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<h1 class="epydoc">Source Code for <a href="Bio.SeqUtils-module.html">Package Bio.SeqUtils</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"># Created: Wed May 29 08:07:18 2002</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"># thomas@cbs.dtu.dk, Cecilia.Alsmark@ebc.uu.se</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 2001 by Thomas Sicheritz-Ponten and Cecilia Alsmark.</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"># All rights reserved.</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>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt><tt class="py-op">,</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="L11"></a><tt class="py-lineno"> 11</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-keyword">import</tt> <tt id="link-2" class="py-name" targets="Package Bio.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-2', 'SeqIO', 'link-2');">SeqIO</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" class="py-name" targets="Module Bio.Translate=Bio.Translate-module.html"><a title="Bio.Translate" class="py-name" href="#" onclick="return doclink('link-4', 'Translate', 'link-4');">Translate</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-5" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-5', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-6" 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-6', 'Seq', 'link-6');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-7', 'Seq', 'link-6');">Seq</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-8', 'Bio', 'link-1');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" 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-9', 'Alphabet', 'link-9');">Alphabet</a></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</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.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'Alphabet', 'link-9');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" 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-12', 'IUPAC', 'link-12');">IUPAC</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Package Bio.Data=Bio.Data-module.html"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-14', 'Data', 'link-14');">Data</a></tt> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name" targets="Module Bio.Data.IUPACData=Bio.Data.IUPACData-module.html"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-15', 'IUPACData', 'link-15');">IUPACData</a></tt><tt class="py-op">,</tt> <tt id="link-16" class="py-name" targets="Module Bio.Data.CodonTable=Bio.Data.CodonTable-module.html,Class Bio.Data.CodonTable.CodonTable=Bio.Data.CodonTable.CodonTable-class.html"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-16', 'CodonTable', 'link-16');">CodonTable</a></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment">######################################</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"># DNA</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">######################</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"># {{{ </tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="reverse"></a><div id="reverse-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="reverse-toggle" onclick="return toggle('reverse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#reverse">reverse</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="reverse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="reverse-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">   <tt class="py-docstring">"""Reverse the sequence. Works on string sequences.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-docstring">   """</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">   <tt class="py-name">r</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-17', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-18" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-18', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">   <tt class="py-name">r</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-19', 'reverse', 'link-19');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">r</tt><tt class="py-op">)</tt> </tt>
</div><a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"> </tt>
<a name="GC"></a><div id="GC-def"><a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="GC-toggle" onclick="return toggle('GC');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#GC">GC</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GC-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GC-expanded"><a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">   <tt class="py-docstring">""" calculates G+C content """</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-comment">#      19/8/03: Iddo: added provision for lowercase</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#      19/8/03: Iddo: divide by the sequence's length rather than by the</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#      A+T+G+C number. In that way, make provision for N.</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"><tt class="py-comment"></tt>        </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">   <tt id="link-20" 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-20', 'd', 'link-20');">d</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">nt</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">'G'</tt><tt class="py-op">,</tt><tt class="py-string">'C'</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">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</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-op">:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">      <tt id="link-21" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-21', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">nt</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-22', 'seq', 'link-18');">seq</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-23', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">nt</tt><tt class="py-op">)</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">      <tt class="py-name">gc</tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-24', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-25" 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-25', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'G'</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-26" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-26', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-27" 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-27', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'C'</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-28" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-28', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-29" 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-29', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'g'</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-30" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-30', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-31" 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-31', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'c'</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="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">           <tt id="link-32" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-32', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-33" 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-33', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'S'</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-34" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-34', 'd', 'link-20');">d</a></tt><tt class="py-op">.</tt><tt id="link-35" 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-35', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'s'</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">   <tt class="py-keyword">if</tt> <tt class="py-name">gc</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-comment">#   return gc*100.0/(d['A'] +d['T'] + gc)</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-comment"></tt>   <tt class="py-keyword">return</tt> <tt class="py-name">gc</tt><tt class="py-op">*</tt><tt class="py-number">100.0</tt><tt class="py-op">/</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-36', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">     </tt>
<a name="GC123"></a><div id="GC123-def"><a name="L47"></a><tt class="py-lineno"> 47</tt> <a class="py-toggle" href="#" id="GC123-toggle" onclick="return toggle('GC123');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#GC123">GC123</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GC123-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GC123-expanded"><a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">   <tt class="py-docstring">" calculates total G+C content plus first, second and third position "</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">   <tt id="link-37" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-37', 'd', 'link-20');">d</a></tt><tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">nt</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">'G'</tt><tt class="py-op">,</tt><tt class="py-string">'C'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">      <tt id="link-38" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-38', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">nt</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-number">0</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-39" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-40', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">      <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-41', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-42', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-39');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> <tt class="py-op">&lt;</tt><tt class="py-number">3</tt><tt class="py-op">:</tt> <tt class="py-name">codon</tt> <tt class="py-op">+=</tt> <tt class="py-string">'  '</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">         <tt class="py-keyword">for</tt> <tt class="py-name">nt</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">'G'</tt><tt class="py-op">,</tt><tt class="py-string">'C'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">codon</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">nt</tt> <tt class="py-keyword">or</tt> <tt class="py-name">codon</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-name">nt</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">                <tt id="link-44" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-44', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">nt</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-45', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-name">nt</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">pos</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt><tt class="py-number">1</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>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">   <tt class="py-name">gc</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">   <tt class="py-name">gcall</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">   <tt class="py-name">nall</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">      <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">         <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt id="link-47" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-47', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'G'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-49" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-49', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'C'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-50" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-50', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt><tt id="link-51" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-51', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'T'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-52" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-52', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-53" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-53', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'A'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-54" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-54', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">         <tt class="py-name">gc</tt><tt class="py-op">[</tt><tt id="link-55" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-55', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-56" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-56', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'G'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-57" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-57', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-58" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-58', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'C'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-59" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-59', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-number">100.0</tt><tt class="py-op">/</tt><tt class="py-name">n</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">      <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">         <tt class="py-name">gc</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-60', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </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 class="py-name">gcall</tt> <tt class="py-op">=</tt> <tt class="py-name">gcall</tt> <tt class="py-op">+</tt> <tt id="link-61" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-61', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'G'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-62', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt id="link-63" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-63', 'd', 'link-20');">d</a></tt><tt class="py-op">[</tt><tt class="py-string">'C'</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt id="link-64" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-64', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">      <tt class="py-name">nall</tt> <tt class="py-op">=</tt> <tt class="py-name">nall</tt> <tt class="py-op">+</tt> <tt class="py-name">n</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">   <tt class="py-name">gcall</tt> <tt class="py-op">=</tt> <tt class="py-number">100.0</tt><tt class="py-op">*</tt><tt class="py-name">gcall</tt><tt class="py-op">/</tt><tt class="py-name">nall</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">gcall</tt><tt class="py-op">,</tt> <tt class="py-name">gc</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">gc</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">gc</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"> </tt>
