<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Data.CodonTable</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Data-module.html">Package Data</a> :: Module CodonTable </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Data.CodonTable-pysrc.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <h1 class="epydoc">Source Code for <a href="Bio.Data.CodonTable-module.html">Module Bio.Data.CodonTable</a></h1> <pre class="py-src"> <a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt> <a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" 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-1', 'Alphabet', 'link-1');">Alphabet</a></tt> </tt> <a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-2', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-3', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" 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-4', 'IUPAC', 'link-4');">IUPAC</a></tt> </tt> <a name="L4"></a><tt class="py-lineno"> 4</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-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name" targets="Package Bio.Data=Bio.Data-module.html"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-6', 'Data', 'link-6');">Data</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" 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-7', 'IUPACData', 'link-7');">IUPACData</a></tt> </tt> <a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"> </tt> <a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt id="link-8" class="py-name" targets="Variable Bio.Data.CodonTable.unambiguous_dna_by_name=Bio.Data.CodonTable-module.html#unambiguous_dna_by_name,Variable Bio.Translate.unambiguous_dna_by_name=Bio.Translate-module.html#unambiguous_dna_by_name"><a title="Bio.Data.CodonTable.unambiguous_dna_by_name Bio.Translate.unambiguous_dna_by_name" class="py-name" href="#" onclick="return doclink('link-8', 'unambiguous_dna_by_name', 'link-8');">unambiguous_dna_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt id="link-9" class="py-name" targets="Variable Bio.Data.CodonTable.unambiguous_dna_by_id=Bio.Data.CodonTable-module.html#unambiguous_dna_by_id,Variable Bio.Translate.unambiguous_dna_by_id=Bio.Translate-module.html#unambiguous_dna_by_id"><a title="Bio.Data.CodonTable.unambiguous_dna_by_id Bio.Translate.unambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-9', 'unambiguous_dna_by_id', 'link-9');">unambiguous_dna_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt id="link-10" class="py-name" targets="Variable Bio.Data.CodonTable.unambiguous_rna_by_name=Bio.Data.CodonTable-module.html#unambiguous_rna_by_name,Variable Bio.Translate.unambiguous_rna_by_name=Bio.Translate-module.html#unambiguous_rna_by_name"><a title="Bio.Data.CodonTable.unambiguous_rna_by_name Bio.Translate.unambiguous_rna_by_name" class="py-name" href="#" onclick="return doclink('link-10', 'unambiguous_rna_by_name', 'link-10');">unambiguous_rna_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt id="link-11" class="py-name" targets="Variable Bio.Data.CodonTable.unambiguous_rna_by_id=Bio.Data.CodonTable-module.html#unambiguous_rna_by_id,Variable Bio.Translate.unambiguous_rna_by_id=Bio.Translate-module.html#unambiguous_rna_by_id"><a title="Bio.Data.CodonTable.unambiguous_rna_by_id Bio.Translate.unambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-11', 'unambiguous_rna_by_id', 'link-11');">unambiguous_rna_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt id="link-12" class="py-name" targets="Variable Bio.Data.CodonTable.generic_by_name=Bio.Data.CodonTable-module.html#generic_by_name"><a title="Bio.Data.CodonTable.generic_by_name" class="py-name" href="#" onclick="return doclink('link-12', 'generic_by_name', 'link-12');">generic_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># unambiguous DNA or RNA</tt> </tt> <a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt id="link-13" class="py-name" targets="Variable Bio.Data.CodonTable.generic_by_id=Bio.Data.CodonTable-module.html#generic_by_id"><a title="Bio.Data.CodonTable.generic_by_id" class="py-name" href="#" onclick="return doclink('link-13', 'generic_by_id', 'link-13');">generic_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># unambiguous DNA or RNA</tt> </tt> <a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt id="link-14" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_generic_by_name=Bio.Data.CodonTable-module.html#ambiguous_generic_by_name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-14', 'ambiguous_generic_by_name', 'link-14');">ambiguous_generic_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># ambiguous DNA or RNA</tt> </tt> <a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt id="link-15" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_generic_by_id=Bio.Data.CodonTable-module.html#ambiguous_generic_by_id"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-15', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># ambiguous DNA or RNA </tt> </tt> <a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt> <a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"># standard IUPAC unambiguous codons</tt> </tt> <a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-16" class="py-name" targets="Variable Bio.Data.CodonTable.standard_dna_table=Bio.Data.CodonTable-module.html#standard_dna_table"><a title="Bio.Data.CodonTable.standard_dna_table" class="py-name" href="#" onclick="return doclink('link-16', 'standard_dna_table', 'link-16');">standard_dna_table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt id="link-17" class="py-name" targets="Variable Bio.Data.CodonTable.standard_rna_table=Bio.Data.CodonTable-module.html#standard_rna_table"><a title="Bio.Data.CodonTable.standard_rna_table" class="py-name" href="#" onclick="return doclink('link-17', 'standard_rna_table', 'link-17');">standard_rna_table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt> <a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt> <a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment"># In the future, the back_table could return a statistically</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"># appropriate distribution of codons, so do not cache the results of</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"># back_table lookups!</tt> </tt> <a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="TranslationError"></a><div id="TranslationError-def"><a name="L23"></a><tt class="py-lineno"> 23</tt> <a class="py-toggle" href="#" id="TranslationError-toggle" onclick="return toggle('TranslationError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.TranslationError-class.html">TranslationError</a><tt class="py-op">(</tt><tt class="py-base-class">Exception</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="TranslationError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="TranslationError-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> </div><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> </tt> <a name="CodonTable"></a><div id="CodonTable-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="CodonTable-toggle" onclick="return toggle('CodonTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.CodonTable-class.html">CodonTable</a><tt class="py-op">:</tt> </tt> </div><div id="CodonTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CodonTable-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt id="link-18" 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-18', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-19', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable Bio.Alphabet.generic_nucleotide=Bio.Alphabet-module.html#generic_nucleotide"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-20', 'generic_nucleotide', 'link-20');">generic_nucleotide</a></tt> </tt> <a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt id="link-21" 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-21', 'protein_alphabet', 'link-21');">protein_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-22', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Variable Bio.Alphabet.generic_protein=Bio.Alphabet-module.html#generic_protein"><a title="Bio.Alphabet.generic_protein" class="py-name" href="#" onclick="return doclink('link-23', 'generic_protein', 'link-23');">generic_protein</a></tt> </tt> <a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt> <a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt id="link-24" 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-24', 'forward_table', 'link-24');">forward_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># only includes codons which actually code</tt> </tt> <a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt id="link-25" 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-25', 'back_table', 'link-25');">back_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># for back translations</tt> </tt> <a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt id="link-26" 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-26', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt id="link-27" 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-27', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-comment"># Not always called from derived classes!</tt> </tt> <a name="CodonTable.__init__"></a><div id="CodonTable.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="CodonTable.__init__-toggle" onclick="return toggle('CodonTable.__init__');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.CodonTable-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">nucleotide_alphabet</tt> <tt class="py-op">=</tt> <tt id="link-28" class="py-name"><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-28', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt><tt class="py-op">,</tt> </tt> <a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-param">protein_alphabet</tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.protein_alphabet Bio.Data.CodonTable.NCBICodonTable.protein_alphabet" class="py-name" href="#" onclick="return doclink('link-29', 'protein_alphabet', 'link-21');">protein_alphabet</a></tt><tt class="py-op">,</tt> </tt> <a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-param">forward_table</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-30', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">,</tt> <tt class="py-param">back_table</tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-31', 'back_table', 'link-25');">back_table</a></tt><tt class="py-op">,</tt> </tt> <a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-param">start_codons</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-32', 'start_codons', 'link-26');">start_codons</a></tt><tt class="py-op">,</tt> <tt class="py-param">stop_codons</tt> <tt class="py-op">=</tt> <tt id="link-33" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-33', 'stop_codons', 'link-27');">stop_codons</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="CodonTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CodonTable.__init__-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><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-34', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><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-35', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> </tt> <a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.protein_alphabet Bio.Data.CodonTable.NCBICodonTable.protein_alphabet" class="py-name" href="#" onclick="return doclink('link-36', 'protein_alphabet', 'link-21');">protein_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.protein_alphabet Bio.Data.CodonTable.NCBICodonTable.protein_alphabet" class="py-name" href="#" onclick="return doclink('link-37', 'protein_alphabet', 'link-21');">protein_alphabet</a></tt> </tt> <a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-38', 'forward_table', 'link-24');">forward_table</a></tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-39', 'forward_table', 'link-24');">forward_table</a></tt> </tt> <a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-40', 'back_table', 'link-25');">back_table</a></tt> <tt class="py-op">=</tt> <tt id="link-41" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-41', 'back_table', 'link-25');">back_table</a></tt> </tt> <a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-42', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt id="link-43" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-43', 'start_codons', 'link-26');">start_codons</a></tt> </tt> <a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-44', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-45', 'stop_codons', 'link-27');">stop_codons</a></tt> </tt> </div><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> </tt> <a name="CodonTable.__str__"></a><div id="CodonTable.__str__-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="CodonTable.__str__-toggle" onclick="return toggle('CodonTable.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.CodonTable-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> </div><div id="CodonTable.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CodonTable.__str__-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a simple text representation of the codon table</tt> </tt> <a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt> <a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt> <a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> >>> import Bio.Data.CodonTable</tt> </tt> <a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> >>> print Bio.Data.CodonTable.standard_dna_table</tt> </tt> <a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> >>> print Bio.Data.CodonTable.generic_by_id[1]"""</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">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Variable Bio.Data.CodonTable.id=Bio.Data.CodonTable-module.html#id,Variable Bio.Encodings.IUPACEncoding.id=Bio.Encodings.IUPACEncoding-module.html#id,Method Bio.GFF.Feature.id()=Bio.GFF.Feature-class.html#id"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-46', 'id', 'link-46');">id</a></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">answer</tt> <tt class="py-op">=</tt> <tt class="py-string">"Table %i"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-47', 'id', 'link-46');">id</a></tt> </tt> <a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">answer</tt> <tt class="py-op">=</tt> <tt class="py-string">"Table ID unknown"</tt> </tt> <a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.Compass._Consumer.names()=Bio.Compass._Consumer-class.html#names"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-48', 'names', 'link-48');">names</a></tt> <tt class="py-op">:</tt> </tt> <a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-name">answer</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-49" class="py-name" targets="Function Bio.FSSP.FSSPTools.filter()=Bio.FSSP.FSSPTools-module.html#filter,Method Bio.FilteredReader.FilteredReader.filter()=Bio.FilteredReader.FilteredReader-class.html#filter,Variable Bio.expressions.swissprot.filter=Bio.expressions.swissprot-module.html#filter"><a title="Bio.FSSP.FSSPTools.filter Bio.FilteredReader.FilteredReader.filter Bio.expressions.swissprot.filter" class="py-name" href="#" onclick="return doclink('link-49', 'filter', 'link-49');">filter</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-50', 'names', 'link-48');">names</a></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> <a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment">#Use the main four letters (and the conventional ordering)</tt> </tt> <a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#even for ambiguous tables</tt> </tt> <a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-51" 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-51', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><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-52', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><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-53', 'letters', 'link-51');">letters</a></tt> </tt> <a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.