <tt class="py-op">+</tt><tt class="py-string">'*'</tt><tt class="py-op">*</tt><tt class="py-number">78</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-comment">#update = config.updatefolder</tt> </tt> <a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-160" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-160', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-161', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="Bio.Restriction.Restriction_Dictionary" class="py-name" href="#" onclick="return doclink('link-162', 'Restriction_Dictionary', 'link-154');">Restriction_Dictionary</a></tt> <tt class="py-keyword">as</tt> <tt id="link-163" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-163', 'rd', 'link-155');">rd</a></tt> </tt> <a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt> <tt class="py-op">:</tt> </tt> <a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-string"> \n Unable to locate the previous Restriction_Dictionary.py module\</tt> </tt> <a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"><tt class="py-string"> \n Aborting installation.'</tt> </tt> <a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># first save the old file in Updates</tt> </tt> <a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">old</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-164', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Bio.Sequencing.Ace.rd" class="py-name" href="#" onclick="return doclink('link-165', 'rd', 'link-155');">rd</a></tt><tt class="py-op">.</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-string">'Restriction_Dictionary.py'</tt><tt class="py-op">)</tt> </tt> <a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt id="link-166" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-166', 'update', 'link-96');">update</a></tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-name">shutil</tt><tt class="py-op">.</tt><tt class="py-name">copyfile</tt><tt class="py-op">(</tt><tt class="py-name">old</tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-167" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-167', 'update', 'link-96');">update</a></tt><tt class="py-op">,</tt> <tt class="py-string">'Restriction_Dictionary.old'</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-name">places</tt> <tt class="py-op">=</tt> <tt id="link-168" class="py-name"><a title="Bio.GenBank.NCBIDictionary.update Bio.Index._InMemoryIndex.update Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update Bio.Prosite.ExPASyDictionary.update Bio.Prosite.Prodoc.ExPASyDictionary.update Bio.PubMed.Dictionary.update Bio.Restriction._Update.Update.RebaseUpdate.update Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-168', 'update', 'link-96');">update</a></tt><tt class="py-op">,</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt id="link-169" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-169', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt id="link-170" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-170', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-171', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name"><a title="Bio.Restriction Bio.Restriction.Restriction" class="py-name" href="#" onclick="return doclink('link-172', 'Restriction', 'link-8');">Restriction</a></tt><tt class="py-op">.</tt><tt class="py-name">__file__</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"\t\tCompilation of the new dictionary : OK.\</tt> </tt> <a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"><tt class="py-string"> \n\t\tInstallation : No.\n\</tt> </tt> <a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"><tt class="py-string"> \n You will find the newly created 'Restriction_Dictionary.py' file\</tt> </tt> <a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"><tt class="py-string"> \n in the folder : \n\</tt> </tt> <a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"><tt class="py-string"> \n\t%s\n\</tt> </tt> <a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"><tt class="py-string"> \n Make a copy of 'Restriction_Dictionary.py' and place it with \</tt> </tt> <a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-string"> \n the other Restriction libraries.\n\</tt> </tt> <a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"><tt class="py-string"> \n note : \</tt> </tt> <a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"><tt class="py-string"> \n This folder should be :\n\</tt> </tt> <a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-string"> \n\t%s\n"</tt> <tt class="py-op">%</tt> <tt class="py-name">places</tt> </tt> <a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n '</tt> <tt class="py-op">+</tt><tt class="py-string">'*'</tt><tt class="py-op">*</tt><tt class="py-number">78</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt> <a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div><a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> </tt> <a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.lastrebasefile"></a><div id="DictionaryBuilder.lastrebasefile-def"><a name="L563"></a><tt class="py-lineno">563</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.lastrebasefile-toggle" onclick="return toggle('DictionaryBuilder.lastrebasefile');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#lastrebasefile">lastrebasefile</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="DictionaryBuilder.lastrebasefile-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.lastrebasefile-expanded"><a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-docstring">"""BD.lastrebasefile() -> None.</tt> </tt> <a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"><tt class="py-docstring"> Check the emboss files are up to date and download them if they are not.</tt> </tt> <a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt> <a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-name">embossnames</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-string">'emboss_e'</tt><tt class="py-op">,</tt> <tt class="py-string">'emboss_r'</tt><tt class="py-op">,</tt> <tt class="py-string">'emboss_s'</tt><tt class="py-op">)</tt> </tt> <a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># first check if we have the last update :</tt> </tt> <a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">emboss_now</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">'.'</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-173" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-173', 'x', 'link-120');">x</a></tt><tt class="py-op">,</tt><tt id="link-174" class="py-name" targets="Function Bio.Restriction._Update.RestrictionCompiler.LocalTime()=Bio.Restriction._Update.RestrictionCompiler-module.html#LocalTime"><a title="Bio.Restriction._Update.RestrictionCompiler.LocalTime" class="py-name" href="#" onclick="return doclink('link-174', 'LocalTime', 'link-174');">LocalTime</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-175" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-175', 'x', 'link-120');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">embossnames</tt><tt class="py-op">]</tt> </tt> <a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-name">update_needed</tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name" targets="Variable Bio.EUtils.POM.False=Bio.EUtils.POM-module.html#False"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-176', 'False', 'link-176');">False</a></tt> </tt> <a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-comment">#dircontent = os.listdir(config.Rebase) # local database content</tt> </tt> <a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dircontent</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">listdir</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-name">base</tt> <tt class="py-op">=</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">getcwd</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># added for biopython current directory</tt> </tt> <a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-177" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-177', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">emboss_now</tt> <tt class="py-op">:</tt> </tt> <a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-178" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-178', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dircontent</tt> <tt class="py-op">:</tt> </tt> <a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-name">update_needed</tt> <tt class="py-op">=</tt> <tt id="link-179" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-179', 'True', 'link-179');">True</a></tt> </tt> <a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> </tt> <a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">update_needed</tt> <tt class="py-op">:</tt> </tt> <a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># nothing to be done</tt> </tt> <a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\n Using the files : %s'</tt><tt class="py-op">%</tt> <tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">emboss_now</tt><tt class="py-op">)</tt> </tt> <a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-180" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-180', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">emboss_now</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># may be download the files.