<a name="GC_skew"></a><div id="GC_skew-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="GC_skew-toggle" onclick="return toggle('GC_skew');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#GC_skew">GC_skew</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">window</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GC_skew-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GC_skew-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">   <tt class="py-docstring">""" calculates GC skew (G-C)/(G+C) """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-comment"># 8/19/03: Iddo: added lowercase </tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-comment"></tt>   <tt id="link-65" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-65', 'values', 'link-65');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-66" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-66', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-67', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">window</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">      <tt id="link-68" 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-68', 's', 'link-68');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-69" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-69', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt id="link-70" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-70', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt> <tt id="link-71" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-71', 'i', 'link-39');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-name">window</tt><tt class="py-op">]</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">      <tt class="py-name">g</tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-72', 's', 'link-68');">s</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-73', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'G'</tt><tt class="py-op">)</tt> <tt class="py-op">+</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-68');">s</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-75', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'g'</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">      <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt id="link-76" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-76', 's', 'link-68');">s</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-77', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'C'</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-78" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-78', 's', 'link-68');">s</a></tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-79', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">'c'</tt><tt class="py-op">)</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">      <tt class="py-name">skew</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">-</tt><tt class="py-name">c</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">g</tt><tt class="py-op">+</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">      <tt id="link-80" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-80', 'values', 'link-65');">values</a></tt><tt class="py-op">.</tt><tt id="link-81" 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-81', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">skew</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt id="link-82" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-82', 'values', 'link-65');">values</a></tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-comment"># 8/19/03 Iddo: moved these imports from within the function as</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># ``import * '' is only</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># allowed within the module</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Brad -- added an import check so you don't have to have Tkinter</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># installed to use other sequtils functions. A little ugly but</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># it really should be fixed by not using 'import *' which I'm not</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># really excited about doing right now.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt class="py-name">Tkinter</tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</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="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">    <tt class="py-keyword">pass</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">math</tt> <tt class="py-keyword">import</tt> <tt id="link-83" class="py-name" targets="Variable Bio.Affy.CelFile.pi=Bio.Affy.CelFile-module.html#pi,Variable Bio.LogisticRegression.pi=Bio.LogisticRegression-module.html#pi,Variable Bio.MarkovModel.pi=Bio.MarkovModel-module.html#pi,Variable Bio.MaxEntropy.pi=Bio.MaxEntropy-module.html#pi,Variable Bio.NaiveBayes.pi=Bio.NaiveBayes-module.html#pi,Variable Bio.PDB.Vector'.pi=Bio.PDB.Vector%27-module.html#pi,Method Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi()=Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint-class.html#pi,Variable Bio.Statistics.lowess.pi=Bio.Statistics.lowess-module.html#pi,Variable Bio.distance.pi=Bio.distance-module.html#pi,Variable Bio.kNN.pi=Bio.kNN-module.html#pi"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-83', 'pi', 'link-83');">pi</a></tt><tt class="py-op">,</tt> <tt id="link-84" class="py-name" targets="Variable Bio.Affy.CelFile.sin=Bio.Affy.CelFile-module.html#sin,Variable Bio.LogisticRegression.sin=Bio.LogisticRegression-module.html#sin,Variable Bio.MarkovModel.sin=Bio.MarkovModel-module.html#sin,Variable Bio.MaxEntropy.sin=Bio.MaxEntropy-module.html#sin,Variable Bio.NaiveBayes.sin=Bio.NaiveBayes-module.html#sin,Variable Bio.PDB.Vector'.sin=Bio.PDB.Vector%27-module.html#sin,Variable Bio.Statistics.lowess.sin=Bio.Statistics.lowess-module.html#sin,Variable Bio.distance.sin=Bio.distance-module.html#sin,Variable Bio.kNN.sin=Bio.kNN-module.html#sin"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-84', 'sin', 'link-84');">sin</a></tt><tt class="py-op">,</tt> <tt id="link-85" class="py-name" targets="Variable Bio.Affy.CelFile.cos=Bio.Affy.CelFile-module.html#cos,Variable Bio.LogisticRegression.cos=Bio.LogisticRegression-module.html#cos,Variable Bio.MarkovModel.cos=Bio.MarkovModel-module.html#cos,Variable Bio.MaxEntropy.cos=Bio.MaxEntropy-module.html#cos,Variable Bio.NaiveBayes.cos=Bio.NaiveBayes-module.html#cos,Variable Bio.PDB.Vector'.cos=Bio.PDB.Vector%27-module.html#cos,Variable Bio.Statistics.lowess.cos=Bio.Statistics.lowess-module.html#cos,Variable Bio.distance.cos=Bio.distance-module.html#cos,Variable Bio.kNN.cos=Bio.kNN-module.html#cos"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-85', 'cos', 'link-85');">cos</a></tt><tt class="py-op">,</tt> <tt id="link-86" class="py-name" targets="Variable Bio.Affy.CelFile.log=Bio.Affy.CelFile-module.html#log,Variable Bio.LogisticRegression.log=Bio.LogisticRegression-module.html#log,Variable Bio.MarkovModel.log=Bio.MarkovModel-module.html#log,Variable Bio.MaxEntropy.log=Bio.MaxEntropy-module.html#log,Variable Bio.NaiveBayes.log=Bio.NaiveBayes-module.html#log,Variable Bio.Statistics.lowess.log=Bio.Statistics.lowess-module.html#log,Variable Bio.distance.log=Bio.distance-module.html#log,Variable Bio.kNN.log=Bio.kNN-module.html#log"><a title="Bio.Affy.CelFile.log
Bio.LogisticRegression.log
Bio.MarkovModel.log
Bio.MaxEntropy.log
Bio.NaiveBayes.log
Bio.Statistics.lowess.log
Bio.distance.log
Bio.kNN.log" class="py-name" href="#" onclick="return doclink('link-86', 'log', 'link-86');">log</a></tt> </tt>
<a name="xGC_skew"></a><div id="xGC_skew-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="xGC_skew-toggle" onclick="return toggle('xGC_skew');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#xGC_skew">xGC_skew</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">window</tt> <tt class="py-op">=</tt> <tt class="py-number">1000</tt><tt class="py-op">,</tt> <tt class="py-param">zoom</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt><tt class="py-op">,</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">                         <tt class="py-param">r</tt> <tt class="py-op">=</tt> <tt class="py-number">300</tt><tt class="py-op">,</tt> <tt class="py-param">px</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt><tt class="py-op">,</tt> <tt class="py-param">py</tt> <tt class="py-op">=</tt> <tt class="py-number">100</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="xGC_skew-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="xGC_skew-expanded"><a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">   <tt class="py-docstring">" calculates and plots normal and accumulated GC skew (GRAPHICS !!!) "</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">    </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">   <tt class="py-name">yscroll</tt> <tt class="py-op">=</tt> <tt class="py-name">Scrollbar</tt><tt class="py-op">(</tt><tt class="py-name">orient</tt> <tt class="py-op">=</tt> <tt class="py-name">VERTICAL</tt><tt class="py-op">)</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">   <tt class="py-name">xscroll</tt> <tt class="py-op">=</tt> <tt class="py-name">Scrollbar</tt><tt class="py-op">(</tt><tt class="py-name">orient</tt> <tt class="py-op">=</tt> <tt class="py-name">HORIZONTAL</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt> <tt class="py-op">=</tt> <tt class="py-name">Canvas</tt><tt class="py-op">(</tt><tt class="py-name">yscrollcommand</tt> <tt class="py-op">=</tt> <tt class="py-name">yscroll</tt><tt class="py-op">.</tt><tt id="link-87" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set,Method Bio.config.DBRegistry.DBObject.set()=Bio.config.DBRegistry.DBObject-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-87', 'set', 'link-87');">set</a></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">xscrollcommand</tt> <tt class="py-op">=</tt> <tt class="py-name">xscroll</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-88', 'set', 'link-87');">set</a></tt><tt class="py-op">,</tt> <tt class="py-name">background</tt> <tt class="py-op">=</tt> <tt class="py-string">'white'</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">win</tt> <tt class="py-op">=</tt> <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">winfo_toplevel</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-name">win</tt><tt class="py-op">.</tt><tt class="py-name">geometry</tt><tt class="py-op">(</tt><tt class="py-string">'700x700'</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">    </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">   <tt class="py-name">yscroll</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name" targets="Package Bio.config=Bio.config-module.html"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-89', 'config', 'link-89');">config</a></tt><tt class="py-op">(</tt><tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">yview</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">   <tt class="py-name">xscroll</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="Bio.config" class="py-name" href="#" onclick="return doclink('link-90', 'config', 'link-89');">config</a></tt><tt class="py-op">(</tt><tt class="py-name">command</tt> <tt class="py-op">=</tt> <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">xview</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">   <tt class="py-name">yscroll</tt><tt class="py-op">.</tt><tt class="py-name">pack</tt><tt class="py-op">(</tt><tt class="py-name">side</tt> <tt class="py-op">=</tt> <tt class="py-name">RIGHT</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-name">Y</tt><tt class="py-op">)</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">   <tt class="py-name">xscroll</tt><tt class="py-op">.</tt><tt class="py-name">pack</tt><tt class="py-op">(</tt><tt class="py-name">side</tt> <tt class="py-op">=</tt> <tt class="py-name">BOTTOM</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-name">X</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">pack</tt><tt class="py-op">(</tt><tt class="py-name">fill</tt><tt class="py-op">=</tt><tt class="py-name">BOTH</tt><tt class="py-op">,</tt> <tt class="py-name">side</tt> <tt class="py-op">=</tt> <tt class="py-name">LEFT</tt><tt class="py-op">,</tt> <tt class="py-name">expand</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt id="link-91" 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-91', 'update', 'link-91');">update</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">   <tt class="py-name">X0</tt><tt class="py-op">,</tt> <tt class="py-name">Y0</tt>  <tt class="py-op">=</tt> <tt class="py-name">r</tt> <tt class="py-op">+</tt> <tt class="py-name">px</tt><tt class="py-op">,</tt> <tt class="py-name">r</tt> <tt class="py-op">+</tt> <tt class="py-name">py</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">   <tt class="py-name">x1</tt><tt class="py-op">,</tt> <tt class="py-name">x2</tt><tt class="py-op">,</tt> <tt class="py-name">y1</tt><tt class="py-op">,</tt> <tt class="py-name">y2</tt> <tt class="py-op">=</tt> <tt class="py-name">X0</tt> <tt class="py-op">-</tt> <tt class="py-name">r</tt><tt class="py-op">,</tt> <tt class="py-name">X0</tt> <tt class="py-op">+</tt> <tt class="py-name">r</tt><tt class="py-op">,</tt> <tt class="py-name">Y0</tt> <tt class="py-op">-</tt><tt class="py-name">r</tt><tt class="py-op">,</tt> <tt class="py-name">Y0</tt> <tt class="py-op">+</tt> <tt class="py-name">r</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">   <tt class="py-name">ty</tt> <tt class="py-op">=</tt> <tt class="py-name">Y0</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_text</tt><tt class="py-op">(</tt><tt class="py-name">X0</tt><tt class="py-op">,</tt> <tt class="py-name">ty</tt><tt class="py-op">,</tt> <tt id="link-92" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-92', 'text', 'link-92');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'%s...