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-54', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-55" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-55', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Class Bio.Alphabet.DNAAlphabet=Bio.Alphabet.DNAAlphabet-class.html"><a title="Bio.Alphabet.DNAAlphabet" class="py-name" href="#" onclick="return doclink('link-56', 'DNAAlphabet', 'link-56');">DNAAlphabet</a></tt><tt class="py-op">)</tt> \ </tt> <a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt id="link-57" class="py-name"><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-57', 'letters', 'link-51');">letters</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-string">"T"</tt> <tt class="py-keyword">in</tt> <tt id="link-58" class="py-name"><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-58', 'letters', 'link-51');">letters</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt id="link-59" class="py-name"><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-59', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"TCAG"</tt> </tt> <a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-comment">#Should be either RNA or generic nucleotides,</tt> </tt> <a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#e.g. Bio.Data.CodonTable.generic_by_id[1]</tt> </tt> <a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-60" class="py-name"><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-60', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"UCAG"</tt> </tt> <a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> </tt> <a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-comment">#Build the table...</tt> </tt> <a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">answer</tt><tt class="py-op">=</tt><tt class="py-name">answer</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n\n |"</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> <a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-op">[</tt><tt class="py-string">" %s "</tt> <tt class="py-op">%</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">in</tt> <tt id="link-61" class="py-name"><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-61', 'letters', 'link-51');">letters</a></tt><tt class="py-op">]</tt> \ </tt> <a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"|"</tt> </tt> <a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">answer</tt><tt class="py-op">=</tt><tt class="py-name">answer</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n--+"</tt> \ </tt> <a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"+"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"---------"</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">in</tt> <tt id="link-62" class="py-name"><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-62', 'letters', 'link-51');">letters</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"+--"</tt> </tt> <a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c1</tt> <tt class="py-keyword">in</tt> <tt id="link-63" class="py-name"><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-63', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">:</tt> </tt> <a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c3</tt> <tt class="py-keyword">in</tt> <tt id="link-64" class="py-name"><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-64', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">:</tt> </tt> <a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">c1</tt> <tt class="py-op">+</tt> <tt class="py-string">" |"</tt> </tt> <a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">in</tt> <tt id="link-65" class="py-name"><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-65', 'letters', 'link-51');">letters</a></tt> <tt class="py-op">:</tt> </tt> <a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">c1</tt><tt class="py-op">+</tt><tt class="py-name">c2</tt><tt class="py-op">+</tt><tt class="py-name">c3</tt> </tt> <a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">+</tt> <tt class="py-string">" %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">codon</tt> </tt> <a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-66', 'stop_codons', 'link-27');">stop_codons</a></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">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">+</tt> <tt class="py-string">" Stop|"</tt> </tt> <a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt> <a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">amino</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-67', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-name">codon</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">except</tt> <tt class="py-name">KeyError</tt> <tt class="py-op">:</tt> </tt> <a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-name">amino</tt> <tt class="py-op">=</tt> <tt class="py-string">"?"</tt> </tt> <a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-68" 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-68', 'TranslationError', 'link-68');">TranslationError</a></tt> <tt class="py-op">:</tt> </tt> <a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">amino</tt> <tt class="py-op">=</tt> <tt class="py-string">"?"</tt> </tt> <a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-69', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">:</tt> </tt> <a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">+</tt> <tt class="py-string">" %s(s)|"</tt> <tt class="py-op">%</tt> <tt class="py-name">amino</tt> </tt> <a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt> <a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">+</tt> <tt class="py-string">" %s |"</tt> <tt class="py-op">%</tt> <tt class="py-name">amino</tt> </tt> <a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt> <tt class="py-op">+</tt> <tt class="py-string">" "</tt> <tt class="py-op">+</tt> <tt class="py-name">c3</tt> </tt> <a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">answer</tt> <tt class="py-op">=</tt> <tt class="py-name">answer</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt><tt class="py-op">+</tt> <tt class="py-name">line</tt> </tt> <a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">answer</tt><tt class="py-op">=</tt><tt class="py-name">answer</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n--+"</tt> \ </tt> <a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">"+"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"---------"</tt> <tt class="py-keyword">for</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">in</tt> <tt id="link-70" class="py-name"><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-70', 'letters', 'link-51');">letters</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt class="py-string">"+--"</tt> </tt> <a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">answer</tt> </tt> </div></div><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt> <a name="make_back_table"></a><div id="make_back_table-def"><a name="L103"></a><tt class="py-lineno">103</tt> <a class="py-toggle" href="#" id="make_back_table-toggle" onclick="return toggle('make_back_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable-module.html#make_back_table">make_back_table</a><tt class="py-op">(</tt><tt class="py-param">table</tt><tt class="py-op">,</tt> <tt class="py-param">default_stop_codon</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="make_back_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="make_back_table-expanded"><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-comment"># ONLY RETURNS A SINGLE CODON</tt> </tt> <a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Do the sort so changes in the hash implementation won't affect</tt> </tt> <a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the result when one amino acid is coded by more than one codon.</tt> </tt> <a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-71" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-71', 'back_table', 'link-25');">back_table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt id="link-72" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-72', 'keys', 'link-72');">keys</a></tt> <tt class="py-op">=</tt> <tt id="link-73" 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-73', 'table', 'link-73');">table</a></tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-74', 'keys', 'link-72');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">;</tt> <tt id="link-75" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-75', 'keys', 'link-72');">keys</a></tt><tt class="py-op">.</tt><tt id="link-76" 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-76', 'sort', 'link-76');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-77" 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-77', 'key', 'link-77');">key</a></tt> <tt class="py-keyword">in</tt> <tt id="link-78" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-78', 'keys', 'link-72');">keys</a></tt><tt class="py-op">:</tt> </tt> <a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt id="link-79" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-79', 'back_table', 'link-25');">back_table</a></tt><tt class="py-op">[</tt><tt id="link-80" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-80', 'table', 'link-73');">table</a></tt><tt class="py-op">[</tt><tt id="link-81" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-81', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-82" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-82', 'key', 'link-77');">key</a></tt> </tt> <a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt id="link-83" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-83', 'back_table', 'link-25');">back_table</a></tt><tt class="py-op">[</tt><tt class="py-name">None</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">default_stop_codon</tt> </tt> <a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-84" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-84', 'back_table', 'link-25');">back_table</a></tt> </tt> </div><a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> </tt> <a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt> <a name="NCBICodonTable"></a><div id="NCBICodonTable-def"><a name="L115"></a><tt class="py-lineno">115</tt> <a class="py-toggle" href="#" id="NCBICodonTable-toggle" onclick="return toggle('NCBICodonTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.NCBICodonTable-class.html">NCBICodonTable</a><tt class="py-op">(</tt><tt class="py-base-class">CodonTable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="NCBICodonTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NCBICodonTable-expanded"><a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt id="link-85" class="py-name"><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-85', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-86" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-86', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="Bio.Alphabet.generic_nucleotide" class="py-name" href="#" onclick="return doclink('link-87', 'generic_nucleotide', 'link-20');">generic_nucleotide</a></tt> </tt> <a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.protein_alphabet Bio.Data.CodonTable.NCBICodonTable.protein_alphabet" class="py-name" href="#" onclick="return doclink('link-88', 'protein_alphabet', 'link-21');">protein_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-89" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-89', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-90" class="py-name" targets="Variable Bio.Alphabet.IUPAC.protein=Bio.Alphabet.IUPAC-module.html#protein"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-90', 'protein', 'link-90');">protein</a></tt> </tt> <a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt> <a name="NCBICodonTable.__init__"></a><div id="NCBICodonTable.__init__-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="NCBICodonTable.__init__-toggle" onclick="return toggle('NCBICodonTable.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.NCBICodonTable-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">id</tt><tt class="py-op">,</tt> <tt class="py-param">names</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt><tt class="py-op">,</tt> <tt class="py-param">start_codons</tt><tt class="py-op">,</tt> <tt class="py-param">stop_codons</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="NCBICodonTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NCBICodonTable.__init__-expanded"><a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-91" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-91', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt id="link-92" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-92', 'id', 'link-46');">id</a></tt> </tt> <a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-93', 'names', 'link-48');">names</a></tt> <tt class="py-op">=</tt> <tt id="link-94" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-94', 'names', 'link-48');">names</a></tt> </tt> <a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-95', 'forward_table', 'link-24');">forward_table</a></tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-96', 'table', 'link-73');">table</a></tt> </tt> <a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-97" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-97', 'back_table', 'link-25');">back_table</a></tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name" targets="Function Bio.Data.CodonTable.make_back_table()=Bio.Data.CodonTable-module.html#make_back_table"><a title="Bio.Data.CodonTable.make_back_table" class="py-name" href="#" onclick="return doclink('link-98', 'make_back_table', 'link-98');">make_back_table</a></tt><tt class="py-op">(</tt><tt id="link-99" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-99', 'table', 'link-73');">table</a></tt><tt class="py-op">,</tt> <tt id="link-100" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-100', 'stop_codons', 'link-27');">stop_codons</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="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-101', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt id="link-102" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-102', 'start_codons', 'link-26');">start_codons</a></tt> </tt> <a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-103', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt id="link-104" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-104', 'stop_codons', 'link-27');">stop_codons</a></tt> </tt> </div></div><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt> <a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt> <a name="NCBICodonTableDNA"></a><div id="NCBICodonTableDNA-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="NCBICodonTableDNA-toggle" onclick="return toggle('NCBICodonTableDNA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.NCBICodonTableDNA-class.html">NCBICodonTableDNA</a><tt class="py-op">(</tt><tt class="py-base-class">NCBICodonTable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="NCBICodonTableDNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NCBICodonTableDNA-expanded"><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><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-105', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-106', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-107" 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-107', 'unambiguous_dna', 'link-107');">unambiguous_dna</a></tt> </tt> </div><a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> </tt> <a name="NCBICodonTableRNA"></a><div id="NCBICodonTableRNA-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="NCBICodonTableRNA-toggle" onclick="return toggle('NCBICodonTableRNA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.NCBICodonTableRNA-class.html">NCBICodonTableRNA</a><tt class="py-op">(</tt><tt class="py-base-class">NCBICodonTable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="NCBICodonTableRNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NCBICodonTableRNA-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><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-108', 'nucleotide_alphabet', 'link-18');">nucleotide_alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-109', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-110" class="py-name" targets="Variable Bio.Alphabet.IUPAC.unambiguous_rna=Bio.Alphabet.IUPAC-module.html#unambiguous_rna"><a title="Bio.Alphabet.IUPAC.unambiguous_rna" class="py-name" href="#" onclick="return doclink('link-110', 'unambiguous_rna', 'link-110');">unambiguous_rna</a></tt> </tt> </div><a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> </tt> <a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt> <a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> </tt> <a name="register_ncbi_table"></a><div id="register_ncbi_table-def"><a name="L136"></a><tt class="py-lineno">136</tt> <a class="py-toggle" href="#" id="register_ncbi_table-toggle" onclick="return toggle('register_ncbi_table');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable-module.html#register_ncbi_table">register_ncbi_table</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">,</tt> <tt class="py-param">alt_name</tt><tt class="py-op">,</tt> <tt class="py-param">id</tt><tt class="py-op">,</tt> </tt> <a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> <tt class="py-param">table</tt><tt class="py-op">,</tt> <tt class="py-param">start_codons</tt><tt class="py-op">,</tt> <tt class="py-param">stop_codons</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="register_ncbi_table-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="register_ncbi_table-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt id="link-111" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-111', 'names', 'link-48');">names</a></tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-112" 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-112', 'split', 'link-112');">split</a></tt><tt class="py-op">(</tt><tt id="link-113" 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-113', 'name', 'link-113');">name</a></tt><tt class="py-op">,</tt> <tt class="py-string">"; "</tt><tt class="py-op">)</tt> </tt> <a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> </tt> <a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt id="link-114" class="py-name" targets="Class Bio.Data.CodonTable.NCBICodonTableDNA=Bio.Data.CodonTable.NCBICodonTableDNA-class.html"><a title="Bio.Data.CodonTable.NCBICodonTableDNA" class="py-name" href="#" onclick="return doclink('link-114', 'NCBICodonTableDNA', 'link-114');">NCBICodonTableDNA</a></tt><tt class="py-op">(</tt><tt id="link-115" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-115', 'id', 'link-46');">id</a></tt><tt class="py-op">,</tt> <tt id="link-116" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-116', 'names', 'link-48');">names</a></tt> <tt class="py-op">+</tt> <tt class="py-op">[</tt><tt class="py-name">alt_name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-117', 'table', 'link-73');">table</a></tt><tt class="py-op">,</tt> <tt id="link-118" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-118', 'start_codons', 'link-26');">start_codons</a></tt><tt class="py-op">,</tt> </tt> <a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt id="link-119" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-119', 'stop_codons', 'link-27');">stop_codons</a></tt><tt class="py-op">)</tt> </tt> <a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-comment"># replace all T's with U's for the RNA tables</tt> </tt> <a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rna_table</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">generic_table</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">codon</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-120" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-120', 'table', 'link-73');">table</a></tt><tt class="py-op">.