</tt> </tt> <a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\n The rebase files are more than one month old.\</tt> </tt> <a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"><tt class="py-string"> \n Would you like to update them before proceeding?(y/n)'</tt> </tt> <a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt class="py-name">raw_input</tt><tt class="py-op">(</tt><tt class="py-string">' update [n] >>> '</tt><tt class="py-op">)</tt> </tt> <a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">r</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-string">'y'</tt><tt class="py-op">,</tt> <tt class="py-string">'yes'</tt><tt class="py-op">,</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'Yes'</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-name">updt</tt> <tt class="py-op">=</tt> <tt id="link-181" class="py-name"><a title="Bio.Restriction._Update.Update.RebaseUpdate" class="py-name" href="#" onclick="return doclink('link-181', 'RebaseUpdate', 'link-39');">RebaseUpdate</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rebase_pass</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">proxy</tt><tt class="py-op">)</tt> </tt> <a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-name">updt</tt><tt class="py-op">.</tt><tt id="link-182" class="py-name" targets="Method Bio.Restriction._Update.Update.RebaseUpdate.openRebase()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#openRebase"><a title="Bio.Restriction._Update.Update.RebaseUpdate.openRebase" class="py-name" href="#" onclick="return doclink('link-182', 'openRebase', 'link-182');">openRebase</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-name">updt</tt><tt class="py-op">.</tt><tt id="link-183" class="py-name" targets="Method Bio.Restriction._Update.Update.RebaseUpdate.getfiles()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#getfiles"><a title="Bio.Restriction._Update.Update.RebaseUpdate.getfiles" class="py-name" href="#" onclick="return doclink('link-183', 'getfiles', 'link-183');">getfiles</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt class="py-name">updt</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="Bio.FilteredReader.FilteredReader.close Bio.Mindy.BerkeleyDB.BerkeleyDB.close Bio.Mindy.FlatDB.MemoryFlatDB.close BioSQL.BioSeqDatabase.Adaptor.close Martel.Parser.Parser.close Martel.Parser.RecordParser.close" class="py-name" href="#" onclick="return doclink('link-184', 'close', 'link-111');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n Update complete. Creating the dictionaries.\n'</tt> </tt> <a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\n Using the files : %s'</tt><tt class="py-op">%</tt> <tt class="py-string">', '</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">emboss_now</tt><tt class="py-op">)</tt> </tt> <a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-185" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-185', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">n</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">n</tt> <tt class="py-keyword">in</tt> <tt class="py-name">emboss_now</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># we will use the last files found without updating.</tt> </tt> <a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># But first we check we have some file to use.</tt> </tt> <a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">class</tt> <tt class="py-def-name">NotFoundError</tt><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> </div><a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-186" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-186', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">embossnames</tt> <tt class="py-op">:</tt> </tt> <a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dircontent</tt> <tt class="py-op">:</tt> </tt> <a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-187', 'name', 'link-68');">name</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotFoundError</tt> </tt> <a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">NotFoundError</tt> <tt class="py-op">:</tt> </tt> <a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"\nNo %s file found. Upgrade is impossible.\n"</tt><tt class="py-op">%</tt><tt id="link-188" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-188', 'name', 'link-68');">name</a></tt> </tt> <a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># now find the last file.</tt> </tt> <a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">last</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt class="py-name">dircontent</tt> <tt class="py-op">:</tt> </tt> <a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-name">fs</tt> <tt class="py-op">=</tt> <tt class="py-name">file</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-189', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'.'</tt><tt class="py-op">)</tt> </tt> <a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-name">embossnames</tt> <tt class="py-keyword">and</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> <tt class="py-name">last</tt><tt class="py-op">.</tt><tt id="link-190" 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-190', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">fs</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt> <a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt> </tt> <a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt class="py-name">last</tt><tt class="py-op">.</tt><tt id="link-191" 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-191', 'sort', 'link-191');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-name">last</tt> <tt class="py-op">=</tt> <tt class="py-name">last</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</tt><tt class="py-op">]</tt> </tt> <a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">100</tt> <tt class="py-op">:</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">last</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">number</tt> <tt class="py-keyword">in</tt> <tt class="py-name">last</tt> <tt class="py-op">:</tt> </tt> <a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt id="link-192" class="py-name" targets="Variable Bio.expressions.hmmpfam.files=Bio.expressions.hmmpfam-module.html#files"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-192', 'files', 'link-192');">files</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-193" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-193', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt id="link-194" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-194', 'name', 'link-68');">name</a></tt><tt class="py-op">+</tt><tt class="py-string">'.%s'</tt><tt class="py-op">%</tt><tt class="py-name">number</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-195" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-195', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">embossnames</tt><tt class="py-op">]</tt> </tt> <a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-name">strmess</tt> <tt class="py-op">=</tt> <tt class="py-string">'\nLast EMBOSS files found are :\n'</tt> </tt> <a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-196" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-196', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt><tt class="py-name">file</tt> <tt class="py-keyword">in</tt> <tt id="link-197" class="py-name"><a title="Bio.expressions.hmmpfam.files" class="py-name" href="#" onclick="return doclink('link-197', 'files', 'link-192');">files</a></tt> <tt class="py-op">:</tt> </tt> <a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">isfile</tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-name">strmess</tt> <tt class="py-op">+=</tt> <tt class="py-string">'\t%s.\n'</tt><tt class="py-op">%</tt><tt class="py-name">file</tt> </tt> <a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt> </tt> <a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">strmess</tt> </tt> <a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-name">emboss_e</tt> <tt class="py-op">=</tt> <tt id="link-198" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-198', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-string">'emboss_e.%s'</tt><tt class="py-op">%</tt><tt class="py-name">number</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt> <a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-name">emboss_r</tt> <tt class="py-op">=</tt> <tt id="link-199" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-199', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-string">'emboss_r.