%s (%d nt)'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-93', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-94" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-94', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">7</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-95" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-95', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">   <tt class="py-name">ty</tt> <tt class="py-op">+=</tt><tt class="py-number">20</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_text</tt><tt class="py-op">(</tt><tt class="py-name">X0</tt><tt class="py-op">,</tt> <tt class="py-name">ty</tt><tt class="py-op">,</tt> <tt id="link-96" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-96', 'text', 'link-92');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'GC %3.2f%%'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-97" class="py-name" targets="Function Bio.SeqUtils.GC()=Bio.SeqUtils-module.html#GC"><a title="Bio.SeqUtils.GC" class="py-name" href="#" onclick="return doclink('link-97', 'GC', 'link-97');">GC</a></tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-98', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">   <tt class="py-name">ty</tt> <tt class="py-op">+=</tt><tt class="py-number">20</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_text</tt><tt class="py-op">(</tt><tt class="py-name">X0</tt><tt class="py-op">,</tt> <tt class="py-name">ty</tt><tt class="py-op">,</tt> <tt id="link-99" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-99', 'text', 'link-92');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'GC Skew'</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-string">'blue'</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">   <tt class="py-name">ty</tt> <tt class="py-op">+=</tt><tt class="py-number">20</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_text</tt><tt class="py-op">(</tt><tt class="py-name">X0</tt><tt class="py-op">,</tt> <tt class="py-name">ty</tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-100', 'text', 'link-92');">text</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Accumulated GC Skew'</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-string">'magenta'</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">   <tt class="py-name">ty</tt> <tt class="py-op">+=</tt><tt class="py-number">20</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_oval</tt><tt class="py-op">(</tt><tt class="py-name">x1</tt><tt class="py-op">,</tt><tt class="py-name">y1</tt><tt class="py-op">,</tt> <tt class="py-name">x2</tt><tt class="py-op">,</tt> <tt class="py-name">y2</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">   <tt id="link-101" class="py-name" targets="Variable Bio.FSSP.fssp_rec.align.acc=Bio.FSSP.fssp_rec.align-class.html#acc"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-101', 'acc', 'link-101');">acc</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">   <tt id="link-102" 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-102', 'start', 'link-102');">start</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">gc</tt> <tt class="py-keyword">in</tt> <tt id="link-103" class="py-name" targets="Function Bio.SeqUtils.GC_skew()=Bio.SeqUtils-module.html#GC_skew"><a title="Bio.SeqUtils.GC_skew" class="py-name" href="#" onclick="return doclink('link-103', 'GC_skew', 'link-103');">GC_skew</a></tt><tt class="py-op">(</tt><tt id="link-104" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-104', 'seq', 'link-18');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">window</tt><tt class="py-op">)</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">r1</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">      <tt id="link-105" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-105', 'acc', 'link-101');">acc</a></tt><tt class="py-op">+=</tt><tt class="py-name">gc</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">      <tt class="py-comment"># GC skew</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-comment"></tt>      <tt class="py-name">alpha</tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-106', 'pi', 'link-83');">pi</a></tt> <tt class="py-op">-</tt> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">*</tt><tt id="link-107" class="py-name"><a title="Bio.Affy.CelFile.pi
Bio.LogisticRegression.pi
Bio.MarkovModel.pi
Bio.MaxEntropy.pi
Bio.NaiveBayes.pi
Bio.PDB.Vector'.pi
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.pi
Bio.Statistics.lowess.pi
Bio.distance.pi
Bio.kNN.pi" class="py-name" href="#" onclick="return doclink('link-107', 'pi', 'link-83');">pi</a></tt><tt class="py-op">*</tt><tt id="link-108" 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-108', 'start', 'link-102');">start</a></tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-109" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-109', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">      <tt class="py-name">r2</tt> <tt class="py-op">=</tt> <tt class="py-name">r1</tt> <tt class="py-op">-</tt> <tt class="py-name">gc</tt><tt class="py-op">*</tt><tt class="py-name">zoom</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">      <tt class="py-name">x1</tt> <tt class="py-op">=</tt> <tt class="py-name">X0</tt> <tt class="py-op">+</tt> <tt class="py-name">r1</tt> <tt class="py-op">*</tt> <tt id="link-110" class="py-name"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-110', 'sin', 'link-84');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">      <tt class="py-name">y1</tt> <tt class="py-op">=</tt> <tt class="py-name">Y0</tt> <tt class="py-op">+</tt> <tt class="py-name">r1</tt> <tt class="py-op">*</tt> <tt id="link-111" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-111', 'cos', 'link-85');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">      <tt class="py-name">x2</tt> <tt class="py-op">=</tt> <tt class="py-name">X0</tt> <tt class="py-op">+</tt> <tt class="py-name">r2</tt> <tt class="py-op">*</tt> <tt id="link-112" class="py-name"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-112', 'sin', 'link-84');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">      <tt class="py-name">y2</tt> <tt class="py-op">=</tt> <tt class="py-name">Y0</tt> <tt class="py-op">+</tt> <tt class="py-name">r2</tt> <tt class="py-op">*</tt> <tt id="link-113" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-113', 'cos', 'link-85');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</tt><tt class="py-op">)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">      <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_line</tt><tt class="py-op">(</tt><tt class="py-name">x1</tt><tt class="py-op">,</tt><tt class="py-name">y1</tt><tt class="py-op">,</tt><tt class="py-name">x2</tt><tt class="py-op">,</tt><tt class="py-name">y2</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-string">'blue'</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">      <tt class="py-comment"># accumulated GC skew</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-comment"></tt>      <tt class="py-name">r1</tt> <tt class="py-op">=</tt> <tt class="py-name">r</tt> <tt class="py-op">-</tt> <tt class="py-number">50</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">      <tt class="py-name">r2</tt> <tt class="py-op">=</tt> <tt class="py-name">r1</tt> <tt class="py-op">-</tt> <tt id="link-114" class="py-name"><a title="Bio.FSSP.fssp_rec.align.acc" class="py-name" href="#" onclick="return doclink('link-114', 'acc', 'link-101');">acc</a></tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">      <tt class="py-name">x1</tt> <tt class="py-op">=</tt> <tt class="py-name">X0</tt> <tt class="py-op">+</tt> <tt class="py-name">r1</tt> <tt class="py-op">*</tt> <tt id="link-115" class="py-name"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-115', 'sin', 'link-84');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</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">y1</tt> <tt class="py-op">=</tt> <tt class="py-name">Y0</tt> <tt class="py-op">+</tt> <tt class="py-name">r1</tt> <tt class="py-op">*</tt> <tt id="link-116" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-116', 'cos', 'link-85');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</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">x2</tt> <tt class="py-op">=</tt> <tt class="py-name">X0</tt> <tt class="py-op">+</tt> <tt class="py-name">r2</tt> <tt class="py-op">*</tt> <tt id="link-117" class="py-name"><a title="Bio.Affy.CelFile.sin
Bio.LogisticRegression.sin
Bio.MarkovModel.sin
Bio.MaxEntropy.sin
Bio.NaiveBayes.sin
Bio.PDB.Vector'.sin
Bio.Statistics.lowess.sin
Bio.distance.sin
Bio.kNN.sin" class="py-name" href="#" onclick="return doclink('link-117', 'sin', 'link-84');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</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">y2</tt> <tt class="py-op">=</tt> <tt class="py-name">Y0</tt> <tt class="py-op">+</tt> <tt class="py-name">r2</tt> <tt class="py-op">*</tt> <tt id="link-118" class="py-name"><a title="Bio.Affy.CelFile.cos
Bio.LogisticRegression.cos
Bio.MarkovModel.cos
Bio.MaxEntropy.cos
Bio.NaiveBayes.cos
Bio.PDB.Vector'.cos
Bio.Statistics.lowess.cos
Bio.distance.cos
Bio.kNN.cos" class="py-name" href="#" onclick="return doclink('link-118', 'cos', 'link-85');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">alpha</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">canvas</tt><tt class="py-op">.</tt><tt class="py-name">create_line</tt><tt class="py-op">(</tt><tt class="py-name">x1</tt><tt class="py-op">,</tt><tt class="py-name">y1</tt><tt class="py-op">,</tt><tt class="py-name">x2</tt><tt class="py-op">,</tt><tt class="py-name">y2</tt><tt class="py-op">,</tt> <tt class="py-name">fill</tt> <tt class="py-op">=</tt> <tt class="py-string">'magenta'</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">      <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt id="link-119" 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-119', 'update', 'link-91');">update</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">      <tt id="link-120" 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-120', 'start', 'link-102');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-121" 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-121', 'start', 'link-102');">start</a></tt> <tt class="py-op">+</tt> <tt class="py-name">window</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">       </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">   <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">configure</tt><tt class="py-op">(</tt><tt class="py-name">scrollregion</tt> <tt class="py-op">=</tt> <tt class="py-name">canvas</tt><tt class="py-op">.</tt><tt class="py-name">bbox</tt><tt class="py-op">(</tt><tt class="py-name">ALL</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"> </tt>
<a name="molecular_weight"></a><div id="molecular_weight-def"><a name="L164"></a><tt class="py-lineno">164</tt> <a class="py-toggle" href="#" id="molecular_weight-toggle" onclick="return toggle('molecular_weight');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#molecular_weight">molecular_weight</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="molecular_weight-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="molecular_weight-expanded"><a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">   <tt class="py-keyword">if</tt> <tt id="link-122" 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-122', 'type', 'link-122');">type</a></tt><tt class="py-op">(</tt><tt id="link-123" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-123', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-124" class="py-name"><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-124', 'type', 'link-122');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">''</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt id="link-125" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-125', 'seq', 'link-18');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-126" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-126', 'Seq', 'link-6');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-127" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-127', 'seq', 'link-18');">seq</a></tt><tt class="py-op">,</tt> <tt id="link-128" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-128', 'IUPAC', 'link-12');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-129" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_dna=Bio.Alphabet.IUPAC-module.html#unambiguous_dna"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-129', 'unambiguous_dna', 'link-129');">unambiguous_dna</a></tt><tt class="py-op">)</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">   <tt class="py-name">weight_table</tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-130', 'IUPACData', 'link-15');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name" targets="Variable Bio.Data.IUPACData.unambiguous_dna_weights=Bio.Data.IUPACData-module.html#unambiguous_dna_weights"><a title="Bio.Data.IUPACData.unambiguous_dna_weights" class="py-name" href="#" onclick="return doclink('link-131', 'unambiguous_dna_weights', 'link-131');">unambiguous_dna_weights</a></tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">   <tt id="link-132" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.sum()=Bio.Nexus.Nexus.StepMatrix-class.html#sum,Function Bio.utils.sum()=Bio.utils-module.html#sum"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-132', 'sum', 'link-132');">sum</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-133" 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-133', 'x', 'link-133');">x</a></tt> <tt class="py-keyword">in</tt> <tt id="link-134" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-134', 'seq', 'link-18');">seq</a></tt><tt class="py-op">:</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">      <tt id="link-135" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-135', 'sum', 'link-132');">sum</a></tt> <tt class="py-op">+=</tt> <tt class="py-name">weight_table</tt><tt class="py-op">[</tt><tt id="link-136" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-136', 'x', 'link-133');">x</a></tt><tt class="py-op">]</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt id="link-137" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.sum
Bio.utils.sum" class="py-name" href="#" onclick="return doclink('link-137', 'sum', 'link-132');">sum</a></tt> </tt>
</div><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"> </tt>