</tt><tt id="link-121" 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-121', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">generic_table</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt> <a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">codon</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"T"</tt><tt class="py-op">,</tt> <tt class="py-string">"U"</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">generic_table</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt> <a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">rna_table</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt> </tt> <a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">rna_start_codons</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">generic_start_codons</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt id="link-122" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-122', 'start_codons', 'link-26');">start_codons</a></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">generic_start_codons</tt><tt class="py-op">.</tt><tt id="link-123" 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-123', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</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">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">codon</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"T"</tt><tt class="py-op">,</tt> <tt class="py-string">"U"</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">generic_start_codons</tt><tt class="py-op">.</tt><tt id="link-124" 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-124', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</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">rna_start_codons</tt><tt class="py-op">.</tt><tt id="link-125" 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-125', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">rna_stop_codons</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">generic_stop_codons</tt> <tt class="py-op">=</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 class="py-keyword">for</tt> <tt class="py-name">codon</tt> <tt class="py-keyword">in</tt> <tt id="link-126" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-126', 'stop_codons', 'link-27');">stop_codons</a></tt><tt class="py-op">:</tt> </tt> <a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">generic_stop_codons</tt><tt class="py-op">.</tt><tt id="link-127" 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-127', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">codon</tt> <tt class="py-op">=</tt> <tt class="py-name">codon</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"T"</tt><tt class="py-op">,</tt> <tt class="py-string">"U"</tt><tt class="py-op">)</tt> </tt> <a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-name">generic_stop_codons</tt><tt class="py-op">.</tt><tt id="link-128" 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-128', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">rna_stop_codons</tt><tt class="py-op">.</tt><tt id="link-129" 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-129', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt> <a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">generic</tt> <tt class="py-op">=</tt> <tt id="link-130" class="py-name" targets="Class Bio.Data.CodonTable.NCBICodonTable=Bio.Data.CodonTable.NCBICodonTable-class.html"><a title="Bio.Data.CodonTable.NCBICodonTable" class="py-name" href="#" onclick="return doclink('link-130', 'NCBICodonTable', 'link-130');">NCBICodonTable</a></tt><tt class="py-op">(</tt><tt id="link-131" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-131', 'id', 'link-46');">id</a></tt><tt class="py-op">,</tt> <tt id="link-132" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-132', 'names', 'link-48');">names</a></tt> <tt class="py-op">+</tt> <tt class="py-op">[</tt><tt class="py-name">alt_name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">generic_table</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">generic_start_codons</tt><tt class="py-op">,</tt> <tt class="py-name">generic_stop_codons</tt><tt class="py-op">)</tt> </tt> <a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-name">rna</tt> <tt class="py-op">=</tt> <tt id="link-133" class="py-name" targets="Class Bio.Data.CodonTable.NCBICodonTableRNA=Bio.Data.CodonTable.NCBICodonTableRNA-class.html"><a title="Bio.Data.CodonTable.NCBICodonTableRNA" class="py-name" href="#" onclick="return doclink('link-133', 'NCBICodonTableRNA', 'link-133');">NCBICodonTableRNA</a></tt><tt class="py-op">(</tt><tt id="link-134" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-134', 'id', 'link-46');">id</a></tt><tt class="py-op">,</tt> <tt id="link-135" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-135', 'names', 'link-48');">names</a></tt> <tt class="py-op">+</tt> <tt class="py-op">[</tt><tt class="py-name">alt_name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">rna_table</tt><tt class="py-op">,</tt> </tt> <a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">rna_start_codons</tt><tt class="py-op">,</tt> <tt class="py-name">rna_stop_codons</tt><tt class="py-op">)</tt> </tt> <a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt> <a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-136" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-136', 'id', 'link-46');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt> <a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">global</tt> <tt id="link-137" class="py-name"><a title="Bio.Data.CodonTable.standard_dna_table" class="py-name" href="#" onclick="return doclink('link-137', 'standard_dna_table', 'link-16');">standard_dna_table</a></tt><tt class="py-op">,</tt> <tt id="link-138" class="py-name"><a title="Bio.Data.CodonTable.standard_rna_table" class="py-name" href="#" onclick="return doclink('link-138', 'standard_rna_table', 'link-17');">standard_rna_table</a></tt> </tt> <a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt id="link-139" class="py-name"><a title="Bio.Data.CodonTable.standard_dna_table" class="py-name" href="#" onclick="return doclink('link-139', 'standard_dna_table', 'link-16');">standard_dna_table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dna</tt> </tt> <a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt id="link-140" class="py-name"><a title="Bio.Data.CodonTable.standard_rna_table" class="py-name" href="#" onclick="return doclink('link-140', 'standard_rna_table', 'link-17');">standard_rna_table</a></tt> <tt class="py-op">=</tt> <tt class="py-name">rna</tt> </tt> <a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> </tt> <a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-141" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_dna_by_id Bio.Translate.unambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-141', 'unambiguous_dna_by_id', 'link-9');">unambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-142" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-142', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">dna</tt> </tt> <a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-143" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_rna_by_id Bio.Translate.unambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-143', 'unambiguous_rna_by_id', 'link-11');">unambiguous_rna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-144" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-144', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">rna</tt> </tt> <a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt id="link-145" class="py-name"><a title="Bio.Data.CodonTable.generic_by_id" class="py-name" href="#" onclick="return doclink('link-145', 'generic_by_id', 'link-13');">generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-146" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-146', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">generic</tt> </tt> <a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt> <a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">alt_name</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt> <a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt id="link-147" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-147', 'names', 'link-48');">names</a></tt><tt class="py-op">.</tt><tt id="link-148" 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-148', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">alt_name</tt><tt class="py-op">)</tt> </tt> <a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt> <a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-149" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-149', 'name', 'link-113');">name</a></tt> <tt class="py-keyword">in</tt> <tt id="link-150" class="py-name"><a title="Bio.Compass._Consumer.names" class="py-name" href="#" onclick="return doclink('link-150', 'names', 'link-48');">names</a></tt><tt class="py-op">:</tt> </tt> <a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt id="link-151" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_dna_by_name Bio.Translate.unambiguous_dna_by_name" class="py-name" href="#" onclick="return doclink('link-151', 'unambiguous_dna_by_name', 'link-8');">unambiguous_dna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-152" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-152', 'name', 'link-113');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">dna</tt> </tt> <a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt id="link-153" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_rna_by_name Bio.Translate.unambiguous_rna_by_name" class="py-name" href="#" onclick="return doclink('link-153', 'unambiguous_rna_by_name', 'link-10');">unambiguous_rna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-154" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-154', 'name', 'link-113');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">rna</tt> </tt> <a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt id="link-155" class="py-name"><a title="Bio.Data.CodonTable.generic_by_name" class="py-name" href="#" onclick="return doclink('link-155', 'generic_by_name', 'link-12');">generic_by_name</a></tt><tt class="py-op">[</tt><tt id="link-156" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-156', 'name', 'link-113');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">generic</tt> </tt> </div><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> </tt> <a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-comment">### These tables created from the data file</tt> </tt> <a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### ftp://ncbi.nlm.nih.gov/entrez/misc/data/gc.prt</tt> </tt> <a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">### using the following:</tt> </tt> <a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##import re</tt> </tt> <a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">##for line in open("gc.prt").readlines():</tt> </tt> <a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if line[:2] == " {":</tt> </tt> <a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## names = []</tt> </tt> <a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## id = None</tt> </tt> <a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## aa = None</tt> </tt> <a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## start = None</tt> </tt> <a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## bases = []</tt> </tt> <a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:6] == " name":</tt> </tt> <a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## names.append(re.search('"([^"]*)"', line).group(1))</tt> </tt> <a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:8] == " name":</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">## names.append(re.search('"(.*)$', line).group(1))</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">## elif line == ' Mitochondrial; Mycoplasma; Spiroplasma" ,\n':</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">## names[-1] = names[-1] + " Mitochondrial; Mycoplasma; Spiroplasma"</tt> </tt> <a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:4] == " id":</tt> </tt> <a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## id = int(re.search('(\d+)', line).group(1))</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">## elif line[:10] == " ncbieaa ":</tt> </tt> <a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## aa = line[12:12+64]</tt> </tt> <a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:10] == " sncbieaa":</tt> </tt> <a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## start = line[12:12+64]</tt> </tt> <a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:9] == " -- Base":</tt> </tt> <a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## bases.append(line[12:12+64])</tt> </tt> <a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif line[:2] == " }":</tt> </tt> <a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## assert names != [] and id is not None and aa is not None</tt> </tt> <a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## assert start is not None and bases != []</tt> </tt> <a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if len(names) == 1:</tt> </tt> <a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## names.append(None)</tt> </tt> <a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print "register_ncbi_table(name = %s," % repr(names[0])</tt> </tt> <a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print " alt_name = %s, id = %d", % \</tt> </tt> <a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## (repr(names[1]), id)</tt> </tt> <a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print " table = {"</tt> </tt> <a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = " "</tt> </tt> <a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## for i in range(64):</tt> </tt> <a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if aa[i] != "*":</tt> </tt> <a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## t = " '%s%s%s': '%s'," % (bases[0][i], bases[1][i],</tt> </tt> <a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## bases[2][i], aa[i])</tt> </tt> <a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if len(s) + len(t) > 75:</tt> </tt> <a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s</tt> </tt> <a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = " " + t</tt> </tt> <a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt> <a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = s + t</tt> </tt> <a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s, "},"</tt> </tt> <a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment">## s = " stop_codons = ["</tt> </tt> <a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## for i in range(64):</tt> </tt> <a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if aa[i] == "*":</tt> </tt> <a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## t = " '%s%s%s'," % (bases[0][i], bases[1][i], bases[2][i])</tt> </tt> <a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if len(s) + len(t) > 75:</tt> </tt> <a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s</tt> </tt> <a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = " " + t</tt> </tt> <a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt> <a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = s + t</tt> </tt> <a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s, "],"</tt> </tt> <a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment">## s = " start_codons = ["</tt> </tt> <a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## for i in range(64):</tt> </tt> <a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if start[i] == "M":</tt> </tt> <a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## t = " '%s%s%s'," % (bases[0][i], bases[1][i], bases[2][i])</tt> </tt> <a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if len(s) + len(t) > 75:</tt> </tt> <a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s</tt> </tt> <a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = " " + t</tt> </tt> <a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt> <a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = s + t</tt> </tt> <a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print s, "]"</tt> </tt> <a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## print " )"</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">## elif line[:2] == "--" or line == "\n" or line == "}\n" or \</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">## line == 'Genetic-code-table ::= {\n':</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">## pass</tt> </tt> <a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt> <a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## raise "Unparsed", repr(line)</tt> </tt> <a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt id="link-157" class="py-name" targets="Function Bio.Data.CodonTable.register_ncbi_table()=Bio.Data.CodonTable-module.html#register_ncbi_table"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-157', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-158" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-158', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Standard'</tt><tt class="py-op">,</tt> </tt> <a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC0'</tt><tt class="py-op">,</tt> <tt id="link-159" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-159', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> </tt> <a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt id="link-160" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-160', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> </tt> <a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt> <a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt> <a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt id="link-161" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-161', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt id="link-162" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-162', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt id="link-163" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-163', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-164" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-164', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Vertebrate Mitochondrial'</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">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC1'</tt><tt class="py-op">,</tt> <tt id="link-165" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-165', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> </tt> <a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt id="link-166" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-166', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt> <a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> </tt> <a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt id="link-167" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-167', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">,</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-168" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-168', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</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 class="py-op">)</tt> </tt> <a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt id="link-169" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-169', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-170" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-170', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Yeast Mitochondrial'</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">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC2'</tt><tt class="py-op">,</tt> <tt id="link-171" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-171', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> </tt> <a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt id="link-172" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-172', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt id="link-173" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-173', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt id="link-174" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-174', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt id="link-175" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-175', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-176" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-176', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma'</tt><tt class="py-op">,</tt> </tt> <a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC3'</tt><tt class="py-op">,</tt> <tt id="link-177" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-177', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">4</tt><tt class="py-op">,</tt> </tt> <a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt id="link-178" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-178', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt id="link-179" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-179', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt id="link-180" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-180', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">,</tt> </tt> <a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-string">'ATA'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt id="link-181" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-181', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-182', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Invertebrate Mitochondrial'</tt><tt class="py-op">,</tt> </tt> <a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC4'</tt><tt class="py-op">,</tt> <tt id="link-183" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-183', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">5</tt><tt class="py-op">,</tt> </tt> <a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-184" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-184', 'table', 'link-73');">table</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 class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</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-185" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-185', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt id="link-186" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-186', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> </tt> <a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-string">'GTG'</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 class="py-op">)</tt> </tt> <a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt id="link-187" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-187', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-188" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-188', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear'</tt><tt class="py-op">,</tt> </tt> <a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC5'</tt><tt class="py-op">,</tt> <tt id="link-189" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-189', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">6</tt><tt class="py-op">,</tt> </tt> <a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt id="link-190" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-190', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-string">'TAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> </tt> <a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> </tt> <a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> </tt> <a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'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-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt id="link-191" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-191', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt id="link-192" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-192', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt id="link-193" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-193', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-194" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-194', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Echinoderm Mitochondrial'</tt><tt class="py-op">,</tt> </tt> <a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC8'</tt><tt class="py-op">,</tt> <tt id="link-195" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-195', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">9</tt><tt class="py-op">,</tt> </tt> <a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt id="link-196" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-196', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</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 id="link-197" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-197', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt id="link-198" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-198', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt id="link-199" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-199', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-200" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-200', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Euplotid Nuclear'</tt><tt class="py-op">,</tt> </tt> <a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-string">'SGC9'</tt><tt class="py-op">,</tt> <tt id="link-201" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-201', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">10</tt><tt class="py-op">,</tt> </tt> <a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt id="link-202" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-202', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</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">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</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">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</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">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</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 id="link-203" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-203', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt id="link-204" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-204', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"><tt id="link-205" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-205', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-206', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Bacterial'</tt><tt class="py-op">,</tt> </tt> <a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-207" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-207', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">11</tt><tt class="py-op">,</tt> </tt> <a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt id="link-208" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-208', 'table', 'link-73');">table</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-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> </tt> <a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt> <a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt> <a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt id="link-209" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-209', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt id="link-210" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-210', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">,</tt> </tt> <a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</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-op">)</tt> </tt> <a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt id="link-211" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-211', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-212" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-212', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Alternative Yeast Nuclear'</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">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-213" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-213', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">12</tt><tt class="py-op">,</tt> </tt> <a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt id="link-214" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-214', 'table', 'link-73');">table</a></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-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> </tt> <a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> </tt> <a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt> <a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt id="link-215" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-215', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt id="link-216" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-216', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt id="link-217" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-217', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-218" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-218', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Ascidian Mitochondrial'</tt><tt class="py-op">,</tt> </tt> <a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-219" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-219', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">13</tt><tt class="py-op">,</tt> </tt> <a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt id="link-220" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-220', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt id="link-221" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-221', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt id="link-222" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-222', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt id="link-223" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-223', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-224" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-224', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Flatworm Mitochondrial'</tt><tt class="py-op">,</tt> </tt> <a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-225" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-225', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">14</tt><tt class="py-op">,</tt> </tt> <a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt id="link-226" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-226', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-string">'TAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> </tt> <a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> </tt> <a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> </tt> <a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> </tt> <a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt id="link-227" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-227', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt id="link-228" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-228', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt id="link-229" class="py-name"><a title="Bio.Data.CodonTable.register_ncbi_table" class="py-name" href="#" onclick="return doclink('link-229', 'register_ncbi_table', 'link-157');">register_ncbi_table</a></tt><tt class="py-op">(</tt><tt id="link-230" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-230', 'name', 'link-113');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">'Blepharisma Macronuclear'</tt><tt class="py-op">,</tt> </tt> <a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">alt_name</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-231" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-231', 'id', 'link-46');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-number">15</tt><tt class="py-op">,</tt> </tt> <a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt id="link-232" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-232', 'table', 'link-73');">table</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt> <a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-string">'TTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'F'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> </tt> <a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-string">'TCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> <tt class="py-string">'TAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'Y'</tt><tt class="py-op">,</tt> </tt> <a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-string">'TAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'C'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'W'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> </tt> <a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt class="py-string">'CTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'L'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> </tt> <a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-string">'CCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'P'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'H'</tt><tt class="py-op">,</tt> <tt class="py-string">'CAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> </tt> <a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-string">'CAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'Q'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'CGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-string">'ATT'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATC'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATA'</tt><tt class="py-op">:</tt> <tt class="py-string">'I'</tt><tt class="py-op">,</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">:</tt> <tt class="py-string">'M'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACT'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> </tt> <a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"> <tt class="py-string">'ACC'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACA'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'ACG'</tt><tt class="py-op">:</tt> <tt class="py-string">'T'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'N'</tt><tt class="py-op">,</tt> </tt> <a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-string">'AAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'K'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'S'</tt><tt class="py-op">,</tt> <tt class="py-string">'AGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> </tt> <a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-string">'AGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'R'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTT'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTC'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTA'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> <tt class="py-string">'GTG'</tt><tt class="py-op">:</tt> <tt class="py-string">'V'</tt><tt class="py-op">,</tt> </tt> <a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-string">'GCT'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCC'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCA'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GCG'</tt><tt class="py-op">:</tt> <tt class="py-string">'A'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAT'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> </tt> <a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-string">'GAC'</tt><tt class="py-op">:</tt> <tt class="py-string">'D'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAA'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GAG'</tt><tt class="py-op">:</tt> <tt class="py-string">'E'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGT'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGC'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> </tt> <a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-string">'GGA'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-string">'GGG'</tt><tt class="py-op">:</tt> <tt class="py-string">'G'</tt><tt class="py-op">,</tt> <tt class="py-op">}</tt><tt class="py-op">,</tt> </tt> <a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt id="link-233" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-233', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'TAA'</tt><tt class="py-op">,</tt> <tt class="py-string">'TGA'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt><tt class="py-op">,</tt> </tt> <a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt id="link-234" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-234', 'start_codons', 'link-26');">start_codons</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt> <tt class="py-string">'ATG'</tt><tt class="py-op">,</tt> <tt class="py-op">]</tt> </tt> <a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> </tt> <a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-comment">######### Deal with ambiguous forward translations</tt> </tt> <a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="AmbiguousCodonTable"></a><div id="AmbiguousCodonTable-def"><a name="L513"></a><tt class="py-lineno">513</tt> <a class="py-toggle" href="#" id="AmbiguousCodonTable-toggle" onclick="return toggle('AmbiguousCodonTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousCodonTable-class.html">AmbiguousCodonTable</a><tt class="py-op">(</tt><tt class="py-base-class">CodonTable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AmbiguousCodonTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AmbiguousCodonTable-expanded"><a name="AmbiguousCodonTable.__init__"></a><div id="AmbiguousCodonTable.__init__-def"><a name="L514"></a><tt class="py-lineno">514</tt> <a class="py-toggle" href="#" id="AmbiguousCodonTable.__init__-toggle" onclick="return toggle('AmbiguousCodonTable.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousCodonTable-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">codon_table</tt><tt class="py-op">,</tt> </tt> <a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt class="py-param">ambiguous_nucleotide_alphabet</tt><tt class="py-op">,</tt> </tt> <a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt class="py-param">ambiguous_nucleotide_values</tt><tt class="py-op">,</tt> </tt> <a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt class="py-param">ambiguous_protein_alphabet</tt><tt class="py-op">,</tt> </tt> <a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"> <tt class="py-param">ambiguous_protein_values</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AmbiguousCodonTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AmbiguousCodonTable.__init__-expanded"><a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt id="link-235" 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-235', 'CodonTable', 'link-235');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-236" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method 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Bio.SwissProt.KeyWList._Scanner.__init__ Bio.SwissProt.SProt.Dictionary.__init__ Bio.SwissProt.SProt.ExPASyDictionary.__init__ Bio.SwissProt.SProt.Iterator.__init__ Bio.SwissProt.SProt.Record.__init__ Bio.SwissProt.SProt.RecordParser.__init__ Bio.SwissProt.SProt.Reference.__init__ Bio.SwissProt.SProt.SequenceParser.__init__ Bio.SwissProt.SProt._RecordConsumer.__init__ Bio.SwissProt.SProt._SequenceConsumer.__init__ Bio.Transcribe.Transcribe.__init__ Bio.Translate.Translator.__init__ Bio.UniGene.Iterator.__init__ Bio.UniGene.RecordParser.__init__ Bio.UniGene.UnigeneProtsimRecord.__init__ Bio.UniGene.UnigeneRecord.__init__ Bio.UniGene.UnigeneSTSRecord.__init__ Bio.UniGene.UnigeneSequenceRecord.__init__ Bio.UniGene._RecordConsumer.__init__ Bio.WWW.RequestLimiter.__init__ Bio.Wise.dnal.Statistics.__init__ Bio.Wise.psw.AlignmentColumn.__init__ Bio.Wise.psw.ColumnUnit.__init__ Bio.Writer.Writer.__init__ Bio.biblio.Biblio.__init__ Bio.biblio.BiblioCollection.__init__ Bio.builders.Search.search.BuildSearch.__init__ Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__ Bio.config.DBRegistry.BioCorbaDB.__init__ Bio.config.DBRegistry.BioSQLDB.__init__ Bio.config.DBRegistry.CGIDB.__init__ Bio.config.DBRegistry.DBGroup.__init__ Bio.config.DBRegistry.DBObject.__init__ Bio.config.DBRegistry.DBRegistry.__init__ Bio.config.DBRegistry.EUtilsDB.__init__ Bio.config.DBRegistry.IndexedFileDB.__init__ Bio.config.FormatRegistry.FormatGroup.__init__ Bio.config.FormatRegistry.FormatObject.__init__ Bio.config.FormatRegistry.FormatRegistry.__init__ Bio.config.Registry.RegisterableGroup.__init__ Bio.config.Registry.RegisterableObject.__init__ Bio.config.Registry.Registry.__init__ Bio.config.SeqDBRegistry.SeqDBRegistry.__init__ Bio.config._stanzaformat.Stanza.__init__ Bio.config._stanzaformat.StanzaFormat.__init__ Bio.config._support.make_cached_expression.__init__ Bio.config._support.make_rate_limited_function.__init__ Bio.kNN.kNN.__init__ Bio.pairwise2.affine_penalty.__init__ Bio.pairwise2.dictionary_match.__init__ Bio.pairwise2.identity_match.__init__ Bio.writers.SeqRecord.embl.WriteEmbl.__init__ Bio.writers.SeqRecord.fasta.WriteFasta.__init__ BioSQL.BioSeq.DBSeq.__init__ BioSQL.BioSeq.DBSeqRecord.__init__ BioSQL.BioSeqDatabase.Adaptor.__init__ BioSQL.BioSeqDatabase.BioSeqDatabase.__init__ BioSQL.BioSeqDatabase.DBServer.__init__ BioSQL.DBUtils.Generic_dbutils.__init__ BioSQL.Loader.DatabaseLoader.__init__ BioSQL.Loader.DatabaseRemover.__init__ Martel.Dispatch.Callback.__init__ Martel.Dispatch.DispatchHandler.__init__ Martel.Dispatch.Dispatcher.__init__ Martel.Dispatch.Multicall.__init__ Martel.Dispatch.RemapEnd.__init__ Martel.Dispatch.RemapStart.__init__ Martel.Expression.Alt.__init__ Martel.Expression.Any.__init__ Martel.Expression.Assert.__init__ Martel.Expression.Debug.__init__ Martel.Expression.FastFeature.__init__ Martel.Expression.Group.__init__ Martel.Expression.GroupRef.__init__ Martel.Expression.HeaderFooter.__init__ Martel.Expression.Literal.__init__ Martel.Expression.MaxRepeat.__init__ Martel.Expression.NullOp.__init__ Martel.Expression.ParseRecords.__init__ Martel.Expression.PassThrough.__init__ Martel.Expression.Seq.__init__ Martel.Expression.Str.__init__ Martel.Generate.CheckAssert.__init__ Martel.Generate.CheckAssertNot.__init__ Martel.Generate.CheckGroupRef.__init__ Martel.Generate.GeneratorState.__init__ Martel.Generate.HandleRepeatCount.__init__ Martel.Generate.SetGroupValue.__init__ Martel.Generate._call_call.__init__ Martel.Generate._call_calltag.__init__ Martel.Generate.print_debug.__init__ Martel.Generate.print_info.__init__ Martel.IterParser.IterHeaderFooter.__init__ Martel.IterParser.IterRecords.__init__ Martel.Iterator.EventStream.__init__ Martel.Iterator.HeaderFooterEventStream.__init__ Martel.Iterator.Iterate.__init__ Martel.Iterator.Iterator.__init__ Martel.Iterator.IteratorHeaderFooter.__init__ Martel.Iterator.IteratorRecords.__init__ Martel.Iterator.RecordEventStream.__init__ Martel.Iterator.StoreEvents.__init__ Martel.LAX.ElementInfo.__init__ Martel.LAX.LAX.__init__ Martel.Parser.HeaderFooterParser.__init__ Martel.Parser.Parser.__init__ Martel.Parser.ParserIncompleteException.__init__ Martel.Parser.ParserPositionException.__init__ Martel.Parser.RecordParser.__init__ Martel.RecordReader.CountLines.__init__ Martel.RecordReader.EndsWith.__init__ Martel.RecordReader.Everything.__init__ Martel.RecordReader.Nothing.__init__ Martel.RecordReader.RecordReader.__init__ Martel.RecordReader.StartsWith.__init__ Martel.RecordReader.Until.__init__ Martel.convert_re.GroupNames.__init__ Martel.msre_parse.Pattern.__init__ Martel.msre_parse.SubPattern.__init__ Martel.msre_parse.Tokenizer.__init__ Martel.test.support.CheckGood.__init__ Martel.test.support.Dump.__init__ Martel.test.support.Storage.__init__ Martel.test.test_Parser.CountErrors.__init__ Martel.test.test_Parser.CountRecords.__init__ Martel.test.test_delimiter.CatchFields.__init__ Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-236', '__init__', 'link-236');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> </tt> <a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt class="py-name">ambiguous_nucleotide_alphabet</tt><tt class="py-op">,</tt> </tt> <a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-name">ambiguous_protein_alphabet</tt><tt class="py-op">,</tt> </tt> <a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> <tt id="link-237" class="py-name" targets="Class Bio.Data.CodonTable.AmbiguousForwardTable=Bio.Data.CodonTable.AmbiguousForwardTable-class.html"><a title="Bio.Data.CodonTable.AmbiguousForwardTable" class="py-name" href="#" onclick="return doclink('link-237', 'AmbiguousForwardTable', 'link-237');">AmbiguousForwardTable</a></tt><tt class="py-op">(</tt><tt class="py-name">codon_table</tt><tt class="py-op">.</tt><tt id="link-238" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-238', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">,</tt> </tt> <a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> <tt class="py-name">ambiguous_nucleotide_values</tt><tt class="py-op">,</tt> </tt> <a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"> <tt class="py-name">ambiguous_protein_values</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-name">codon_table</tt><tt class="py-op">.</tt><tt id="link-239" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.back_table" class="py-name" href="#" onclick="return doclink('link-239', 'back_table', 'link-25');">back_table</a></tt><tt class="py-op">,</tt> </tt> <a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"> </tt> <a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"> <tt class="py-comment"># These two are WRONG! I need to get the</tt> </tt> <a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"> <tt class="py-comment"># list of ambiguous codons which code for</tt> </tt> <a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"> <tt class="py-comment"># the stop codons XXX</tt> </tt> <a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt id="link-240" class="py-name" targets="Function Bio.Data.CodonTable.list_ambiguous_codons()=Bio.Data.CodonTable-module.html#list_ambiguous_codons"><a title="Bio.Data.CodonTable.list_ambiguous_codons" class="py-name" href="#" onclick="return doclink('link-240', 'list_ambiguous_codons', 'link-240');">list_ambiguous_codons</a></tt><tt class="py-op">(</tt><tt class="py-name">codon_table</tt><tt class="py-op">.</tt><tt id="link-241" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.start_codons" class="py-name" href="#" onclick="return doclink('link-241', 'start_codons', 'link-26');">start_codons</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt id="link-242" class="py-name"><a title="Bio.Data.CodonTable.list_ambiguous_codons" class="py-name" href="#" onclick="return doclink('link-242', 'list_ambiguous_codons', 'link-240');">list_ambiguous_codons</a></tt><tt class="py-op">(</tt><tt class="py-name">codon_table</tt><tt class="py-op">.</tt><tt id="link-243" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-243', 'stop_codons', 'link-27');">stop_codons</a></tt><tt class="py-op">)</tt> </tt> <a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt> <a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_codon_table</tt> <tt class="py-op">=</tt> <tt class="py-name">codon_table</tt> </tt> </div><a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> </tt> <a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-comment"># Be sneaky and forward attribute lookups to the original table.</tt> </tt> <a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># This lets us get the names, if the original table is an NCBI</tt> </tt> <a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># table.</tt> </tt> <a name="AmbiguousCodonTable.__getattr__"></a><div id="AmbiguousCodonTable.__getattr__-def"><a name="L538"></a><tt class="py-lineno">538</tt> <a class="py-toggle" href="#" id="AmbiguousCodonTable.