%s'</tt><tt class="py-op">%</tt><tt class="py-name">number</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt> <a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-name">emboss_s</tt> <tt class="py-op">=</tt> <tt id="link-200" class="py-name"><a title="Bio.Mindy.FlatDB.open Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-200', 'open', 'link-142');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">os</tt><tt class="py-op">.</tt><tt class="py-name">path</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">base</tt><tt class="py-op">,</tt> <tt class="py-string">'emboss_s.%s'</tt><tt class="py-op">%</tt><tt class="py-name">number</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt> <a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">emboss_e</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_r</tt><tt class="py-op">,</tt> <tt class="py-name">emboss_s</tt> </tt> <a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt> </tt> <a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> </div><a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.parseline"></a><div id="DictionaryBuilder.parseline-def"><a name="L658"></a><tt class="py-lineno">658</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.parseline-toggle" onclick="return toggle('DictionaryBuilder.parseline');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#parseline">parseline</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">line</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="DictionaryBuilder.parseline-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.parseline-expanded"><a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</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">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</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">int</tt><tt class="py-op">(</tt><tt id="link-201" 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-201', 'i', 'link-201');">i</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-202" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-202', 'i', 'link-201');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-number">9</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">9</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt> <a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt id="link-203" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-203', 'name', 'link-68');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt class="py-name">site</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-comment"># sequence of the recognition site</tt> </tt> <a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt id="link-204" class="py-name"><a title="Bio.Restriction.Restriction.DNA Bio.Restriction._Update.RestrictionCompiler.DNA" class="py-name" href="#" onclick="return doclink('link-204', 'DNA', 'link-45');">DNA</a></tt><tt class="py-op">(</tt><tt class="py-name">site</tt><tt class="py-op">)</tt> </tt> <a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt id="link-205" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-205', 'size', 'link-69');">size</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-comment"># size of the recognition site</tt> </tt> <a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Calculate the overhang.</tt> </tt> <a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fst5</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt> <tt class="py-comment"># first site sense strand </tt> </tt> <a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-name">fst3</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt> <tt class="py-comment"># first site antisense strand</tt> </tt> <a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-name">scd5</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> <tt class="py-comment"># second site sense strand</tt> </tt> <a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-name">scd3</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">8</tt><tt class="py-op">]</tt> <tt class="py-comment"># second site antisense strand</tt> </tt> <a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> </tt> <a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the overhang is the difference between the two cut</tt> </tt> <a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">fst5</tt> <tt class="py-op">-</tt> <tt class="py-name">fst3</tt> </tt> <a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> <tt class="py-name">ovhg2</tt> <tt class="py-op">=</tt> <tt class="py-name">scd5</tt> <tt class="py-op">-</tt> <tt class="py-name">scd3</tt> </tt> <a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> </tt> <a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 0 has the meaning 'do not cut' in rebase. So we get short of 1</tt> </tt> <a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># for the negative numbers so we add 1 to negative sites for now.</tt> </tt> <a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># We will deal with the record later.</tt> </tt> <a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">fst5</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fst3</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">fst3</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">scd5</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">scd5</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">scd3</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">scd3</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> </tt> <a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">ovhg2</tt> <tt class="py-op">!=</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">!=</tt> <tt class="py-name">ovhg2</tt> <tt class="py-op">:</tt> </tt> <a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># different length of the overhang of the first and second cut</tt> </tt> <a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># it's a pain to deal with and at the moment it concerns only</tt> </tt> <a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># one enzyme which is not commercially available (HaeIV).</tt> </tt> <a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># So we don't deal with it but we check the progression</tt> </tt> <a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># of the affair.</tt> </tt> <a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Should HaeIV become commercially available or other similar</tt> </tt> <a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># new enzymes be added, this might be modified.</tt> </tt> <a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\</tt> </tt> <a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-string"> \nWARNING : %s cut twice with different overhang length each time.\</tt> </tt> <a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"><tt class="py-string"> \n\tUnable to deal with this behaviour. \</tt> </tt> <a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"><tt class="py-string"> \n\tThis enzyme will not be included in the database. Sorry.'</tt> <tt class="py-op">%</tt><tt id="link-206" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-206', 'name', 'link-68');">name</a></tt> </tt> <a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'\tChecking :'</tt><tt class="py-op">,</tt> </tt> <a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-207" class="py-name" targets="Class Bio.Restriction._Update.RestrictionCompiler.OverhangError=Bio.Restriction._Update.RestrictionCompiler.OverhangError-class.html"><a title="Bio.Restriction._Update.RestrictionCompiler.OverhangError" class="py-name" href="#" onclick="return doclink('link-207', 'OverhangError', 'link-207');">OverhangError</a></tt> </tt> <a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><=</tt> <tt id="link-208" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-208', 'size', 'link-69');">size</a></tt> <tt class="py-keyword">and</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt class="py-name">fst3</tt> <tt class="py-op"><=</tt> <tt id="link-209" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-209', 'size', 'link-69');">size</a></tt> <tt class="py-op">:</tt> </tt> <a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># cut inside recognition site</tt> </tt> <a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' overhang</tt> </tt> <a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-name">fst5</tt><tt class="py-op">:</tt><tt class="py-name">fst3</tt><tt class="py-op">]</tt> </tt> <a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">fst5</tt> <tt class="py-op">></tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' overhang</tt> </tt> <a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-name">fst3</tt><tt class="py-op">:</tt><tt class="py-name">fst5</tt><tt