<a name="nt_search"></a><div id="nt_search-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="nt_search-toggle" onclick="return toggle('nt_search');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#nt_search">nt_search</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">subseq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="nt_search-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="nt_search-expanded"><a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">   <tt class="py-docstring">""" search for a DNA subseq in sequence</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">       use ambiguous values (like N = A or T or C or G, R = A or G etc.)</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line"><tt class="py-docstring">       searches only on forward strand</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line"><tt class="py-docstring">   """</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">   <tt id="link-138" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-138', 'pattern', 'link-138');">pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">nt</tt> <tt class="py-keyword">in</tt> <tt class="py-name">subseq</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">      <tt id="link-139" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-139', 'value', 'link-139');">value</a></tt> <tt class="py-op">=</tt> <tt id="link-140" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-140', 'IUPACData', 'link-15');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-141" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_dna_values=Bio.Data.IUPACData-module.html#ambiguous_dna_values"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-141', 'ambiguous_dna_values', 'link-141');">ambiguous_dna_values</a></tt><tt class="py-op">[</tt><tt class="py-name">nt</tt><tt class="py-op">]</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-142" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-142', 'value', 'link-139');">value</a></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="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">         <tt id="link-143" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-143', 'pattern', 'link-138');">pattern</a></tt> <tt class="py-op">+=</tt> <tt id="link-144" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-144', 'value', 'link-139');">value</a></tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">      <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">         <tt id="link-145" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-145', 'pattern', 'link-138');">pattern</a></tt> <tt class="py-op">+=</tt> <tt class="py-string">'[%s]'</tt> <tt class="py-op">%</tt> <tt id="link-146" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-146', 'value', 'link-139');">value</a></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">   <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">   <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-147" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-147', 'pattern', 'link-138');">pattern</a></tt><tt class="py-op">]</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">   <tt class="py-name">l</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-148" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-148', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">   <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">      <tt class="py-name">pos</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">      <tt id="link-149" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-149', 's', 'link-68');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-150" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-150', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">pos</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">m</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-151" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-151', 'search', 'link-151');">search</a></tt><tt class="py-op">(</tt><tt id="link-152" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-152', 'pattern', 'link-138');">pattern</a></tt><tt class="py-op">,</tt> <tt id="link-153" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-153', 's', 'link-68');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">m</tt><tt class="py-op">:</tt> <tt class="py-keyword">break</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">      <tt class="py-name">pos</tt> <tt class="py-op">+=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">.</tt><tt id="link-154" 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-154', 'start', 'link-102');">start</a></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="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">      <tt class="py-name">result</tt><tt class="py-op">.</tt><tt id="link-155" 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-155', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">)</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">result</tt> </tt>
</div><a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"><tt class="py-comment"># }}}</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-comment"></tt>    </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-comment">######################################</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Protein</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">######################</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"># {{{ </tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line"><tt class="py-comment"># temporary hack for exception free translation of "dirty" DNA</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"># should be moved to ???</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="ProteinX"></a><div id="ProteinX-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="ProteinX-toggle" onclick="return toggle('ProteinX');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqUtils.ProteinX-class.html">ProteinX</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ProteinX-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ProteinX-expanded"><a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">   <tt id="link-156" class="py-name" targets="Variable Bio.Alphabet.Alphabet.letters=Bio.Alphabet.Alphabet-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACProtein.letters=Bio.Alphabet.IUPAC.IUPACProtein-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html#letters,Variable Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html#letters,Variable Bio.Alphabet.Reduced.HPModel.letters=Bio.Alphabet.Reduced.HPModel-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy10.letters=Bio.Alphabet.Reduced.Murphy10-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy15.letters=Bio.Alphabet.Reduced.Murphy15-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy4.letters=Bio.Alphabet.Reduced.Murphy4-class.html#letters,Variable Bio.Alphabet.Reduced.Murphy8.letters=Bio.Alphabet.Reduced.Murphy8-class.html#letters,Variable Bio.Alphabet.Reduced.PC5.letters=Bio.Alphabet.Reduced.PC5-class.html#letters,Variable Bio.Alphabet.SecondaryStructure.letters=Bio.Alphabet.SecondaryStructure-class.html#letters,Variable Bio.Alphabet.SingleLetterAlphabet.letters=Bio.Alphabet.SingleLetterAlphabet-class.html#letters,Variable Bio.Alphabet.ThreeLetterProtein.letters=Bio.Alphabet.ThreeLetterProtein-class.html#letters,Variable Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters=Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet-class.html#letters,Variable Bio.SeqUtils.ProteinX.letters=Bio.SeqUtils.ProteinX-class.html#letters"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-156', 'letters', 'link-156');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-157" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-157', 'IUPACData', 'link-15');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-158" class="py-name" targets="Variable Bio.Data.IUPACData.extended_protein_letters=Bio.Data.IUPACData-module.html#extended_protein_letters"><a title="Bio.Data.IUPACData.extended_protein_letters" class="py-name" href="#" onclick="return doclink('link-158', 'extended_protein_letters', 'link-158');">extended_protein_letters</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"X"</tt> </tt>
</div><a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line"> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line"><tt id="link-159" class="py-name" targets="Variable Bio.SeqUtils.proteinX=Bio.SeqUtils-module.html#proteinX"><a title="Bio.SeqUtils.proteinX" class="py-name" href="#" onclick="return doclink('link-159', 'proteinX', 'link-159');">proteinX</a></tt> <tt class="py-op">=</tt> <tt id="link-160" class="py-name" targets="Class Bio.SeqUtils.ProteinX=Bio.SeqUtils.ProteinX-class.html"><a title="Bio.SeqUtils.ProteinX" class="py-name" href="#" onclick="return doclink('link-160', 'ProteinX', 'link-160');">ProteinX</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"> </tt>
<a name="MissingTable"></a><div id="MissingTable-def"><a name="L213"></a><tt class="py-lineno">213</tt> <a class="py-toggle" href="#" id="MissingTable-toggle" onclick="return toggle('MissingTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqUtils.MissingTable-class.html">MissingTable</a><tt class="py-op">:</tt> </tt>
</div><div id="MissingTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MissingTable-expanded"><a name="MissingTable.__init__"></a><div id="MissingTable.__init__-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="MissingTable.__init__-toggle" onclick="return toggle('MissingTable.__init__');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.MissingTable-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">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MissingTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="MissingTable.__init__-expanded"><a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_table</tt> <tt class="py-op">=</tt> <tt id="link-161" class="py-name" targets="Variable Bio.CDD.cdd_format.table=Bio.CDD.cdd_format-module.html#table,Variable Bio.expressions.blast.ncbiblast.table=Bio.expressions.blast.ncbiblast-module.html#table"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-161', 'table', 'link-161');">table</a></tt> </tt>
</div><a name="MissingTable.get"></a><div id="MissingTable.get-def"><a name="L216"></a><tt class="py-lineno">216</tt> <a class="py-toggle" href="#" id="MissingTable.get-toggle" onclick="return toggle('MissingTable.get');">-</a><tt class="py-line">  <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils.MissingTable-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">codon</tt><tt class="py-op">,</tt> <tt class="py-param">stop_symbol</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MissingTable.get-collapsed" style="display:none;" pad="+++" indent="++++++"></div><div id="MissingTable.get-expanded"><a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">      <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_table</tt><tt class="py-op">.</tt><tt id="link-162" 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-162', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">,</tt> <tt class="py-name">stop_symbol</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">    <tt class="py-keyword">except</tt> <tt id="link-163" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-163', 'CodonTable', 'link-16');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-164" class="py-name" targets="Class Bio.Data.CodonTable.TranslationError=Bio.Data.CodonTable.TranslationError-class.html"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-164', 'TranslationError', 'link-164');">TranslationError</a></tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">      <tt class="py-keyword">return</tt> <tt class="py-string">'X'</tt> </tt>
</div></div><a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line"> </tt>
<a name="makeTableX"></a><div id="makeTableX-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="makeTableX-toggle" onclick="return toggle('makeTableX');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#makeTableX">makeTableX</a><tt class="py-op">(</tt><tt class="py-param">table</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="makeTableX-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="makeTableX-expanded"><a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">  <tt class="py-keyword">assert</tt> <tt id="link-165" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-165', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-166" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.protein_alphabet=Bio.Data.CodonTable.CodonTable-class.html#protein_alphabet,Variable Bio.Data.CodonTable.NCBICodonTable.protein_alphabet=Bio.Data.CodonTable.NCBICodonTable-class.html#protein_alphabet"><a title="Bio.Data.CodonTable.CodonTable.protein_alphabet
Bio.Data.CodonTable.NCBICodonTable.protein_alphabet" class="py-name" href="#" onclick="return doclink('link-166', 'protein_alphabet', 'link-166');">protein_alphabet</a></tt> <tt class="py-op">==</tt> <tt id="link-167" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-167', 'IUPAC', 'link-12');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name" targets="Variable Bio.Alphabet.IUPAC.extended_protein=Bio.Alphabet.IUPAC-module.html#extended_protein"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-168', 'extended_protein', 'link-168');">extended_protein</a></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">  <tt class="py-keyword">return</tt> <tt id="link-169" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-169', 'CodonTable', 'link-16');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-170" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-170', 'CodonTable', 'link-16');">CodonTable</a></tt><tt class="py-op">(</tt><tt id="link-171" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-171', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-172" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.nucleotide_alphabet=Bio.Data.CodonTable.CodonTable-class.html#nucleotide_alphabet,Variable Bio.Data.CodonTable.NCBICodonTable.nucleotide_alphabet=Bio.Data.CodonTable.NCBICodonTable-class.html#nucleotide_alphabet,Variable Bio.Data.CodonTable.NCBICodonTableDNA.nucleotide_alphabet=Bio.Data.CodonTable.NCBICodonTableDNA-class.html#nucleotide_alphabet,Variable Bio.Data.CodonTable.NCBICodonTableRNA.nucleotide_alphabet=Bio.Data.CodonTable.NCBICodonTableRNA-class.html#nucleotide_alphabet"><a title="Bio.Data.CodonTable.CodonTable.nucleotide_alphabet
Bio.Data.CodonTable.NCBICodonTable.nucleotide_alphabet
Bio.Data.CodonTable.NCBICodonTableDNA.nucleotide_alphabet
Bio.Data.CodonTable.NCBICodonTableRNA.nucleotide_alphabet" class="py-name" href="#" onclick="return doclink('link-172', 'nucleotide_alphabet', 'link-172');">nucleotide_alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-173" class="py-name"><a title="Bio.SeqUtils.proteinX" class="py-name" href="#" onclick="return doclink('link-173', 'proteinX', 'link-159');">proteinX</a></tt><tt class="py-op">,</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">                               <tt id="link-174" class="py-name" targets="Class Bio.SeqUtils.MissingTable=Bio.SeqUtils.MissingTable-class.html"><a title="Bio.SeqUtils.MissingTable" class="py-name" href="#" onclick="return doclink('link-174', 'MissingTable', 'link-174');">MissingTable</a></tt><tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-175', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-176" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.forward_table=Bio.Data.CodonTable.CodonTable-class.html#forward_table"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-176', 'forward_table', 'link-176');">forward_table</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">                               <tt id="link-177" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-177', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-178" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.back_table=Bio.Data.CodonTable.CodonTable-class.html#back_table"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-178', 'back_table', 'link-178');">back_table</a></tt><tt class="py-op">,</tt> <tt id="link-179" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-179', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-180" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.start_codons=Bio.Data.CodonTable.CodonTable-class.html#start_codons"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-180', 'start_codons', 'link-180');">start_codons</a></tt><tt class="py-op">,</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">                               <tt id="link-181" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-181', 'table', 'link-161');">table</a></tt><tt class="py-op">.