__getattr__-toggle" onclick="return toggle('AmbiguousCodonTable.__getattr__');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousCodonTable-class.html#__getattr__">__getattr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AmbiguousCodonTable.__getattr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AmbiguousCodonTable.__getattr__-expanded"><a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_codon_table</tt><tt class="py-op">,</tt> <tt id="link-244" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-244', 'name', 'link-113');">name</a></tt><tt class="py-op">)</tt> </tt> </div></div><a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> </tt> <a name="list_possible_proteins"></a><div id="list_possible_proteins-def"><a name="L541"></a><tt class="py-lineno">541</tt> <a class="py-toggle" href="#" id="list_possible_proteins-toggle" onclick="return toggle('list_possible_proteins');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable-module.html#list_possible_proteins">list_possible_proteins</a><tt class="py-op">(</tt><tt class="py-param">codon</tt><tt class="py-op">,</tt> <tt class="py-param">forward_table</tt><tt class="py-op">,</tt> <tt class="py-param">ambiguous_nucleotide_values</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="list_possible_proteins-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="list_possible_proteins-expanded"><a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-name">c1</tt><tt class="py-op">,</tt> <tt class="py-name">c2</tt><tt class="py-op">,</tt> <tt class="py-name">c3</tt> <tt class="py-op">=</tt> <tt class="py-name">codon</tt> </tt> <a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-name">x1</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_nucleotide_values</tt><tt class="py-op">[</tt><tt class="py-name">c1</tt><tt class="py-op">]</tt> </tt> <a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-name">x2</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_nucleotide_values</tt><tt class="py-op">[</tt><tt class="py-name">c2</tt><tt class="py-op">]</tt> </tt> <a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-name">x3</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_nucleotide_values</tt><tt class="py-op">[</tt><tt class="py-name">c3</tt><tt class="py-op">]</tt> </tt> <a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-name">possible</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-name">stops</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y1</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x1</tt><tt class="py-op">:</tt> </tt> <a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x2</tt><tt class="py-op">:</tt> </tt> <a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">y3</tt> <tt class="py-keyword">in</tt> <tt class="py-name">x3</tt><tt class="py-op">:</tt> </tt> <a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-name">possible</tt><tt class="py-op">[</tt><tt id="link-245" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-245', 'forward_table', 'link-24');">forward_table</a></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">y3</tt><tt class="py-op">]</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-comment"># If tripping over a stop codon</tt> </tt> <a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">stops</tt><tt class="py-op">.</tt><tt id="link-246" 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-246', 'append', 'link-123');">append</a></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">y3</tt><tt class="py-op">)</tt> </tt> <a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stops</tt><tt class="py-op">:</tt> </tt> <a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">possible</tt><tt class="py-op">.</tt><tt id="link-247" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-247', 'keys', 'link-72');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-248" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-248', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"ambiguous codon codes for both proteins and stop codons"</tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-comment"># This is a true stop codon - tell the caller about it</tt> </tt> <a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> </tt> <a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">possible</tt><tt class="py-op">.</tt><tt id="link-249" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-249', 'keys', 'link-72');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> </div><a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> </tt> <a name="list_ambiguous_codons"></a><div id="list_ambiguous_codons-def"><a name="L563"></a><tt class="py-lineno">563</tt> <a class="py-toggle" href="#" id="list_ambiguous_codons-toggle" onclick="return toggle('list_ambiguous_codons');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable-module.html#list_ambiguous_codons">list_ambiguous_codons</a><tt class="py-op">(</tt><tt class="py-param">codons</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="list_ambiguous_codons-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="list_ambiguous_codons-expanded"><a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-comment"># XXX not implemented!</tt> </tt> <a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">codons</tt> </tt> </div><a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> </tt> <a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"><tt class="py-comment"># Forward translation is "onto", that is, any given codon always maps</tt> </tt> <a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># to the same protein, or it doesn't map at all. Thus, I can build</tt> </tt> <a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># off of an existing table to produce the ambiguous mappings.</tt> </tt> <a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt> <a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This handles the general case. Perhaps it's overkill?</tt> </tt> <a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> t = CodonTable.ambiguous_dna_by_id[1]</tt> </tt> <a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> t.forward_table["AAT"]</tt> </tt> <a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'N'</tt> </tt> <a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> t.forward_table["GAT"]</tt> </tt> <a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'D'</tt> </tt> <a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> t.forward_table["RAT"]</tt> </tt> <a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'B'</tt> </tt> <a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># >>> t.forward_table["YTA"]</tt> </tt> <a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># 'L'</tt> </tt> <a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt> <a name="AmbiguousForwardTable"></a><div id="AmbiguousForwardTable-def"><a name="L582"></a><tt class="py-lineno">582</tt> <a class="py-toggle" href="#" id="AmbiguousForwardTable-toggle" onclick="return toggle('AmbiguousForwardTable');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousForwardTable-class.html">AmbiguousForwardTable</a><tt class="py-op">:</tt> </tt> </div><div id="AmbiguousForwardTable-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AmbiguousForwardTable-expanded"><a name="AmbiguousForwardTable.__init__"></a><div id="AmbiguousForwardTable.__init__-def"><a name="L583"></a><tt class="py-lineno">583</tt> <a class="py-toggle" href="#" id="AmbiguousForwardTable.__init__-toggle" onclick="return toggle('AmbiguousForwardTable.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousForwardTable-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">forward_table</tt><tt class="py-op">,</tt> <tt class="py-param">ambiguous_nucleotide</tt><tt class="py-op">,</tt> <tt class="py-param">ambiguous_protein</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> </div><div id="AmbiguousForwardTable.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AmbiguousForwardTable.__init__-expanded"><a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-250', 'forward_table', 'link-24');">forward_table</a></tt> <tt class="py-op">=</tt> <tt id="link-251" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-251', 'forward_table', 'link-24');">forward_table</a></tt> </tt> <a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> </tt> <a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ambiguous_nucleotide</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_nucleotide</tt> </tt> <a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ambiguous_protein</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_protein</tt> </tt> <a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> </tt> <a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-name">inverted</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-252" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-252', 'name', 'link-113');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ambiguous_protein</tt><tt class="py-op">.</tt><tt id="link-253" 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-253', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">val</tt><tt class="py-op">:</tt> </tt> <a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt id="link-254" 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-254', 'x', 'link-254');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">inverted</tt><tt class="py-op">.</tt><tt id="link-255" 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-255', 'get', 'link-255');">get</a></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-op">}</tt><tt class="py-op">)</tt> </tt> <a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt id="link-256" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-256', 'x', 'link-254');">x</a></tt><tt class="py-op">[</tt><tt id="link-257" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-257', 'name', 'link-113');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt> <a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt class="py-name">inverted</tt><tt class="py-op">[</tt><tt class="py-name">c</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-258" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-258', 'x', 'link-254');">x</a></tt> </tt> <a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-259" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-259', 'name', 'link-113');">name</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">inverted</tt><tt class="py-op">.</tt><tt id="link-260" 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-260', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-name">inverted</tt><tt class="py-op">[</tt><tt id="link-261" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-261', 'name', 'link-113');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">val</tt><tt class="py-op">.</tt><tt id="link-262" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-262', 'keys', 'link-72');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt> <a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_inverted</tt> <tt class="py-op">=</tt> <tt class="py-name">inverted</tt> </tt> <a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> </tt> <a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> </div><a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> </tt> <a name="AmbiguousForwardTable.get"></a><div id="AmbiguousForwardTable.get-def"><a name="L601"></a><tt class="py-lineno">601</tt> <a class="py-toggle" href="#" id="AmbiguousForwardTable.get-toggle" onclick="return toggle('AmbiguousForwardTable.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousForwardTable-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">failobj</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="AmbiguousForwardTable.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AmbiguousForwardTable.get-expanded"><a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-263" class="py-name" targets="Method Bio.Align.AlignInfo.PSSM.__getitem__()=Bio.Align.AlignInfo.PSSM-class.html#__getitem__,Method Bio.Crystal.Chain.__getitem__()=Bio.Crystal.Chain-class.html#__getitem__,Method Bio.Crystal.Crystal.__getitem__()=Bio.Crystal.Crystal-class.html#__getitem__,Method Bio.DBXRef.BioformatDBName.__getitem__()=Bio.DBXRef.BioformatDBName-class.html#__getitem__,Method Bio.DBXRef.UnknownDBName.__getitem__()=Bio.DBXRef.UnknownDBName-class.html#__getitem__,Method Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__getitem__,Method Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__()=Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet-class.html#__getitem__,Method Bio.EUtils.Datatypes.DBIds.__getitem__()=Bio.EUtils.Datatypes.DBIds-class.html#__getitem__,Method Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__()=Bio.EUtils.HistoryClient.BaseHistoryRecordSet-class.html#__getitem__,Method Bio.EUtils.MultiDict._BaseMultiDict.__getitem__()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#__getitem__,Method Bio.EUtils.POM.ElementNode.__getitem__()=Bio.EUtils.POM.ElementNode-class.html#__getitem__,Method Bio.FSSP.fssp_rec.fff_rec.__getitem__()=Bio.FSSP.fssp_rec.fff_rec-class.html#__getitem__,Method Bio.GFF.GenericTools.ForgivingDictionary.__getitem__()=Bio.GFF.GenericTools.ForgivingDictionary-class.html#__getitem__,Method Bio.GFF.easy.FeatureDict.__getitem__()=Bio.GFF.easy.FeatureDict-class.html#__getitem__,Method Bio.GenBank.NCBIDictionary.__getitem__()=Bio.GenBank.NCBIDictionary-class.html#__getitem__,Method Bio.Gobase.Dictionary.__getitem__()=Bio.Gobase.Dictionary-class.html#__getitem__,Method Bio.Mindy.BaseDB.DictLookup.__getitem__()=Bio.Mindy.BaseDB.DictLookup-class.html#__getitem__,Method Bio.Mindy.BaseDB.OpenDB.__getitem__()=Bio.Mindy.BaseDB.OpenDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__()=Bio.Mindy.BerkeleyDB.BerkeleyDB-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.BisectFile.__getitem__()=Bio.Mindy.FlatDB.BisectFile-class.html#__getitem__,Method Bio.Mindy.FlatDB.DiskFlatDB.__getitem__()=Bio.Mindy.FlatDB.DiskFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__()=Bio.Mindy.FlatDB.MemoryFlatDB-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.PrimaryTable.__getitem__()=Bio.Mindy.FlatDB.PrimaryTable-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#__getitem__,Method Bio.Mindy.FlatDB.SecondaryTable.__getitem__()=Bio.Mindy.FlatDB.SecondaryTable-class.html#__getitem__,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#__getitem__,Method Bio.PDB.Chain.Chain.__getitem__()=Bio.PDB.Chain.Chain-class.html#__getitem__,Method Bio.PDB.Entity.Entity.__getitem__()=Bio.PDB.Entity.Entity-class.html#__getitem__,Method Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#__getitem__,Method Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__()=Bio.PDB.MMCIF2Dict.MMCIF2Dict-class.html#__getitem__,Method Bio.PDB.Vector'.Vector.__getitem__()=Bio.PDB.Vector%27.Vector-class.html#__getitem__,Method Bio.PropertyManager.CreateDict.__getitem__()=Bio.PropertyManager.CreateDict-class.html#__getitem__,Method Bio.Prosite.Dictionary.__getitem__()=Bio.Prosite.Dictionary-class.html#__getitem__,Method Bio.Prosite.ExPASyDictionary.__getitem__()=Bio.Prosite.ExPASyDictionary-class.html#__getitem__,Method Bio.Prosite.Pattern.Prosite.__getitem__()=Bio.Prosite.Pattern.Prosite-class.html#__getitem__,Method Bio.Prosite.Pattern.PrositeMatch.__getitem__()=Bio.Prosite.Pattern.PrositeMatch-class.html#__getitem__,Method Bio.Prosite.Prodoc.Dictionary.__getitem__()=Bio.Prosite.Prodoc.Dictionary-class.html#__getitem__,Method Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#__getitem__,Method Bio.PubMed.Dictionary.__getitem__()=Bio.PubMed.Dictionary-class.html#__getitem__,Method Bio.Rebase.Dictionary.__getitem__()=Bio.Rebase.Dictionary-class.html#__getitem__,Method Bio.Restriction.Restriction.FormattedSeq.__getitem__()=Bio.Restriction.Restriction.FormattedSeq-class.html#__getitem__,Method Bio.SCOP.Cla.Index.__getitem__()=Bio.SCOP.Cla.Index-class.html#__getitem__,Method Bio.SCOP.FileIndex.FileIndex.__getitem__()=Bio.SCOP.FileIndex.FileIndex-class.html#__getitem__,Method Bio.SCOP.FileIndex.defaultdict.__getitem__()=Bio.SCOP.FileIndex.defaultdict-class.html#__getitem__,Method Bio.SCOP.Raf.SeqMapIndex.__getitem__()=Bio.SCOP.Raf.SeqMapIndex-class.html#__getitem__,Method Bio.Seq.MutableSeq.__getitem__()=Bio.Seq.MutableSeq-class.html#__getitem__,Method Bio.Seq.Seq.__getitem__()=Bio.Seq.Seq-class.html#__getitem__,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#__getitem__,Method Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__()=Bio.SeqIO.StockholmIO.StockholmIterator-class.html#__getitem__,Method Bio.SwissProt.SProt.Dictionary.__getitem__()=Bio.SwissProt.SProt.Dictionary-class.html#__getitem__,Method Bio.SwissProt.SProt.ExPASyDictionary.__getitem__()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#__getitem__,Method Bio.config.DBRegistry.DBGroup.