class="py-op">]</tt> </tt> <a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># blunt</tt> </tt> <a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-string">'NRYWMSKHDBV'</tt> <tt class="py-op">:</tt> </tt> <a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">base</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">:</tt> </tt> <a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># site and overhang degenerated</tt> </tt> <a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">ovhg1</tt> </tt> <a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ovhg1</tt><tt class="py-op">)</tt> </tt> <a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">ovhg1</tt><tt class="py-op">)</tt> </tt> <a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt> <a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><=</tt> <tt id="link-210" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-210', 'size', 'link-69');">size</a></tt> <tt class="py-op">:</tt> </tt> <a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' cut inside the site 3' outside</tt> </tt> <a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' cut after the site</tt> </tt> <a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-name">fst5</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">fst3</tt> <tt class="py-op">-</tt> <tt id="link-211" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-211', 'size', 'link-69');">size</a></tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-string">'N'</tt> </tt> <a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">fst5</tt> <tt class="py-op">></tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' cut before the site</tt> </tt> <a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt id="link-212" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.abs()=Bio.FSSP.FSSPAlignDict-class.html#abs"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-212', 'abs', 'link-212');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">fst3</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-string">'N'</tt> <tt class="py-op">+</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">fst5</tt><tt class="py-op">]</tt> </tt> <a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># blunt outside</tt> </tt> <a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhg1</tt> <tt class="py-op">=</tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-number">0</tt> <tt class="py-op"><=</tt> <tt class="py-name">fst3</tt> <tt class="py-op"><=</tt> <tt id="link-213" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-213', 'size', 'link-69');">size</a></tt> <tt class="py-op">:</tt> </tt> <a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' cut inside the site, 5' outside</tt> </tt> <a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' cut before the site</tt> </tt> <a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt id="link-214" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-214', 'abs', 'link-212');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">fst5</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-string">'N'</tt> <tt class="py-op">+</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">fst3</tt><tt class="py-op">]</tt> </tt> <a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">fst5</tt> <tt class="py-op">></tt> <tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' cut after the site</tt> </tt> <a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-name">site</tt><tt class="py-op">[</tt><tt class="py-name">fst3</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">fst5</tt> <tt class="py-op">-</tt> <tt id="link-215" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-215', 'size', 'link-69');">size</a></tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-string">'N'</tt> </tt> <a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># should not happend</tt> </tt> <a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">'Error in #1'</tt> </tt> <a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">fst3</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt id="link-216" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-216', 'size', 'link-69');">size</a></tt> <tt class="py-op"><</tt> <tt class="py-name">fst5</tt> <tt class="py-op">:</tt> </tt> <a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 3' overhang. site is included.</tt> </tt> <a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt id="link-217" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-217', 'abs', 'link-212');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">fst3</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-string">'N'</tt> <tt class="py-op">+</tt> <tt class="py-name">site</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">fst5</tt><tt class="py-op">-</tt><tt id="link-218" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-218', 'size', 'link-69');">size</a></tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-string">'N'</tt> </tt> <a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">fst5</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt id="link-219" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-219', 'size', 'link-69');">size</a></tt> <tt class="py-op"><</tt><tt class="py-name">fst3</tt> <tt class="py-op">:</tt> </tt> <a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' overhang. site is included.</tt> </tt> <a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt id="link-220" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-220', 'abs', 'link-212');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">fst5</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-string">'N'</tt> <tt class="py-op">+</tt> <tt class="py-name">site</tt> <tt class="py-op">+</tt> <tt class="py-op">(</tt><tt class="py-name">fst3</tt><tt class="py-op">-</tt><tt id="link-221" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-221', 'size', 'link-69');">size</a></tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-string">'N'</tt> </tt> <a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># 5' and 3' outside of the site</tt> </tt> <a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ovhgseq</tt> <tt class="py-op">=</tt> <tt class="py-string">'N'</tt> <tt class="py-op">*</tt> <tt id="link-222" class="py-name"><a title="Bio.FSSP.FSSPAlignDict.abs" class="py-name" href="#" onclick="return doclink('link-222', 'abs', 'link-212');">abs</a></tt><tt class="py-op">(</tt><tt class="py-name">ovhg1</tt><tt class="py-op">)</tt> </tt> <a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Now line[5] to [8] are the location of the cut but we have to</tt> </tt> <a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># deal with the weird mathematics of biologists.</tt> </tt> <a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># EMBOSS sequence numbering give :</tt> </tt> <a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># DNA = 'a c g t A C G T'</tt> </tt> <a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># -1 1 2 3 4</tt> </tt> <a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Biologists do not know about 0. Too much use of latin certainly.</tt> </tt> <a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># To compensate, we add 1 to the positions if they are negative.</tt> </tt> <a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># No need to modify 0 as it means no cut and will not been used.</tt> </tt> <a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Positive numbers should be ok since our sequence starts 1.</tt> </tt> <a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Moreover line[6] and line[8] represent cut on the reverse strand.</tt> </tt> <a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># They will be used for non palindromic sites and sre.finditer</tt> </tt> <a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># will detect the site in inverse orientation so we need to add the</tt> </tt> <a name="L805"></a><tt class="py-lineno">805</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># length of the site to compensate (+1 if they are negative).