</tt><tt id="link-182" class="py-name" targets="Variable Bio.Data.CodonTable.CodonTable.stop_codons=Bio.Data.CodonTable.CodonTable-class.html#stop_codons"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-182', 'stop_codons', 'link-182');">stop_codons</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line"><tt class="py-comment"># end of hacks</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="seq3"></a><div id="seq3-def"><a name="L232"></a><tt class="py-lineno">232</tt> <a class="py-toggle" href="#" id="seq3-toggle" onclick="return toggle('seq3');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#seq3">seq3</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="seq3-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="seq3-expanded"><a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">   <tt class="py-docstring">"""</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line"><tt class="py-docstring">   Method that returns the amino acid sequence as a</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line"><tt class="py-docstring">   list of three letter codes. Output follows the IUPAC standard plus 'Ter' for</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line"><tt class="py-docstring">   terminator. Any unknown character, including the default</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-docstring">   unknown character 'X', is changed into 'Xaa'. A noncoded</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line"><tt class="py-docstring">   aminoacid selenocystein is recognized (Sel, U).</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-docstring">   """</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">   <tt class="py-name">threecode</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">'Ala'</tt><tt class="py-op">,</tt> <tt class="py-string">'B'</tt><tt class="py-op">:</tt><tt class="py-string">'Asx'</tt><tt class="py-op">,</tt> <tt class="py-string">'C'</tt><tt class="py-op">:</tt><tt class="py-string">'Cys'</tt><tt class="py-op">,</tt> <tt class="py-string">'D'</tt><tt class="py-op">:</tt><tt class="py-string">'Asp'</tt><tt class="py-op">,</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line">                <tt class="py-string">'E'</tt><tt class="py-op">:</tt><tt class="py-string">'Glu'</tt><tt class="py-op">,</tt> <tt class="py-string">'F'</tt><tt class="py-op">:</tt><tt class="py-string">'Phe'</tt><tt class="py-op">,</tt> <tt class="py-string">'G'</tt><tt class="py-op">:</tt><tt class="py-string">'Gly'</tt><tt class="py-op">,</tt> <tt class="py-string">'H'</tt><tt class="py-op">:</tt><tt class="py-string">'His'</tt><tt class="py-op">,</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line">                <tt class="py-string">'I'</tt><tt class="py-op">:</tt><tt class="py-string">'Ile'</tt><tt class="py-op">,</tt> <tt class="py-string">'K'</tt><tt class="py-op">:</tt><tt class="py-string">'Lys'</tt><tt class="py-op">,</tt> <tt class="py-string">'L'</tt><tt class="py-op">:</tt><tt class="py-string">'Leu'</tt><tt class="py-op">,</tt> <tt class="py-string">'M'</tt><tt class="py-op">:</tt><tt class="py-string">'Met'</tt><tt class="py-op">,</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt>  <tt class="py-line">                <tt class="py-string">'N'</tt><tt class="py-op">:</tt><tt class="py-string">'Asn'</tt><tt class="py-op">,</tt> <tt class="py-string">'P'</tt><tt class="py-op">:</tt><tt class="py-string">'Pro'</tt><tt class="py-op">,</tt> <tt class="py-string">'Q'</tt><tt class="py-op">:</tt><tt class="py-string">'Gln'</tt><tt class="py-op">,</tt> <tt class="py-string">'R'</tt><tt class="py-op">:</tt><tt class="py-string">'Arg'</tt><tt class="py-op">,</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">                <tt class="py-string">'S'</tt><tt class="py-op">:</tt><tt class="py-string">'Ser'</tt><tt class="py-op">,</tt> <tt class="py-string">'T'</tt><tt class="py-op">:</tt><tt class="py-string">'Thr'</tt><tt class="py-op">,</tt> <tt class="py-string">'V'</tt><tt class="py-op">:</tt><tt class="py-string">'Val'</tt><tt class="py-op">,</tt> <tt class="py-string">'W'</tt><tt class="py-op">:</tt><tt class="py-string">'Trp'</tt><tt class="py-op">,</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line">                <tt class="py-string">'Y'</tt><tt class="py-op">:</tt><tt class="py-string">'Tyr'</tt><tt class="py-op">,</tt> <tt class="py-string">'Z'</tt><tt class="py-op">:</tt><tt class="py-string">'Glx'</tt><tt class="py-op">,</tt> <tt class="py-string">'X'</tt><tt class="py-op">:</tt><tt class="py-string">'Xaa'</tt><tt class="py-op">,</tt> <tt class="py-string">'*'</tt><tt class="py-op">:</tt><tt class="py-string">'Ter'</tt><tt class="py-op">,</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line">                <tt class="py-string">'U'</tt><tt class="py-op">:</tt><tt class="py-string">'Sel'</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt>  <tt class="py-line">                <tt class="py-op">}</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line"> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">threecode</tt><tt class="py-op">.</tt><tt id="link-183" 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-183', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">aa</tt><tt class="py-op">,</tt><tt class="py-string">'Xer'</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">aa</tt> <tt class="py-keyword">in</tt> <tt id="link-184" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-184', 'seq', 'link-18');">seq</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line"> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line"><tt class="py-comment"># }}}</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line"><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-comment"># Mixed ??? </tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">######################</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># {{{ </tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="translate"></a><div id="translate-def"><a name="L259"></a><tt class="py-lineno">259</tt> <a class="py-toggle" href="#" id="translate-toggle" onclick="return toggle('translate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#translate">translate</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">frame</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">genetic_code</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">translator</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="translate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="translate-expanded"><a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line">   <tt class="py-docstring">" translation of DNA in one of the six different reading frames "</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt>  <tt class="py-line">   <tt class="py-keyword">if</tt> <tt id="link-185" class="py-name" targets="Method Bio.Blast.NCBIStandalone._HSPConsumer.frame()=Bio.Blast.NCBIStandalone._HSPConsumer-class.html#frame,Variable Bio.expressions.blast.ncbiblast.frame=Bio.expressions.blast.ncbiblast-module.html#frame"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-185', 'frame', 'link-185');">frame</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-number">2</tt><tt class="py-op">,</tt><tt class="py-number">3</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-number">2</tt><tt class="py-op">,</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt>  <tt class="py-line">      <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">'invalid frame'</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt>  <tt class="py-line"> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt>  <tt class="py-line">   <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">translator</tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt>  <tt class="py-line">      <tt id="link-186" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-186', 'table', 'link-161');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-187" class="py-name" targets="Function Bio.SeqUtils.makeTableX()=Bio.SeqUtils-module.html#makeTableX"><a title="Bio.SeqUtils.makeTableX" class="py-name" href="#" onclick="return doclink('link-187', 'makeTableX', 'link-187');">makeTableX</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-188', 'CodonTable', 'link-16');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-189" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_dna_by_id=Bio.Data.CodonTable-module.html#ambiguous_dna_by_id,Variable Bio.Translate.ambiguous_dna_by_id=Bio.Translate-module.html#ambiguous_dna_by_id"><a title="Bio.Data.CodonTable.ambiguous_dna_by_id
Bio.Translate.ambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-189', 'ambiguous_dna_by_id', 'link-189');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt class="py-name">genetic_code</tt><tt class="py-op">]</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">translator</tt> <tt class="py-op">=</tt> <tt id="link-190" class="py-name"><a title="Bio.Translate" class="py-name" href="#" onclick="return doclink('link-190', 'Translate', 'link-4');">Translate</a></tt><tt class="py-op">.</tt><tt id="link-191" class="py-name" targets="Class Bio.Translate.Translator=Bio.Translate.Translator-class.html"><a title="Bio.Translate.Translator" class="py-name" href="#" onclick="return doclink('link-191', 'Translator', 'link-191');">Translator</a></tt><tt class="py-op">(</tt><tt id="link-192" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-192', 'table', 'link-161');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt>  <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">translator</tt><tt class="py-op">.</tt><tt id="link-193" class="py-name" targets="Method Bio.GFF.Feature.translate()=Bio.GFF.Feature-class.html#translate,Method Bio.GFF.FeatureAggregate.translate()=Bio.GFF.FeatureAggregate-class.html#translate,Function Bio.Seq.translate()=Bio.Seq-module.html#translate,Function Bio.SeqUtils.translate()=Bio.SeqUtils-module.html#translate,Method Bio.Translate.Translator.translate()=Bio.Translate.Translator-class.html#translate,Function Bio.utils.translate()=Bio.utils-module.html#translate"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-193', 'translate', 'link-193');">translate</a></tt><tt class="py-op">(</tt><tt id="link-194" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-194', 'Seq', 'link-6');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-195', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt id="link-196" class="py-name"><a title="Bio.Blast.NCBIStandalone._HSPConsumer.frame
Bio.expressions.blast.ncbiblast.frame" class="py-name" href="#" onclick="return doclink('link-196', 'frame', 'link-185');">frame</a></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 id="link-197" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-197', 'IUPAC', 'link-12');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-198" class="py-name" targets="Variable Bio.Alphabet.IUPAC.ambiguous_dna=Bio.Alphabet.IUPAC-module.html#ambiguous_dna"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-198', 'ambiguous_dna', 'link-198');">ambiguous_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-199', 'data', 'link-199');">data</a></tt> </tt>
</div><a name="L269"></a><tt class="py-lineno">269</tt>  <tt class="py-line"> </tt>
<a name="GC_Frame"></a><div id="GC_Frame-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="GC_Frame-toggle" onclick="return toggle('GC_Frame');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#GC_Frame">GC_Frame</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">genetic_code</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="GC_Frame-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="GC_Frame-expanded"><a name="L271"></a><tt class="py-lineno">271</tt>  <tt class="py-line">   <tt class="py-docstring">" just an alias for six_frame_translations "</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt id="link-200" class="py-name" targets="Function Bio.SeqUtils.six_frame_translations()=Bio.SeqUtils-module.html#six_frame_translations"><a title="Bio.SeqUtils.six_frame_translations" class="py-name" href="#" onclick="return doclink('link-200', 'six_frame_translations', 'link-200');">six_frame_translations</a></tt><tt class="py-op">(</tt><tt id="link-201" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-201', 'seq', 'link-18');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">genetic_code</tt><tt class="py-op">)</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt>  <tt class="py-line"> </tt>
<a name="six_frame_translations"></a><div id="six_frame_translations-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="six_frame_translations-toggle" onclick="return toggle('six_frame_translations');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#six_frame_translations">six_frame_translations</a><tt class="py-op">(</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt> <tt class="py-param">genetic_code</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="six_frame_translations-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="six_frame_translations-expanded"><a name="L275"></a><tt class="py-lineno">275</tt>  <tt class="py-line">   <tt class="py-docstring">"""</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt>  <tt class="py-line"><tt class="py-docstring">   nice looking 6 frame translation with GC content - code from xbbtools</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt>  <tt class="py-line"><tt class="py-docstring">   similar to DNA Striders six-frame translation</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt>  <tt class="py-line"><tt class="py-docstring">   """</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt>  <tt class="py-line">   <tt class="py-keyword">from</tt> <tt id="link-202" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-202', 'Bio', 'link-1');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-203', 'Seq', 'link-6');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-204" class="py-name" targets="Method Bio.Seq.MutableSeq.reverse_complement()=Bio.Seq.MutableSeq-class.html#reverse_complement,Method Bio.Seq.Seq.reverse_complement()=Bio.Seq.Seq-class.html#reverse_complement,Function Bio.Seq.reverse_complement()=Bio.Seq-module.html#reverse_complement"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-204', 'reverse_complement', 'link-204');">reverse_complement</a></tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt>  <tt class="py-line">   <tt class="py-name">anti</tt> <tt class="py-op">=</tt> <tt id="link-205" class="py-name"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-205', 'reverse_complement', 'link-204');">reverse_complement</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-206', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt>  <tt class="py-line">   <tt class="py-name">comp</tt> <tt class="py-op">=</tt> <tt class="py-name">anti</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="L282"></a><tt class="py-lineno">282</tt>  <tt class="py-line">   <tt id="link-207" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.length()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#length,Method Bio.GFF.easy.Location.length()=Bio.GFF.easy.Location-class.html#length"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-207', 'length', 'link-207');">length</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-208" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-208', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt>  <tt class="py-line">   <tt class="py-name">frames</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-209" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-209', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt>  <tt class="py-line">      <tt class="py-name">frames</tt><tt class="py-op">[</tt><tt id="link-210" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-210', 'i', 'link-39');">i</a></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-211" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-211', 'translate', 'link-193');">translate</a></tt><tt class="py-op">(</tt><tt id="link-212" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-212', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt id="link-213" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-213', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">genetic_code</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt>  <tt class="py-line">      <tt class="py-name">frames</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt id="link-214" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-214', 'i', 'link-39');">i</a></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 id="link-215" class="py-name"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-215', 'reverse', 'link-19');">reverse</a></tt><tt class="py-op">(</tt><tt id="link-216" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-216', 'translate', 'link-193');">translate</a></tt><tt class="py-op">(</tt><tt class="py-name">anti</tt><tt class="py-op">[</tt><tt id="link-217" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-217', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">genetic_code</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<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-comment"># create header</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt>  <tt class="py-line"><tt class="py-comment"></tt>   <tt class="py-keyword">if</tt> <tt id="link-218" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-218', 'length', 'link-207');">length</a></tt> <tt class="py-op">&gt;</tt> <tt class="py-number">20</tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt>  <tt class="py-line">      <tt class="py-name">short</tt> <tt class="py-op">=</tt> <tt class="py-string">'%s ... %s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-219" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-219', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">10</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-220" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-220', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</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-op">)</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt>  <tt class="py-line">   <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt>  <tt class="py-line">      <tt class="py-name">short</tt> <tt class="py-op">=</tt> <tt id="link-221" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-221', 'seq', 'link-18');">seq</a></tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt>  <tt class="py-line">   <tt id="link-222" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.date()=Bio.GenBank._FeatureConsumer-class.html#date,Method Bio.GenBank._RecordConsumer.date()=Bio.GenBank._RecordConsumer-class.html#date,Method Bio.Prosite._RecordConsumer.date()=Bio.Prosite._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._RecordConsumer.date()=Bio.SwissProt.SProt._RecordConsumer-class.html#date,Method Bio.SwissProt.SProt._SequenceConsumer.date()=Bio.SwissProt.SProt._SequenceConsumer-class.html#date,Variable Bio.expressions.embl.embl65.date=Bio.expressions.embl.embl65-module.html#date,Variable Bio.expressions.genbank.date=Bio.expressions.genbank-module.html#date"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-222', 'date', 'link-222');">date</a></tt> <tt class="py-op">=</tt> <tt id="link-223" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-223', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt class="py-name">strftime</tt><tt class="py-op">(</tt><tt class="py-string">'%y %b %d, %X'</tt><tt class="py-op">,</tt> <tt id="link-224" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-224', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt id="link-225" class="py-name" targets="Method Bio.Restriction._Update.Update.RebaseUpdate.localtime()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#localtime"><a title="Bio.Restriction._Update.Update.RebaseUpdate.localtime" class="py-name" href="#" onclick="return doclink('link-225', 'localtime', 'link-225');">localtime</a></tt><tt class="py-op">(</tt><tt id="link-226" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-226', 'time', 'link-0');">time</a></tt><tt class="py-op">.</tt><tt id="link-227" class="py-name"><a title="Bio.Sequencing.Phd._RecordConsumer.time" class="py-name" href="#" onclick="return doclink('link-227', 'time', 'link-0');">time</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="L294"></a><tt class="py-lineno">294</tt>  <tt class="py-line">   <tt id="link-228" class="py-name" targets="Variable Bio.Wise.dnal.Statistics.header=Bio.Wise.dnal.Statistics-class.html#header,Variable Bio.expressions.blast.ncbiblast.header=Bio.expressions.blast.ncbiblast-module.html#header,Variable Bio.expressions.blast.wublast.header=Bio.expressions.blast.wublast-module.html#header,Variable Bio.expressions.blocks.header=Bio.expressions.blocks-module.html#header,Variable Bio.expressions.genbank.header=Bio.expressions.genbank-module.html#header,Variable Bio.expressions.hmmpfam.header=Bio.expressions.hmmpfam-module.html#header"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-228', 'header', 'link-228');">header</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'GC_Frame: %s, '</tt> <tt class="py-op">%</tt> <tt id="link-229" class="py-name"><a title="Bio.GenBank._FeatureConsumer.date
Bio.GenBank._RecordConsumer.date
Bio.Prosite._RecordConsumer.date
Bio.SwissProt.SProt._RecordConsumer.date
Bio.SwissProt.SProt._SequenceConsumer.date
Bio.expressions.embl.embl65.date
Bio.expressions.genbank.date" class="py-name" href="#" onclick="return doclink('link-229', 'date', 'link-222');">date</a></tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">nt</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">'g'</tt><tt class="py-op">,</tt><tt class="py-string">'c'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt>  <tt class="py-line">      <tt id="link-230" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-230', 'header', 'link-228');">header</a></tt> <tt class="py-op">+=</tt> <tt class="py-string">'%s:%d '</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">nt</tt><tt class="py-op">,</tt> <tt id="link-231" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-231', 'seq', 'link-18');">seq</a></tt><tt class="py-op">.</tt><tt id="link-232" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-232', 'count', 'link-23');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">nt</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>
<a name="L297"></a><tt class="py-lineno">297</tt>  <tt class="py-line">       </tt>
<a name="L298"></a><tt class="py-lineno">298</tt>  <tt class="py-line">   <tt id="link-233" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-233', 'header', 'link-228');">header</a></tt> <tt class="py-op">+=</tt> <tt class="py-string">'\nSequence: %s, %d nt, %0.2f %%GC\n\n\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">short</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt id="link-234" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-234', 'length', 'link-207');">length</a></tt><tt class="py-op">,</tt> <tt id="link-235" class="py-name"><a title="Bio.SeqUtils.GC" class="py-name" href="#" onclick="return doclink('link-235', 'GC', 'link-97');">GC</a></tt><tt class="py-op">(</tt><tt id="link-236" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-236', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt>        </tt>
<a name="L299"></a><tt class="py-lineno">299</tt>  <tt class="py-line">   <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt id="link-237" class="py-name"><a title="Bio.Wise.dnal.Statistics.header
Bio.expressions.blast.ncbiblast.header
Bio.expressions.blast.wublast.header
Bio.expressions.blocks.header
Bio.expressions.genbank.header
Bio.expressions.hmmpfam.header" class="py-name" href="#" onclick="return doclink('link-237', 'header', 'link-228');">header</a></tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt>  <tt class="py-line">    </tt>
<a name="L301"></a><tt class="py-lineno">301</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-238" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-238', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt id="link-239" class="py-name"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.length
Bio.GFF.easy.Location.length" class="py-name" href="#" onclick="return doclink('link-239', 'length', 'link-207');">length</a></tt><tt class="py-op">,</tt><tt class="py-number">60</tt><tt class="py-op">)</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">subseq</tt> <tt class="py-op">=</tt> <tt id="link-240" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-240', 'seq', 'link-18');">seq</a></tt><tt class="py-op">[</tt><tt id="link-241" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-241', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt><tt id="link-242" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-242', 'i', 'link-39');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">60</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">csubseq</tt> <tt class="py-op">=</tt> <tt class="py-name">comp</tt><tt class="py-op">[</tt><tt id="link-243" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-243', 'i', 'link-39');">i</a></tt><tt class="py-op">:</tt><tt id="link-244" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-244', 'i', 'link-39');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">60</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">p</tt> <tt class="py-op">=</tt> <tt id="link-245" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-245', 'i', 'link-39');">i</a></tt><tt class="py-op">/</tt><tt class="py-number">3</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">'%d/%d\n'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-246" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-246', 'i', 'link-39');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-247" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-247', 'i', 'link-39');">i</a></tt><tt class="py-op">/</tt><tt class="py-number">3</tt><tt class="py-op">+</tt><tt class="py-number">1</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">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">'  '</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 id="link-248" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-248', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</tt><tt class="py-op">[</tt><tt class="py-number">3</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">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">'\n'</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</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 id="link-249" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-249', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</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-name">p</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">'\n'</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</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 id="link-250" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-250', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</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">p</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">'\n'</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt>  <tt class="py-line">      <tt class="py-comment"># seq</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt>  <tt class="py-line"><tt class="py-comment"></tt>      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-name">subseq</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'%5d %%\n'</tt> <tt class="py-op">%</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-251" class="py-name"><a title="Bio.SeqUtils.GC" class="py-name" href="#" onclick="return doclink('link-251', 'GC', 'link-97');">GC</a></tt><tt class="py-op">(</tt><tt class="py-name">subseq</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-name">csubseq</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt>  <tt class="py-line">      <tt class="py-comment"># - frames</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">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</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 id="link-252" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-252', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</tt><tt class="py-op">[</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-name">p</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">' \n'</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">' '</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 id="link-253" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-253', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</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">p</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">'\n'</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt>  <tt class="py-line">      <tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-name">res</tt> <tt class="py-op">+</tt> <tt class="py-string">'  '</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 id="link-254" class="py-name"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-254', 'map', 'link-17');">map</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">frames</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">:</tt><tt class="py-name">p</tt><tt class="py-op">+</tt><tt class="py-number">20</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">'\n\n'</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">res</tt> </tt>