__getitem__()=Bio.config.DBRegistry.DBGroup-class.html#__getitem__,Method Bio.config.DBRegistry.DBObject.__getitem__()=Bio.config.DBRegistry.DBObject-class.html#__getitem__,Method Bio.config.Registry.Registry.__getitem__()=Bio.config.Registry.Registry-class.html#__getitem__,Method Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__()=Bio.config.SeqDBRegistry.SeqDBRegistry-class.html#__getitem__,Method BioSQL.BioSeq.DBSeq.__getitem__()=BioSQL.BioSeq.DBSeq-class.html#__getitem__,Method BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#__getitem__,Method BioSQL.BioSeqDatabase.DBServer.__getitem__()=BioSQL.BioSeqDatabase.DBServer-class.html#__getitem__,Method Martel.Iterator.Iterate.__getitem__()=Martel.Iterator.Iterate-class.html#__getitem__,Method Martel.Parser.MartelAttributeList.__getitem__()=Martel.Parser.MartelAttributeList-class.html#__getitem__,Method Martel.msre_parse.SubPattern.__getitem__()=Martel.msre_parse.SubPattern-class.html#__getitem__,Method Martel.test.support.Storage.__getitem__()=Martel.test.support.Storage-class.html#__getitem__"><a title="Bio.Align.AlignInfo.PSSM.__getitem__ Bio.Crystal.Chain.__getitem__ Bio.Crystal.Crystal.__getitem__ Bio.DBXRef.BioformatDBName.__getitem__ Bio.DBXRef.UnknownDBName.__getitem__ Bio.Data.CodonTable.AmbiguousForwardTable.__getitem__ Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__getitem__ Bio.EUtils.Datatypes.DBIds.__getitem__ Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__getitem__ Bio.EUtils.MultiDict._BaseMultiDict.__getitem__ Bio.EUtils.POM.ElementNode.__getitem__ Bio.FSSP.fssp_rec.fff_rec.__getitem__ Bio.GFF.GenericTools.ForgivingDictionary.__getitem__ Bio.GFF.easy.FeatureDict.__getitem__ Bio.GenBank.NCBIDictionary.__getitem__ Bio.Gobase.Dictionary.__getitem__ Bio.Mindy.BaseDB.DictLookup.__getitem__ Bio.Mindy.BaseDB.OpenDB.__getitem__ Bio.Mindy.BerkeleyDB.BerkeleyDB.__getitem__ Bio.Mindy.BerkeleyDB.PrimaryNamespace.__getitem__ Bio.Mindy.BerkeleyDB.SecondaryNamespace.__getitem__ Bio.Mindy.FlatDB.BisectFile.__getitem__ Bio.Mindy.FlatDB.DiskFlatDB.__getitem__ Bio.Mindy.FlatDB.MemoryFlatDB.__getitem__ Bio.Mindy.FlatDB.PrimaryNamespace.__getitem__ Bio.Mindy.FlatDB.PrimaryTable.__getitem__ Bio.Mindy.FlatDB.SecondaryNamespace.__getitem__ Bio.Mindy.FlatDB.SecondaryTable.__getitem__ Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__getitem__ Bio.PDB.Chain.Chain.__getitem__ Bio.PDB.Entity.Entity.__getitem__ Bio.PDB.FragmentMapper'.FragmentMapper.__getitem__ Bio.PDB.MMCIF2Dict.MMCIF2Dict.__getitem__ Bio.PDB.Vector'.Vector.__getitem__ Bio.PropertyManager.CreateDict.__getitem__ Bio.Prosite.Dictionary.__getitem__ Bio.Prosite.ExPASyDictionary.__getitem__ Bio.Prosite.Pattern.Prosite.__getitem__ Bio.Prosite.Pattern.PrositeMatch.__getitem__ Bio.Prosite.Prodoc.Dictionary.__getitem__ Bio.Prosite.Prodoc.ExPASyDictionary.__getitem__ Bio.PubMed.Dictionary.__getitem__ Bio.Rebase.Dictionary.__getitem__ Bio.Restriction.Restriction.FormattedSeq.__getitem__ Bio.SCOP.Cla.Index.__getitem__ Bio.SCOP.FileIndex.FileIndex.__getitem__ Bio.SCOP.FileIndex.defaultdict.__getitem__ Bio.SCOP.Raf.SeqMapIndex.__getitem__ Bio.Seq.MutableSeq.__getitem__ Bio.Seq.Seq.__getitem__ Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__getitem__ Bio.SeqIO.StockholmIO.StockholmIterator.__getitem__ Bio.SwissProt.SProt.Dictionary.__getitem__ Bio.SwissProt.SProt.ExPASyDictionary.__getitem__ Bio.config.DBRegistry.DBGroup.__getitem__ Bio.config.DBRegistry.DBObject.__getitem__ Bio.config.Registry.Registry.__getitem__ Bio.config.SeqDBRegistry.SeqDBRegistry.__getitem__ BioSQL.BioSeq.DBSeq.__getitem__ BioSQL.BioSeqDatabase.BioSeqDatabase.__getitem__ BioSQL.BioSeqDatabase.DBServer.__getitem__ Martel.Iterator.Iterate.__getitem__ Martel.Parser.MartelAttributeList.__getitem__ Martel.msre_parse.SubPattern.__getitem__ Martel.test.support.Storage.__getitem__" class="py-name" href="#" onclick="return doclink('link-263', '__getitem__', 'link-263');">__getitem__</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">)</tt> </tt> <a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">failobj</tt> </tt> </div><a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> </tt> <a name="AmbiguousForwardTable.__getitem__"></a><div id="AmbiguousForwardTable.__getitem__-def"><a name="L607"></a><tt class="py-lineno">607</tt> <a class="py-toggle" href="#" id="AmbiguousForwardTable.__getitem__-toggle" onclick="return toggle('AmbiguousForwardTable.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Data.CodonTable.AmbiguousForwardTable-class.html#__getitem__">__getitem__</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-op">:</tt> </tt> </div><div id="AmbiguousForwardTable.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AmbiguousForwardTable.__getitem__-expanded"><a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt id="link-264" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-264', 'x', 'link-254');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> </tt> <a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt> <a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-265" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-265', 'x', 'link-254');">x</a></tt> <tt class="py-keyword">is</tt> <tt id="link-266" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-266', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">:</tt> </tt> <a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-267" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-267', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> <tt class="py-comment"># no unique translation</tt> </tt> <a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-268" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-268', 'x', 'link-254');">x</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> <tt class="py-comment"># it's a stop codon</tt> </tt> <a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-269" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-269', 'x', 'link-254');">x</a></tt> </tt> <a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt id="link-270" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-270', 'x', 'link-254');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-271', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> </tt> <a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-272" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-272', 'x', 'link-254');">x</a></tt> </tt> <a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-273" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-273', 'x', 'link-254');">x</a></tt> </tt> <a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt> <a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> </tt> <a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-comment"># XXX Need to make part of this into a method which returns</tt> </tt> <a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># a list of all possible encodings for a codon!</tt> </tt> <a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt> <a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt class="py-name">possible</tt> <tt class="py-op">=</tt> <tt id="link-274" class="py-name" targets="Function Bio.Data.CodonTable.list_possible_proteins()=Bio.Data.CodonTable-module.html#list_possible_proteins"><a title="Bio.Data.CodonTable.list_possible_proteins" class="py-name" href="#" onclick="return doclink('link-274', 'list_possible_proteins', 'link-274');">list_possible_proteins</a></tt><tt class="py-op">(</tt><tt class="py-name">codon</tt><tt class="py-op">,</tt> </tt> <a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-275', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">,</tt> </tt> <a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ambiguous_nucleotide</tt><tt class="py-op">)</tt> </tt> <a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt> <a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">KeyError</tt> </tt> <a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> <tt class="py-comment"># stop codon</tt> </tt> <a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-276" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-276', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">:</tt> </tt> <a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-277" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-277', 'TranslationError', 'link-68');">TranslationError</a></tt> </tt> <a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-278" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-278', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> <tt class="py-comment"># does not code</tt> </tt> <a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">possible</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-string">"unambiguous codons must code"</tt> </tt> <a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> </tt> <a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-comment"># Hah! Only one possible protein, so use it</tt> </tt> <a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">possible</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="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">possible</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">possible</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> </tt> <a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-comment"># See if there's an ambiguous protein encoding for the multiples.</tt> </tt> <a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Find residues which exist in every coding set.</tt> </tt> <a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">ambiguous_possible</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">amino</tt> <tt class="py-keyword">in</tt> <tt class="py-name">possible</tt><tt class="py-op">:</tt> </tt> <a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">term</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_inverted</tt><tt class="py-op">[</tt><tt class="py-name">amino</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt> <a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-name">ambiguous_possible</tt><tt class="py-op">[</tt><tt class="py-name">term</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">ambiguous_possible</tt><tt class="py-op">.</tt><tt id="link-279" 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-279', 'get', 'link-255');">get</a></tt><tt class="py-op">(</tt><tt class="py-name">term</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-number">1</tt> </tt> <a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> </tt> <a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"> <tt class="py-name">n</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">possible</tt><tt class="py-op">)</tt> </tt> <a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-name">possible</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt> <a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">amino</tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ambiguous_possible</tt><tt class="py-op">.</tt><tt id="link-280" 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-280', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">val</tt> <tt class="py-op">==</tt> <tt class="py-name">n</tt><tt class="py-op">:</tt> </tt> <a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-name">possible</tt><tt class="py-op">.</tt><tt id="link-281" 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-281', 'append', 'link-123');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">amino</tt><tt class="py-op">)</tt> </tt> <a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> </tt> <a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"> <tt class="py-comment"># No amino acid encoding for the results</tt> </tt> <a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">possible</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="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-282" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-282', 'TranslationError', 'link-68');">TranslationError</a></tt> </tt> <a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-283" class="py-name"><a title="Bio.Data.CodonTable.TranslationError" class="py-name" href="#" onclick="return doclink('link-283', 'TranslationError', 'link-68');">TranslationError</a></tt><tt class="py-op">,</tt> <tt class="py-name">codon</tt> <tt class="py-comment"># no valid translation</tt> </tt> <a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> </tt> <a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-comment"># All of these are valid, so choose one</tt> </tt> <a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># To be unique, sort by smallet ambiguity then alphabetically</tt> </tt> <a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Can get this if "X" encodes for everything.</tt> </tt> <a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <tt class="py-def-name">_sort</tt><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ambiguous_protein</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-284" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-284', 'table', 'link-73');">table</a></tt><tt class="py-op">[</tt><tt id="link-285" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-285', 'x', 'link-254');">x</a></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-286" class="py-name"><a title="Bio.CDD.cdd_format.table Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-286', 'table', 'link-73');">table</a></tt><tt class="py-op">[</tt><tt class="py-name">y</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">a</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt> <a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt id="link-287" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-287', 'x', 'link-254');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">)</tt> </tt> <a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">a</tt> </tt> </div><a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-name">possible</tt><tt class="py-op">.</tt><tt id="link-288" class="py-name"><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-288', 'sort', 'link-76');">sort</a></tt><tt class="py-op">(</tt><tt id="link-289" class="py-name" targets="Method Bio.PDB.Chain.Chain._sort()=Bio.PDB.Chain.Chain-class.html#_sort,Method Bio.PDB.Model.Model._sort()=Bio.PDB.Model.Model-class.html#_sort,Method Bio.PDB.Residue.Residue._sort()=Bio.PDB.Residue.Residue-class.html#_sort,Method Bio.PDB.Structure.Structure._sort()=Bio.PDB.Structure.Structure-class.html#_sort"><a title="Bio.PDB.Chain.Chain._sort Bio.PDB.Model.Model._sort Bio.PDB.Residue.Residue._sort Bio.PDB.Structure.Structure._sort" class="py-name" href="#" onclick="return doclink('link-289', '_sort', 'link-289');">_sort</a></tt><tt class="py-op">)</tt> </tt> <a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> </tt> <a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt id="link-290" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-290', 'x', 'link-254');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">possible</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt> <a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_cache</tt><tt class="py-op">[</tt><tt class="py-name">codon</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-291" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-291', 'x', 'link-254');">x</a></tt> </tt> <a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-292" class="py-name"><a title="Bio.MarkovModel.x Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-292', 'x', 'link-254');">x</a></tt> </tt> </div></div><a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> </tt> <a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"><tt class="py-comment">#Prepare the ambiguous tables for DNA, RNA and Generic (DNA or RNA)</tt> </tt> <a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-293" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_dna_by_name=Bio.Data.CodonTable-module.html#ambiguous_dna_by_name,Variable Bio.Translate.ambiguous_dna_by_name=Bio.Translate-module.html#ambiguous_dna_by_name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_name Bio.Translate.ambiguous_dna_by_name" class="py-name" href="#" onclick="return doclink('link-293', 'ambiguous_dna_by_name', 'link-293');">ambiguous_dna_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-294" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-294', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-295" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_dna_by_name Bio.Translate.unambiguous_dna_by_name" class="py-name" href="#" onclick="return doclink('link-295', 'unambiguous_dna_by_name', 'link-8');">unambiguous_dna_by_name</a></tt><tt class="py-op">.