</tt> </tt> <a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-223" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-223', 'x', 'link-120');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">7</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-224" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-224', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-225" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-225', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-226" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-226', 'x', 'link-120');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-227" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-227', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-228" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-228', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">-=</tt> <tt id="link-229" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-229', 'size', 'link-69');">size</a></tt> </tt> <a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-230" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-230', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op"><</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-231" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-231', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt id="link-232" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-232', 'x', 'link-120');">x</a></tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt id="link-233" class="py-name"><a title="Bio.Affy.CelFile.CelRecord.size Bio.Alphabet.Alphabet.size Bio.Alphabet.Reduced.HPModel.size Bio.Alphabet.Reduced.Murphy10.size Bio.Alphabet.Reduced.Murphy15.size Bio.Alphabet.Reduced.Murphy4.size Bio.Alphabet.Reduced.Murphy8.size Bio.Alphabet.Reduced.PC5.size Bio.Alphabet.SingleLetterAlphabet.size Bio.Alphabet.ThreeLetterProtein.size Bio.GenBank._FeatureConsumer.size Bio.GenBank._RecordConsumer.size Bio.expressions.genbank.size" class="py-name" href="#" onclick="return doclink('link-233', 'size', 'link-69');">size</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt> <a name="L812"></a><tt class="py-lineno">812</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># now is the site palindromic?</tt> </tt> <a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># produce the regular expression which correspond to the site.</tt> </tt> <a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># tag of the regex will be the name of the enzyme for palindromic</tt> </tt> <a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># enzymesband two tags for the other, the name for the sense sequence</tt> </tt> <a name="L817"></a><tt class="py-lineno">817</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># and the name with '_as' at the end for the antisense sequence.</tt> </tt> <a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L819"></a><tt class="py-lineno">819</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rg</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt> <a name="L820"></a><tt class="py-lineno">820</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-234" class="py-name" targets="Function Bio.Restriction._Update.RestrictionCompiler.is_palindrom()=Bio.Restriction._Update.RestrictionCompiler-module.html#is_palindrom"><a title="Bio.Restriction._Update.RestrictionCompiler.is_palindrom" class="py-name" href="#" onclick="return doclink('link-234', 'is_palindrom', 'link-234');">is_palindrom</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L821"></a><tt class="py-lineno">821</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-235" 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-235', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt id="link-236" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-236', 'True', 'link-179');">True</a></tt><tt class="py-op">)</tt> </tt> <a name="L822"></a><tt class="py-lineno">822</tt> <tt class="py-line"> <tt class="py-name">rg</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'(?P<'</tt><tt class="py-op">,</tt> <tt id="link-237" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-237', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">'>'</tt><tt class="py-op">,</tt> <tt id="link-238" class="py-name" targets="Function Bio.Restriction._Update.RestrictionCompiler.regex()=Bio.Restriction._Update.RestrictionCompiler-module.html#regex"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-238', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt class="py-name">site</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">')'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L823"></a><tt class="py-lineno">823</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L824"></a><tt class="py-lineno">824</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-239" 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-239', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt id="link-240" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-240', 'False', 'link-176');">False</a></tt><tt class="py-op">)</tt> </tt> <a name="L825"></a><tt class="py-lineno">825</tt> <tt class="py-line"> <tt class="py-name">sense</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'(?P<'</tt><tt class="py-op">,</tt> <tt id="link-241" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-241', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">'>'</tt><tt class="py-op">,</tt> <tt id="link-242" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-242', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt class="py-name">site</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">')'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L826"></a><tt class="py-lineno">826</tt> <tt class="py-line"> <tt class="py-name">antisense</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'(?P<'</tt><tt class="py-op">,</tt> <tt id="link-243" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-243', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">'_as>'</tt><tt class="py-op">,</tt> </tt> <a name="L827"></a><tt class="py-lineno">827</tt> <tt class="py-line"> <tt id="link-244" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-244', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt id="link-245" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.Antiparallel" class="py-name" href="#" onclick="return doclink('link-245', 'Antiparallel', 'link-62');">Antiparallel</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">')'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L828"></a><tt class="py-lineno">828</tt> <tt class="py-line"> <tt class="py-name">rg</tt> <tt class="py-op">=</tt> <tt class="py-name">sense</tt> <tt class="py-op">+</tt> <tt class="py-string">'|'</tt> <tt class="py-op">+</tt> <tt class="py-name">antisense</tt> </tt> <a name="L829"></a><tt class="py-lineno">829</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L830"></a><tt class="py-lineno">830</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># exact frequency of the site. (ie freq(N) == 1, ...)</tt> </tt> <a name="L831"></a><tt class="py-lineno">831</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L832"></a><tt class="py-lineno">832</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">/</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-246" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.dna_alphabet" class="py-name" href="#" onclick="return doclink('link-246', 'dna_alphabet', 'link-47');">dna_alphabet</a></tt><tt class="py-op">[</tt><tt class="py-name">l</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">site</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt> <a name="L833"></a><tt class="py-lineno">833</tt> <tt class="py-line"> <tt class="py-name">freq</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt id="link-247" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-247', 'x', 'link-120');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-op">:</tt> <tt id="link-248" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-248', 'x', 'link-120');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">f</tt><tt class="py-op">)</tt> </tt> <a name="L834"></a><tt class="py-lineno">834</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-249" 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-249', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">freq</tt><tt class="py-op">)</tt> </tt> <a name="L835"></a><tt class="py-lineno">835</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L836"></a><tt class="py-lineno">836</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># append regex and ovhg1, they have not been appended before not to</tt> </tt> <a name="L837"></a><tt class="py-lineno">837</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># break the factory class. simply to leazy to make the changes there.</tt> </tt> <a name="L838"></a><tt class="py-lineno">838</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L839"></a><tt class="py-lineno">839</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-250" 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-250', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">rg</tt><tt class="py-op">)</tt> </tt> <a name="L840"></a><tt class="py-lineno">840</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-251" 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-251', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ovhg1</tt><tt class="py-op">)</tt> </tt> <a name="L841"></a><tt class="py-lineno">841</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-252" 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-252', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">ovhgseq</tt><tt class="py-op">)</tt> </tt> <a name="L842"></a><tt class="py-lineno">842</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">line</tt> </tt> </div><a name="L843"></a><tt class="py-lineno">843</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.removestart"></a><div id="DictionaryBuilder.removestart-def"><a name="L844"></a><tt class="py-lineno">844</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.removestart-toggle" onclick="return toggle('DictionaryBuilder.removestart');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#removestart">removestart</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">file</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="DictionaryBuilder.removestart-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.removestart-expanded"><a name="L845"></a><tt class="py-lineno">845</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L846"></a><tt class="py-lineno">846</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># remove the heading of the file.