</div><a name="L317"></a><tt class="py-lineno">317</tt>  <tt class="py-line"> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt>  <tt class="py-line"><tt class="py-comment"># }}}</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt>  <tt class="py-line"><tt class="py-comment">######################################</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># FASTA file utilities</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">######################</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"># {{{ </tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="fasta_uniqids"></a><div id="fasta_uniqids-def"><a name="L325"></a><tt class="py-lineno">325</tt> <a class="py-toggle" href="#" id="fasta_uniqids-toggle" onclick="return toggle('fasta_uniqids');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#fasta_uniqids">fasta_uniqids</a><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="fasta_uniqids-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="fasta_uniqids-expanded"><a name="L326"></a><tt class="py-lineno">326</tt>  <tt class="py-line">   <tt class="py-docstring">" checks and changes the name/ID's to be unique identifiers by adding numbers "</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt>  <tt class="py-line">   <tt class="py-name">dict</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">txt</tt> <tt class="py-op">=</tt> <tt id="link-255" 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-255', 'open', 'link-255');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-256" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-256', 'read', 'link-256');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt>  <tt class="py-line">   <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt class="py-name">txt</tt><tt class="py-op">.</tt><tt id="link-257" 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-257', 'split', 'link-257');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'&gt;'</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="L331"></a><tt class="py-lineno">331</tt>  <tt class="py-line">      <tt id="link-258" 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-258', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt id="link-259" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-259', 'seq', 'link-18');">seq</a></tt><tt class="py-op">=</tt> <tt class="py-name">entry</tt><tt class="py-op">.</tt><tt id="link-260" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-260', 'split', 'link-257');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt>  <tt class="py-line">      <tt id="link-261" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-261', 'name', 'link-258');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-262" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-262', 'name', 'link-258');">name</a></tt><tt class="py-op">.</tt><tt id="link-263" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-263', 'split', 'link-257');">split</a></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 id="link-264" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-264', 'split', 'link-257');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">','</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="L333"></a><tt class="py-lineno">333</tt>  <tt class="py-line">       </tt>
<a name="L334"></a><tt class="py-lineno">334</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-265" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-265', 'has_key', 'link-265');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-266" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-266', 'name', 'link-258');">name</a></tt><tt class="py-op">)</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">n</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt>  <tt class="py-line">         <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt>  <tt class="py-line">            <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">n</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt>  <tt class="py-line">            <tt id="link-267" class="py-name" targets="Method Bio.KEGG.Compound.Record._name()=Bio.KEGG.Compound.Record-class.html#_name,Method Bio.KEGG.Enzyme.Record._name()=Bio.KEGG.Enzyme.Record-class.html#_name,Method Bio.MEME.Motif.Motif._name()=Bio.MEME.Motif.Motif-class.html#_name,Variable Bio.Mindy.XPath._name=Bio.Mindy.XPath-module.html#_name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-267', '_name', 'link-267');">_name</a></tt> <tt class="py-op">=</tt> <tt id="link-268" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-268', 'name', 'link-258');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-269" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-269', 'has_key', 'link-265');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-270" class="py-name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-270', '_name', 'link-267');">_name</a></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 id="link-271" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-271', 'name', 'link-258');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name"><a title="Bio.KEGG.Compound.Record._name
Bio.KEGG.Enzyme.Record._name
Bio.MEME.Motif.Motif._name
Bio.Mindy.XPath._name" class="py-name" href="#" onclick="return doclink('link-272', '_name', 'link-267');">_name</a></tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt>  <tt class="py-line">               <tt class="py-keyword">break</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt>  <tt class="py-line">             </tt>
<a name="L343"></a><tt class="py-lineno">343</tt>  <tt class="py-line">      <tt class="py-name">dict</tt><tt class="py-op">[</tt><tt id="link-273" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-273', 'name', 'link-258');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-274" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-274', 'seq', 'link-18');">seq</a></tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt>  <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-275" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-275', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt id="link-276" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-276', 'seq', 'link-18');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">dict</tt><tt class="py-op">.</tt><tt id="link-277" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-277', 'items', 'link-277');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt>  <tt class="py-line">      <tt class="py-keyword">print</tt> <tt class="py-string">'&gt;%s\n%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-278" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-278', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt id="link-279" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-279', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L347"></a><tt class="py-lineno">347</tt>  <tt class="py-line"> </tt>
<a name="quick_FASTA_reader"></a><div id="quick_FASTA_reader-def"><a name="L348"></a><tt class="py-lineno">348</tt> <a class="py-toggle" href="#" id="quick_FASTA_reader-toggle" onclick="return toggle('quick_FASTA_reader');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#quick_FASTA_reader">quick_FASTA_reader</a><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="quick_FASTA_reader-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="quick_FASTA_reader-expanded"><a name="L349"></a><tt class="py-lineno">349</tt>  <tt class="py-line">   <tt class="py-docstring">" simple and FASTA reader, preferable to be used on large files "</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt>  <tt class="py-line">   <tt class="py-name">txt</tt> <tt class="py-op">=</tt> <tt id="link-280" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-280', 'open', 'link-255');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-281" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-281', 'read', 'link-256');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt>  <tt class="py-line">   <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">entry</tt> <tt class="py-keyword">in</tt> <tt class="py-name">txt</tt><tt class="py-op">.</tt><tt id="link-282" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-282', 'split', 'link-257');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'&gt;'</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="L353"></a><tt class="py-lineno">353</tt>  <tt class="py-line">      <tt id="link-283" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-283', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt><tt id="link-284" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-284', 'seq', 'link-18');">seq</a></tt><tt class="py-op">=</tt> <tt class="py-name">entry</tt><tt class="py-op">.</tt><tt id="link-285" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-285', 'split', 'link-257');">split</a></tt><tt class="py-op">(</tt><tt class="py-string">'\n'</tt><tt class="py-op">,</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt>  <tt class="py-line">      <tt id="link-286" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-286', 'seq', 'link-18');">seq</a></tt> <tt class="py-op">=</tt> <tt id="link-287" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-287', 'seq', 'link-18');">seq</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</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-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">' '</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">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt>  <tt class="py-line">      <tt class="py-name">entries</tt><tt class="py-op">.</tt><tt id="link-288" 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-288', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-289" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-289', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt id="link-290" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-290', 'seq', 'link-18');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt>  <tt class="py-line">       </tt>
<a name="L357"></a><tt class="py-lineno">357</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">entries</tt> </tt>
</div><a name="L358"></a><tt class="py-lineno">358</tt>  <tt class="py-line">     </tt>
<a name="apply_on_multi_fasta"></a><div id="apply_on_multi_fasta-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="apply_on_multi_fasta-toggle" onclick="return toggle('apply_on_multi_fasta');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#apply_on_multi_fasta">apply_on_multi_fasta</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">function</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="apply_on_multi_fasta-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="apply_on_multi_fasta-expanded"><a name="L360"></a><tt class="py-lineno">360</tt>  <tt class="py-line">   <tt class="py-docstring">" apply function on each sequence in a multiple FASTA file "</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt>  <tt class="py-line">   <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt>  <tt class="py-line">      <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">globals</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">function</tt><tt class="py-op">]</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt>  <tt class="py-line">   <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt>  <tt class="py-line">      <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"%s not implemented"</tt> <tt class="py-op">%</tt> <tt class="py-name">function</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt>  <tt class="py-line">    </tt>
<a name="L366"></a><tt class="py-lineno">366</tt>  <tt class="py-line">   <tt id="link-291" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-291', 'handle', 'link-291');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-292" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-292', 'open', 'link-255');">open</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt>  <tt class="py-line">   <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-293" class="py-name"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-293', 'SeqIO', 'link-2');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-294" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-294', 'parse', 'link-294');">parse</a></tt><tt class="py-op">(</tt><tt id="link-295" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-295', 'handle', 'link-291');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-string">"fasta"</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt>  <tt class="py-line">   <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-296" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-296', 'record', 'link-296');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt>  <tt class="py-line">      <tt class="py-name">arguments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-297" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-297', 'record', 'link-296');">record</a></tt><tt class="py-op">.</tt><tt id="link-298" 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-298', 'sequence', 'link-298');">sequence</a></tt><tt class="py-op">]</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt class="py-name">arg</tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> <tt class="py-name">arguments</tt><tt class="py-op">.</tt><tt id="link-299" 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-299', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">arg</tt><tt class="py-op">)</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt>  <tt class="py-line">      <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">arguments</tt><tt class="py-op">)</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">result</tt><tt class="py-op">:</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt>  <tt class="py-line">         <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-300" 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-300', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'&gt;%s\n%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-301" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-301', 'record', 'link-296');">record</a></tt><tt class="py-op">.</tt><tt id="link-302" class="py-name" targets="Method Bio.Blast.NCBIStandalone._AlignmentConsumer.title()=Bio.Blast.NCBIStandalone._AlignmentConsumer-class.html#title,Method Bio.GenBank._FeatureConsumer.title()=Bio.GenBank._FeatureConsumer-class.html#title,Method Bio.GenBank._RecordConsumer.title()=Bio.GenBank._RecordConsumer-class.html#title,Method Bio.Medline._RecordConsumer.title()=Bio.Medline._RecordConsumer-class.html#title,Variable Bio.expressions.fasta.title=Bio.expressions.fasta-module.html#title"><a title="Bio.Blast.NCBIStandalone._AlignmentConsumer.title
Bio.GenBank._FeatureConsumer.title
Bio.GenBank._RecordConsumer.title
Bio.Medline._RecordConsumer.title
Bio.expressions.fasta.title" class="py-name" href="#" onclick="return doclink('link-302', 'title', 'link-302');">title</a></tt><tt class="py-op">,</tt> <tt class="py-name">result</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt>
</div><a name="L376"></a><tt class="py-lineno">376</tt>  <tt class="py-line">          </tt>
<a name="quicker_apply_on_multi_fasta"></a><div id="quicker_apply_on_multi_fasta-def"><a name="L377"></a><tt class="py-lineno">377</tt> <a class="py-toggle" href="#" id="quicker_apply_on_multi_fasta-toggle" onclick="return toggle('quicker_apply_on_multi_fasta');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqUtils-module.html#quicker_apply_on_multi_fasta">quicker_apply_on_multi_fasta</a><tt class="py-op">(</tt><tt class="py-param">file</tt><tt class="py-op">,</tt> <tt class="py-param">function</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="quicker_apply_on_multi_fasta-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="quicker_apply_on_multi_fasta-expanded"><a name="L378"></a><tt class="py-lineno">378</tt>  <tt class="py-line">   <tt class="py-docstring">" apply function on each sequence in a multiple FASTA file "</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt>  <tt class="py-line">   <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt>  <tt class="py-line">      <tt class="py-name">f</tt> <tt class="py-op">=</tt> <tt class="py-name">globals</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">function</tt><tt class="py-op">]</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt>  <tt class="py-line">   <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt>  <tt class="py-line">      <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"%s not implemented"</tt> <tt class="py-op">%</tt> <tt class="py-name">function</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt>  <tt class="py-line">    </tt>