</tt> </tt> <a name="L847"></a><tt class="py-lineno">847</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L848"></a><tt class="py-lineno">848</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">l</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">dropwhile</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt><tt class="py-op">:</tt><tt class="py-name">l</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'#'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt> </div><a name="L849"></a><tt class="py-lineno">849</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.getblock"></a><div id="DictionaryBuilder.getblock-def"><a name="L850"></a><tt class="py-lineno">850</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.getblock-toggle" onclick="return toggle('DictionaryBuilder.getblock');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#getblock">getblock</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">file</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="DictionaryBuilder.getblock-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.getblock-expanded"><a name="L851"></a><tt class="py-lineno">851</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L852"></a><tt class="py-lineno">852</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># emboss_r.txt, separation between blocks is //</tt> </tt> <a name="L853"></a><tt class="py-lineno">853</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L854"></a><tt class="py-lineno">854</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-253" class="py-name" targets="Function Bio.listfns.take()=Bio.listfns-module.html#take"><a title="Bio.listfns.take" class="py-name" href="#" onclick="return doclink('link-253', 'take', 'link-253');">take</a></tt> <tt class="py-op">=</tt> <tt class="py-name">itertools</tt><tt class="py-op">.</tt><tt class="py-name">takewhile</tt> </tt> <a name="L855"></a><tt class="py-lineno">855</tt> <tt class="py-line"> <tt class="py-name">block</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">l</tt> <tt class="py-keyword">for</tt> <tt class="py-name">l</tt> <tt class="py-keyword">in</tt> <tt id="link-254" class="py-name"><a title="Bio.listfns.take" class="py-name" href="#" onclick="return doclink('link-254', 'take', 'link-253');">take</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">l</tt> <tt class="py-op">:</tt><tt class="py-keyword">not</tt> <tt class="py-name">l</tt><tt class="py-op">.</tt><tt class="py-name">startswith</tt><tt class="py-op">(</tt><tt class="py-string">'//'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">file</tt><tt class="py-op">[</tt><tt id="link-255" 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-255', 'index', 'link-255');">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="L856"></a><tt class="py-lineno">856</tt> <tt class="py-line"> <tt id="link-256" 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-256', 'index', 'link-255');">index</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">block</tt><tt class="py-op">)</tt><tt class="py-op">+</tt><tt class="py-number">1</tt> </tt> <a name="L857"></a><tt class="py-lineno">857</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">block</tt><tt class="py-op">,</tt> <tt id="link-257" 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-257', 'index', 'link-255');">index</a></tt> </tt> </div><a name="L858"></a><tt class="py-lineno">858</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.get"></a><div id="DictionaryBuilder.get-def"><a name="L859"></a><tt class="py-lineno">859</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.get-toggle" onclick="return toggle('DictionaryBuilder.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">block</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="DictionaryBuilder.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.get-expanded"><a name="L860"></a><tt class="py-lineno">860</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L861"></a><tt class="py-lineno">861</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># take what we want from the block.</tt> </tt> <a name="L862"></a><tt class="py-lineno">862</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Each block correspond to one enzyme.</tt> </tt> <a name="L863"></a><tt class="py-lineno">863</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># block[0] => enzyme name</tt> </tt> <a name="L864"></a><tt class="py-lineno">864</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># block[3] => methylation (position and type)</tt> </tt> <a name="L865"></a><tt class="py-lineno">865</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># block[5] => suppliers (as a string of single letter)</tt> </tt> <a name="L866"></a><tt class="py-lineno">866</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L867"></a><tt class="py-lineno">867</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">bl3</tt> <tt class="py-op">=</tt> <tt class="py-name">block</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-258" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip Bio.File.SGMLStripper.strip Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-258', 'strip', 'link-258');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L868"></a><tt class="py-lineno">868</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">bl3</tt> <tt class="py-op">:</tt> <tt class="py-name">bl3</tt> <tt class="py-op">=</tt> <tt id="link-259" class="py-name"><a title="Bio.EUtils.POM.False" class="py-name" href="#" onclick="return doclink('link-259', 'False', 'link-176');">False</a></tt> <tt class="py-comment"># site is not methylable</tt> </tt> <a name="L869"></a><tt class="py-lineno">869</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">block</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip Bio.File.SGMLStripper.strip Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-260', 'strip', 'link-258');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">bl3</tt><tt class="py-op">,</tt> <tt class="py-name">block</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-261" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip Bio.File.SGMLStripper.strip Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-261', 'strip', 'link-258');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> </div><a name="L870"></a><tt class="py-lineno">870</tt> <tt class="py-line"> </tt> <a name="DictionaryBuilder.information_mixer"></a><div id="DictionaryBuilder.information_mixer-def"><a name="L871"></a><tt class="py-lineno">871</tt> <a class="py-toggle" href="#" id="DictionaryBuilder.information_mixer-toggle" onclick="return toggle('DictionaryBuilder.information_mixer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#information_mixer">information_mixer</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">file1</tt><tt class="py-op">,</tt> <tt class="py-param">file2</tt><tt class="py-op">,</tt> <tt class="py-param">file3</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="DictionaryBuilder.information_mixer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DictionaryBuilder.information_mixer-expanded"><a name="L872"></a><tt class="py-lineno">872</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L873"></a><tt class="py-lineno">873</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Mix all the information from the 3 files and produce a coherent</tt> </tt> <a name="L874"></a><tt class="py-lineno">874</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># restriction record.