<a name="L384"></a><tt class="py-lineno">384</tt>  <tt class="py-line">   <tt class="py-name">entries</tt> <tt class="py-op">=</tt> <tt id="link-303" class="py-name" targets="Function Bio.SeqUtils.quick_FASTA_reader()=Bio.SeqUtils-module.html#quick_FASTA_reader"><a title="Bio.SeqUtils.quick_FASTA_reader" class="py-name" href="#" onclick="return doclink('link-303', 'quick_FASTA_reader', 'link-303');">quick_FASTA_reader</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt>  <tt class="py-line">   <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt id="link-304" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-304', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt id="link-305" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-305', 'seq', 'link-18');">seq</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">entries</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">arguments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-306" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-306', 'seq', 'link-18');">seq</a></tt><tt class="py-op">]</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt class="py-name">arg</tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> <tt class="py-name">arguments</tt><tt class="py-op">.</tt><tt id="link-307" 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-307', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">arg</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt>  <tt class="py-line">      <tt class="py-name">result</tt> <tt class="py-op">=</tt> <tt class="py-name">f</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">arguments</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">result</tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt>  <tt class="py-line">         <tt class="py-name">results</tt><tt class="py-op">.</tt><tt id="link-308" 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-308', 'append', 'link-81');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'&gt;%s\n%s'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt id="link-309" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-309', 'name', 'link-258');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">result</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt>  <tt class="py-line">   <tt class="py-keyword">return</tt> <tt class="py-name">results</tt> </tt>
</div><a name="L393"></a><tt class="py-lineno">393</tt>  <tt class="py-line"> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt>  <tt class="py-line"><tt class="py-comment"># }}}</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt>  <tt class="py-line"><tt class="py-comment">######################################</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Main</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">#####################</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"># {{{ </tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt>  <tt class="py-line">   <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt><tt class="py-op">,</tt> <tt class="py-name">getopt</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt>  <tt class="py-line">   <tt class="py-comment"># crude command line options to use most functions directly on a FASTA file</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt>  <tt class="py-line"><tt class="py-comment"></tt>   <tt class="py-name">options</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'apply_on_multi_fasta'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt>  <tt class="py-line">              <tt class="py-string">'quick'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt>  <tt class="py-line">              <tt class="py-string">'uniq_ids'</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt>  <tt class="py-line">              <tt class="py-op">}</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt>  <tt class="py-line"> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt>  <tt class="py-line">   <tt class="py-name">optlist</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">getopt</tt><tt class="py-op">.</tt><tt class="py-name">getopt</tt><tt class="py-op">(</tt><tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</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-string">''</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-string">'describe'</tt><tt class="py-op">,</tt> <tt class="py-string">'apply_on_multi_fasta='</tt><tt class="py-op">,</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt>  <tt class="py-line">                                                    <tt class="py-string">'help'</tt><tt class="py-op">,</tt> <tt class="py-string">'quick'</tt><tt class="py-op">,</tt> <tt class="py-string">'uniq_ids'</tt><tt class="py-op">,</tt> <tt class="py-string">'search='</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt>  <tt class="py-line">   <tt class="py-keyword">for</tt> <tt class="py-name">arg</tt> <tt class="py-keyword">in</tt> <tt class="py-name">optlist</tt><tt class="py-op">:</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">arg</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-op">[</tt><tt class="py-string">'-h'</tt><tt class="py-op">,</tt> <tt class="py-string">'--help'</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-keyword">pass</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt>  <tt class="py-line">      <tt class="py-keyword">elif</tt> <tt class="py-name">arg</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-op">[</tt><tt class="py-string">'--describe'</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"># get all new functions from this file</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt>  <tt class="py-line"><tt class="py-comment"></tt>         <tt class="py-name">mol_funcs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-310" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-310', 'x', 'link-133');">x</a></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-311" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-311', 'x', 'link-133');">x</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">locals</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-312', 'items', 'link-277');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> <tt id="link-313" class="py-name"><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-313', 'type', 'link-122');">type</a></tt><tt class="py-op">(</tt><tt id="link-314" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-314', 'x', 'link-133');">x</a></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 id="link-315" class="py-name"><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-315', 'type', 'link-122');">type</a></tt><tt class="py-op">(</tt><tt id="link-316" class="py-name"><a title="Bio.SeqUtils.GC" class="py-name" href="#" onclick="return doclink('link-316', 'GC', 'link-97');">GC</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt>  <tt class="py-line">         <tt class="py-name">mol_funcs</tt><tt class="py-op">.</tt><tt id="link-317" 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-317', 'sort', 'link-317');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt>  <tt class="py-line">         <tt class="py-keyword">print</tt> <tt class="py-string">'available functions:'</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt>  <tt class="py-line">         <tt class="py-keyword">for</tt> <tt class="py-name">f</tt> <tt class="py-keyword">in</tt> <tt class="py-name">mol_funcs</tt><tt class="py-op">:</tt> <tt class="py-keyword">print</tt> <tt class="py-string">'\t--%s'</tt> <tt class="py-op">%</tt> <tt class="py-name">f</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt>  <tt class="py-line">         <tt class="py-keyword">print</tt> <tt class="py-string">'\n\ne.g.\n./sequtils.py  --apply_on_multi_fasta GC test.fas'</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt>  <tt class="py-line"> </tt>
<a name="L422"></a><tt class="py-lineno">422</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-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt>  <tt class="py-line">      <tt class="py-keyword">elif</tt> <tt class="py-name">arg</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-op">[</tt><tt class="py-string">'--apply_on_multi_fasta'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt>  <tt class="py-line">         <tt class="py-name">options</tt><tt class="py-op">[</tt><tt class="py-string">'apply_on_multi_fasta'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">arg</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt>  <tt class="py-line">      <tt class="py-keyword">elif</tt> <tt class="py-name">arg</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-op">[</tt><tt class="py-string">'--search'</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt>  <tt class="py-line">         <tt class="py-name">options</tt><tt class="py-op">[</tt><tt class="py-string">'search'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">arg</tt><tt class="py-op">[</tt><tt class="py-number">1</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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt>  <tt class="py-line">         <tt id="link-318" class="py-name" targets="Variable Bio.Translate.key=Bio.Translate-module.html#key"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-318', 'key', 'link-318');">key</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-319" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-319', 'search', 'link-151');">search</a></tt><tt class="py-op">(</tt><tt class="py-string">'-*(.+)'</tt><tt class="py-op">,</tt> <tt class="py-name">arg</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 id="link-320" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-320', 'group', 'link-320');">group</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt>  <tt class="py-line">         <tt class="py-name">options</tt><tt class="py-op">[</tt><tt id="link-321" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-321', 'key', 'link-318');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt>  <tt class="py-line"> </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-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-322" 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-322', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'apply_on_multi_fasta'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt>  <tt class="py-line">      <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt>  <tt class="py-line">      <tt class="py-name">function</tt> <tt class="py-op">=</tt> <tt class="py-name">options</tt><tt class="py-op">[</tt><tt class="py-string">'apply_on_multi_fasta'</tt><tt class="py-op">]</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt>  <tt class="py-line">      <tt class="py-name">arguments</tt> <tt class="py-op">=</tt> <tt class="py-op">[</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">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-323" 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-323', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'search'</tt><tt class="py-op">)</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">arguments</tt> <tt class="py-op">=</tt> <tt class="py-name">options</tt><tt class="py-op">[</tt><tt class="py-string">'search'</tt><tt class="py-op">]</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">function</tt> <tt class="py-op">==</tt> <tt class="py-string">'xGC_skew'</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">arguments</tt> <tt class="py-op">=</tt> <tt class="py-number">1000</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt>  <tt class="py-line">      <tt class="py-keyword">if</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-324" 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-324', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'quick'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt>  <tt class="py-line">         <tt class="py-name">results</tt> <tt class="py-op">=</tt> <tt id="link-325" class="py-name" targets="Function Bio.SeqUtils.quicker_apply_on_multi_fasta()=Bio.SeqUtils-module.html#quicker_apply_on_multi_fasta"><a title="Bio.SeqUtils.quicker_apply_on_multi_fasta" class="py-name" href="#" onclick="return doclink('link-325', 'quicker_apply_on_multi_fasta', 'link-325');">quicker_apply_on_multi_fasta</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">function</tt><tt class="py-op">,</tt> <tt class="py-name">arguments</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">else</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">results</tt> <tt class="py-op">=</tt> <tt id="link-326" class="py-name" targets="Function Bio.SeqUtils.apply_on_multi_fasta()=Bio.SeqUtils-module.html#apply_on_multi_fasta"><a title="Bio.SeqUtils.apply_on_multi_fasta" class="py-name" href="#" onclick="return doclink('link-326', 'apply_on_multi_fasta', 'link-326');">apply_on_multi_fasta</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">,</tt> <tt class="py-name">function</tt><tt class="py-op">,</tt> <tt class="py-name">arguments</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt>  <tt class="py-line">      <tt class="py-keyword">for</tt> <tt class="py-name">result</tt> <tt class="py-keyword">in</tt> <tt class="py-name">results</tt><tt class="py-op">:</tt> <tt class="py-keyword">print</tt> <tt class="py-name">result</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt>  <tt class="py-line">       </tt>
<a name="L446"></a><tt class="py-lineno">446</tt>  <tt class="py-line">   <tt class="py-keyword">elif</tt> <tt class="py-name">options</tt><tt class="py-op">.</tt><tt id="link-327" 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-327', 'get', 'link-25');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">'uniq_ids'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt>  <tt class="py-line">      <tt class="py-name">file</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt>  <tt class="py-line">      <tt id="link-328" class="py-name" targets="Function Bio.SeqUtils.fasta_uniqids()=Bio.SeqUtils-module.html#fasta_uniqids"><a title="Bio.SeqUtils.fasta_uniqids" class="py-name" href="#" onclick="return doclink('link-328', 'fasta_uniqids', 'link-328');">fasta_uniqids</a></tt><tt class="py-op">(</tt><tt class="py-name">file</tt><tt class="py-op">)</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt>  <tt class="py-line"> </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><script type="text/javascript">
<!--
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