</tt> </tt> <a name="L875"></a><tt class="py-lineno">875</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># </tt> </tt> <a name="L876"></a><tt class="py-lineno">876</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">methfile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.removestart()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#removestart"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.removestart" class="py-name" href="#" onclick="return doclink('link-262', 'removestart', 'link-262');">removestart</a></tt><tt class="py-op">(</tt><tt class="py-name">file1</tt><tt class="py-op">)</tt> </tt> <a name="L877"></a><tt class="py-lineno">877</tt> <tt class="py-line"> <tt class="py-name">sitefile</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.removestart" class="py-name" href="#" onclick="return doclink('link-263', 'removestart', 'link-262');">removestart</a></tt><tt class="py-op">(</tt><tt class="py-name">file2</tt><tt class="py-op">)</tt> </tt> <a name="L878"></a><tt class="py-lineno">878</tt> <tt class="py-line"> <tt class="py-name">supplier</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-264" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.removestart" class="py-name" href="#" onclick="return doclink('link-264', 'removestart', 'link-262');">removestart</a></tt><tt class="py-op">(</tt><tt class="py-name">file3</tt><tt class="py-op">)</tt> </tt> <a name="L879"></a><tt class="py-lineno">879</tt> <tt class="py-line"> </tt> <a name="L880"></a><tt class="py-lineno">880</tt> <tt class="py-line"> <tt class="py-name">i1</tt><tt class="py-op">,</tt> <tt class="py-name">i2</tt><tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt> </tt> <a name="L881"></a><tt class="py-lineno">881</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L882"></a><tt class="py-lineno">882</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-265" class="py-name"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-265', 'True', 'link-179');">True</a></tt> <tt class="py-op">:</tt> </tt> <a name="L883"></a><tt class="py-lineno">883</tt> <tt class="py-line"> <tt class="py-name">block</tt><tt class="py-op">,</tt> <tt class="py-name">i1</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-266" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.getblock()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#getblock"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.getblock" class="py-name" href="#" onclick="return doclink('link-266', 'getblock', 'link-266');">getblock</a></tt><tt class="py-op">(</tt><tt class="py-name">methfile</tt><tt class="py-op">,</tt> <tt class="py-name">i1</tt><tt class="py-op">)</tt> </tt> <a name="L884"></a><tt class="py-lineno">884</tt> <tt class="py-line"> <tt class="py-name">bl</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get Bio.Data.CodonTable.AmbiguousForwardTable.get Bio.EUtils.MultiDict._BaseMultiDict.get Bio.EUtils.POM.ElementNode.get Bio.GenBank.NCBIDictionary.get Bio.Mindy.BaseDB.DictLookup.get Bio.Prosite.ExPASyDictionary.get Bio.Prosite.Prodoc.ExPASyDictionary.get Bio.PubMed.Dictionary.get Bio.Restriction.Restriction.RestrictionBatch.get Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get Bio.SeqUtils.MissingTable.get Bio.SwissProt.SProt.ExPASyDictionary.get Bio.config.DBRegistry.DBGroup.get Bio.config.DBRegistry.DBObject.get Bio.config.Registry.Registry.get Martel.Parser.MartelAttributeList.get Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-267', 'get', 'link-267');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">block</tt><tt class="py-op">)</tt> </tt> <a name="L885"></a><tt class="py-lineno">885</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">sitefile</tt><tt class="py-op">[</tt><tt class="py-name">i2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-268" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip Bio.File.SGMLStripper.strip Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-268', 'strip', 'link-258');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-269', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L886"></a><tt class="py-lineno">886</tt> <tt class="py-line"> <tt id="link-270" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-270', 'name', 'link-68');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L887"></a><tt class="py-lineno">887</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-271" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-271', 'name', 'link-68');">name</a></tt> <tt class="py-op">==</tt> <tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L888"></a><tt class="py-lineno">888</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-272" 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-272', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">bl</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-comment"># -> methylation</tt> </tt> <a name="L889"></a><tt class="py-lineno">889</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-273" 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-273', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># -> suppliers</tt> </tt> <a name="L890"></a><tt class="py-lineno">890</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L891"></a><tt class="py-lineno">891</tt> <tt class="py-line"> <tt class="py-name">bl</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-274" class="py-name"><a title="Bio.Crystal.Crystal.get Bio.Data.CodonTable.AmbiguousForwardTable.get Bio.EUtils.MultiDict._BaseMultiDict.get Bio.EUtils.POM.ElementNode.get Bio.GenBank.NCBIDictionary.get Bio.Mindy.BaseDB.DictLookup.get Bio.Prosite.ExPASyDictionary.get Bio.Prosite.Prodoc.ExPASyDictionary.get Bio.PubMed.Dictionary.get Bio.Restriction.Restriction.RestrictionBatch.get Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get Bio.SeqUtils.MissingTable.get Bio.SwissProt.SProt.ExPASyDictionary.get Bio.config.DBRegistry.DBGroup.get Bio.config.DBRegistry.DBObject.get Bio.config.Registry.Registry.get Martel.Parser.MartelAttributeList.get Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-274', 'get', 'link-267');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">oldblock</tt><tt class="py-op">)</tt> </tt> <a name="L892"></a><tt class="py-lineno">892</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L893"></a><tt class="py-lineno">893</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-275" 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-275', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L894"></a><tt class="py-lineno">894</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-276" 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-276', 'append', 'link-126');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L895"></a><tt class="py-lineno">895</tt> <tt class="py-line"> <tt class="py-name">i2</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L896"></a><tt class="py-lineno">896</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt> </tt> <a name="L897"></a><tt class="py-lineno">897</tt> <tt class="py-line"> <tt class="py-name">oldblock</tt> <tt class="py-op">=</tt> <tt class="py-name">block</tt> </tt> <a name="L898"></a><tt class="py-lineno">898</tt> <tt class="py-line"> <tt class="py-name">i2</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt> <a name="L899"></a><tt class="py-lineno">899</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L900"></a><tt class="py-lineno">900</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name" targets="Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.parseline()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#parseline"><a title="Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.parseline" class="py-name" href="#" onclick="return doclink('link-277', 'parseline', 'link-277');">parseline</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt> <a name="L901"></a><tt class="py-lineno">901</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-278" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.OverhangError" class="py-name" href="#" onclick="return doclink('link-278', 'OverhangError', 'link-207');">OverhangError</a></tt> <tt class="py-op">:</tt> <tt class="py-comment"># overhang error </tt> </tt> <a name="L902"></a><tt class="py-lineno">902</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-279" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-279', 'name', 'link-68');">name</a></tt> <tt class="py-comment"># do not include the enzyme</tt> </tt> <a name="L903"></a><tt class="py-lineno">903</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">bl</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt> <a name="L904"></a><tt class="py-lineno">904</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Anyway, %s is not commercially available.\n'</tt> <tt class="py-op">%</tt><tt class="py-name">n</tt> </tt> <a name="L905"></a><tt class="py-lineno">905</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L906"></a><tt class="py-lineno">906</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">'Unfortunately, %s is commercially available.\n'</tt><tt class="py-op">%</tt><tt class="py-name">n</tt> </tt> <a name="L907"></a><tt class="py-lineno">907</tt> <tt class="py-line"> </tt> <a name="L908"></a><tt class="py-lineno">908</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt> <a name="L909"></a><tt class="py-lineno">909</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-280" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-280', 'name', 'link-68');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-281" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-281', 'enzymedict', 'link-49');">enzymedict</a></tt> <tt class="py-op">:</tt> </tt> <a name="L910"></a><tt class="py-lineno">910</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L911"></a><tt class="py-lineno">911</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># deal with TaqII and its two sites.</tt> </tt> <a name="L912"></a><tt class="py-lineno">912</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L913"></a><tt class="py-lineno">913</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\nWARNING :'</tt><tt class="py-op">,</tt> </tt> <a name="L914"></a><tt class="py-lineno">914</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-282" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-282', 'name', 'link-68');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">'has two different sites.\n'</tt> </tt> <a name="L915"></a><tt class="py-lineno">915</tt> <tt class="py-line"> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt id="link-283" class="py-name"><a title="Bio.Restriction.Restriction.DNA Bio.Restriction._Update.RestrictionCompiler.DNA" class="py-name" href="#" onclick="return doclink('link-283', 'DNA', 'link-45');">DNA</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L916"></a><tt class="py-lineno">916</tt> <tt class="py-line"> <tt class="py-name">sense1</tt> <tt class="py-op">=</tt> <tt id="link-284" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-284', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.Crystal.Crystal.tostring Bio.EUtils.POM.ElementNode.tostring Bio.Prosite.Pattern.Prosite.tostring Bio.Seq.MutableSeq.tostring Bio.Seq.Seq.tostring BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-285', 'tostring', 'link-59');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L917"></a><tt class="py-lineno">917</tt> <tt class="py-line"> <tt class="py-name">antisense1</tt> <tt class="py-op">=</tt> <tt id="link-286" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-286', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt id="link-287" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.Antiparallel" class="py-name" href="#" onclick="return doclink('link-287', 'Antiparallel', 'link-62');">Antiparallel</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L918"></a><tt class="py-lineno">918</tt> <tt class="py-line"> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt id="link-288" class="py-name"><a title="Bio.Restriction.Restriction.DNA Bio.Restriction._Update.RestrictionCompiler.DNA" class="py-name" href="#" onclick="return doclink('link-288', 'DNA', 'link-45');">DNA</a></tt><tt class="py-op">(</tt><tt id="link-289" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-289', 'enzymedict', 'link-49');">enzymedict</a></tt><tt class="py-op">[</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L919"></a><tt class="py-lineno">919</tt> <tt class="py-line"> <tt class="py-name">sense2</tt> <tt class="py-op">=</tt> <tt id="link-290" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-290', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">.</tt><tt id="link-291" class="py-name"><a title="Bio.Crystal.Crystal.tostring Bio.EUtils.POM.ElementNode.tostring Bio.Prosite.Pattern.Prosite.tostring Bio.Seq.MutableSeq.tostring Bio.Seq.Seq.tostring BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-291', 'tostring', 'link-59');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L920"></a><tt class="py-lineno">920</tt> <tt class="py-line"> <tt class="py-name">antisense2</tt> <tt class="py-op">=</tt> <tt id="link-292" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.regex" class="py-name" href="#" onclick="return doclink('link-292', 'regex', 'link-238');">regex</a></tt><tt class="py-op">(</tt><tt id="link-293" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.Antiparallel" class="py-name" href="#" onclick="return doclink('link-293', 'Antiparallel', 'link-62');">Antiparallel</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L921"></a><tt class="py-lineno">921</tt> <tt class="py-line"> <tt class="py-name">sense</tt> <tt class="py-op">=</tt> <tt class="py-string">'(?P<'</tt><tt class="py-op">+</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-string">'>'</tt><tt class="py-op">+</tt><tt class="py-name">sense1</tt><tt class="py-op">+</tt><tt class="py-string">'|'</tt><tt class="py-op">+</tt><tt class="py-name">sense2</tt><tt class="py-op">+</tt><tt class="py-string">')'</tt> </tt> <a name="L922"></a><tt class="py-lineno">922</tt> <tt class="py-line"> <tt class="py-name">antisense</tt> <tt class="py-op">=</tt> <tt class="py-string">'(?P<'</tt><tt class="py-op">+</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">+</tt><tt class="py-string">'_as>'</tt><tt class="py-op">+</tt><tt class="py-name">antisense1</tt><tt class="py-op">+</tt><tt class="py-string">'|'</tt><tt class="py-op">+</tt><tt class="py-name">antisense2</tt> <tt class="py-op">+</tt> <tt class="py-string">')'</tt> </tt> <a name="L923"></a><tt class="py-lineno">923</tt> <tt class="py-line"> <tt class="py-name">reg</tt> <tt class="py-op">=</tt> <tt class="py-name">sense</tt> <tt class="py-op">+</tt> <tt class="py-string">'|'</tt> <tt class="py-op">+</tt> <tt class="py-name">antisense</tt> </tt> <a name="L924"></a><tt class="py-lineno">924</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line</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-string">'|'</tt> <tt class="py-op">+</tt> <tt id="link-294" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-294', 'enzymedict', 'link-49');">enzymedict</a></tt><tt class="py-op">[</tt><tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L925"></a><tt class="py-lineno">925</tt> <tt class="py-line"> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">reg</tt> </tt> <a name="L926"></a><tt class="py-lineno">926</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L927"></a><tt class="py-lineno">927</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the data to produce the enzyme class are then stored in</tt> </tt> <a name="L928"></a><tt class="py-lineno">928</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># enzymedict.</tt> </tt> <a name="L929"></a><tt class="py-lineno">929</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L930"></a><tt class="py-lineno">930</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-295" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.enzymedict" class="py-name" href="#" onclick="return doclink('link-295', 'enzymedict', 'link-49');">enzymedict</a></tt><tt class="py-op">[</tt><tt id="link-296" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-296', 'name', 'link-68');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt> <a name="L931"></a><tt class="py-lineno">931</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt> <tt class="py-op">:</tt> </tt> <a name="L932"></a><tt class="py-lineno">932</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L933"></a><tt class="py-lineno">933</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-297" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-297', 'i', 'link-201');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">supplier</tt> <tt class="py-op">:</tt> </tt> <a name="L934"></a><tt class="py-lineno">934</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt> <a name="L935"></a><tt class="py-lineno">935</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># construction of the list of suppliers.</tt> </tt> <a name="L936"></a><tt class="py-lineno">936</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt> <a name="L937"></a><tt class="py-lineno">937</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt id="link-298" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-298', 'i', 'link-201');">i</a></tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip Bio.File.SGMLStripper.strip Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-299', 'strip', 'link-258');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="Bio.Nexus.Trees.Tree.split Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-300', 'split', 'link-54');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt> <a name="L938"></a><tt class="py-lineno">938</tt> <tt class="py-line"> <tt id="link-301" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.suppliersdict" class="py-name" href="#" onclick="return doclink('link-301', 'suppliersdict', 'link-50');">suppliersdict</a></tt><tt class="py-op">[</tt><tt class="py-name">t</tt><tt class="py-op">[</tt><tt class="py-number">0</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">t</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt> <a name="L939"></a><tt class="py-lineno">939</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt> </div></div><a name="L940"></a><tt class="py-lineno">940</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 09:28:09 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>