</tt><tt id="link-296" 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-296', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> <tt id="link-297" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_name Bio.Translate.ambiguous_dna_by_name" class="py-name" href="#" onclick="return doclink('link-297', 'ambiguous_dna_by_name', 'link-293');">ambiguous_dna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-298" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-298', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-299" class="py-name" targets="Class Bio.Data.CodonTable.AmbiguousCodonTable=Bio.Data.CodonTable.AmbiguousCodonTable-class.html"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-299', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt id="link-300" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-300', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-301" 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-301', 'ambiguous_dna', 'link-301');">ambiguous_dna</a></tt><tt class="py-op">,</tt> </tt> <a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt id="link-302" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-302', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-303" 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-303', 'ambiguous_dna_values', 'link-303');">ambiguous_dna_values</a></tt><tt class="py-op">,</tt> </tt> <a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> <tt id="link-304" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-304', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-305" 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-305', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt id="link-306" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-306', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-307" class="py-name" targets="Variable Bio.Data.IUPACData.extended_protein_values=Bio.Data.IUPACData-module.html#extended_protein_values"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-307', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"><tt id="link-308" 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-308', 'ambiguous_dna_by_id', 'link-308');">ambiguous_dna_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-309" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-309', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-310" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_dna_by_id Bio.Translate.unambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-310', 'unambiguous_dna_by_id', 'link-9');">unambiguous_dna_by_id</a></tt><tt class="py-op">.</tt><tt id="link-311" 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-311', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> <tt id="link-312" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_id Bio.Translate.ambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-312', 'ambiguous_dna_by_id', 'link-308');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-313" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-313', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-314" class="py-name"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-314', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt id="link-315" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-315', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-316" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-316', 'ambiguous_dna', 'link-301');">ambiguous_dna</a></tt><tt class="py-op">,</tt> </tt> <a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> <tt id="link-317" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-317', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-318" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-318', 'ambiguous_dna_values', 'link-303');">ambiguous_dna_values</a></tt><tt class="py-op">,</tt> </tt> <a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> <tt id="link-319" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-319', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-320" class="py-name"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-320', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"> <tt id="link-321" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-321', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-322" class="py-name"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-322', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> </tt> <a name="L692"></a><tt class="py-lineno">692</tt> <tt class="py-line"><tt id="link-323" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_rna_by_name=Bio.Data.CodonTable-module.html#ambiguous_rna_by_name,Variable Bio.Translate.ambiguous_rna_by_name=Bio.Translate-module.html#ambiguous_rna_by_name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_name Bio.Translate.ambiguous_rna_by_name" class="py-name" href="#" onclick="return doclink('link-323', 'ambiguous_rna_by_name', 'link-323');">ambiguous_rna_by_name</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-324" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-324', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-325" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_rna_by_name Bio.Translate.unambiguous_rna_by_name" class="py-name" href="#" onclick="return doclink('link-325', 'unambiguous_rna_by_name', 'link-10');">unambiguous_rna_by_name</a></tt><tt class="py-op">.</tt><tt id="link-326" 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-326', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"> <tt id="link-327" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_name Bio.Translate.ambiguous_rna_by_name" class="py-name" href="#" onclick="return doclink('link-327', 'ambiguous_rna_by_name', 'link-323');">ambiguous_rna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-328" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-328', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-329" class="py-name"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-329', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"> <tt id="link-330" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-330', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-331" class="py-name" targets="Variable Bio.Alphabet.IUPAC.ambiguous_rna=Bio.Alphabet.IUPAC-module.html#ambiguous_rna"><a title="Bio.Alphabet.IUPAC.ambiguous_rna" class="py-name" href="#" onclick="return doclink('link-331', 'ambiguous_rna', 'link-331');">ambiguous_rna</a></tt><tt class="py-op">,</tt> </tt> <a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> <tt id="link-332" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-332', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_rna_values=Bio.Data.IUPACData-module.html#ambiguous_rna_values"><a title="Bio.Data.IUPACData.ambiguous_rna_values" class="py-name" href="#" onclick="return doclink('link-333', 'ambiguous_rna_values', 'link-333');">ambiguous_rna_values</a></tt><tt class="py-op">,</tt> </tt> <a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"> <tt id="link-334" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-334', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-335" class="py-name"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-335', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"> <tt id="link-336" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-336', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-337" class="py-name"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-337', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"><tt id="link-338" class="py-name" targets="Variable Bio.Data.CodonTable.ambiguous_rna_by_id=Bio.Data.CodonTable-module.html#ambiguous_rna_by_id,Variable Bio.Translate.ambiguous_rna_by_id=Bio.Translate-module.html#ambiguous_rna_by_id"><a title="Bio.Data.CodonTable.ambiguous_rna_by_id Bio.Translate.ambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-338', 'ambiguous_rna_by_id', 'link-338');">ambiguous_rna_by_id</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt> <a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-339" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-339', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-340" class="py-name"><a title="Bio.Data.CodonTable.unambiguous_rna_by_id Bio.Translate.unambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-340', 'unambiguous_rna_by_id', 'link-11');">unambiguous_rna_by_id</a></tt><tt class="py-op">.</tt><tt id="link-341" 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-341', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"> <tt id="link-342" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_id Bio.Translate.ambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-342', 'ambiguous_rna_by_id', 'link-338');">ambiguous_rna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-343" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-343', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-344" class="py-name"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-344', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"> <tt id="link-345" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-345', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-346" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_rna" class="py-name" href="#" onclick="return doclink('link-346', 'ambiguous_rna', 'link-331');">ambiguous_rna</a></tt><tt class="py-op">,</tt> </tt> <a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> <tt id="link-347" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-347', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-348" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_values" class="py-name" href="#" onclick="return doclink('link-348', 'ambiguous_rna_values', 'link-333');">ambiguous_rna_values</a></tt><tt class="py-op">,</tt> </tt> <a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt id="link-349" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-349', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-350" class="py-name"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-350', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt id="link-351" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-351', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-352" class="py-name"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-352', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> </tt> <a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"><tt class="py-comment">#The following isn't very elegant, but seems to work nicely.</tt> </tt> <a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-name">_merged_values</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt id="link-353" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-353', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-354" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_values" class="py-name" href="#" onclick="return doclink('link-354', 'ambiguous_rna_values', 'link-333');">ambiguous_rna_values</a></tt><tt class="py-op">.</tt><tt class="py-name">iteritems</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt> <a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"><tt class="py-name">_merged_values</tt><tt class="py-op">[</tt><tt class="py-string">"T"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-string">"U"</tt> </tt> <a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> </tt> <a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-355" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-355', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-356" class="py-name"><a title="Bio.Data.CodonTable.generic_by_name" class="py-name" href="#" onclick="return doclink('link-356', 'generic_by_name', 'link-12');">generic_by_name</a></tt><tt class="py-op">.</tt><tt id="link-357" 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-357', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> <tt id="link-358" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-358', 'ambiguous_generic_by_name', 'link-14');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt id="link-359" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-359', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-360" class="py-name"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-360', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"> <tt id="link-361" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-361', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-362" class="py-name" targets="Class Bio.Alphabet.NucleotideAlphabet=Bio.Alphabet.NucleotideAlphabet-class.html"><a title="Bio.Alphabet.NucleotideAlphabet" class="py-name" href="#" onclick="return doclink('link-362', 'NucleotideAlphabet', 'link-362');">NucleotideAlphabet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-name">_merged_values</tt><tt class="py-op">,</tt> </tt> <a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"> <tt id="link-363" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-363', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-364" class="py-name"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-364', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"> <tt id="link-365" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-365', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-366" class="py-name"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-366', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> </tt> <a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"><tt class="py-keyword">for</tt> <tt id="link-367" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-367', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt id="link-368" class="py-name"><a title="Bio.Data.CodonTable.generic_by_id" class="py-name" href="#" onclick="return doclink('link-368', 'generic_by_id', 'link-13');">generic_by_id</a></tt><tt class="py-op">.</tt><tt id="link-369" 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-369', 'items', 'link-121');">items</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt> <a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> <tt id="link-370" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-370', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-371" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-371', 'key', 'link-77');">key</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-372" class="py-name"><a title="Bio.Data.CodonTable.AmbiguousCodonTable" class="py-name" href="#" onclick="return doclink('link-372', 'AmbiguousCodonTable', 'link-299');">AmbiguousCodonTable</a></tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">,</tt> </tt> <a name="L720"></a><tt class="py-lineno">720</tt> <tt class="py-line"> <tt id="link-373" class="py-name"><a title="Bio.Alphabet Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-373', 'Alphabet', 'link-1');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-374" class="py-name"><a title="Bio.Alphabet.NucleotideAlphabet" class="py-name" href="#" onclick="return doclink('link-374', 'NucleotideAlphabet', 'link-362');">NucleotideAlphabet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt> <a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-name">_merged_values</tt><tt class="py-op">,</tt> </tt> <a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"> <tt id="link-375" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-375', 'IUPAC', 'link-4');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-376" class="py-name"><a title="Bio.Alphabet.IUPAC.extended_protein" class="py-name" href="#" onclick="return doclink('link-376', 'extended_protein', 'link-305');">extended_protein</a></tt><tt class="py-op">,</tt> </tt> <a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"> <tt id="link-377" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-377', 'IUPACData', 'link-7');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-378" class="py-name"><a title="Bio.Data.IUPACData.extended_protein_values" class="py-name" href="#" onclick="return doclink('link-378', 'extended_protein_values', 'link-307');">extended_protein_values</a></tt><tt class="py-op">)</tt> </tt> <a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> </tt> <a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"><tt class="py-comment">#Basic sanity test,</tt> </tt> <a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">for</tt> <tt id="link-379" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-379', 'id', 'link-46');">id</a></tt> <tt class="py-keyword">in</tt> <tt id="link-380" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-380', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">.</tt><tt id="link-381" class="py-name"><a title="Bio.Crystal.Crystal.keys Bio.EUtils.MultiDict._BaseMultiDict.keys Bio.GenBank.NCBIDictionary.keys Bio.Mindy.BaseDB.DictLookup.keys Bio.Mindy.BaseDB.OpenDB.keys Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.PrimaryNamespace.keys Bio.Mindy.FlatDB.PrimaryTable.keys Bio.Mindy.FlatDB.SecondaryNamespace.keys Bio.Mindy.FlatDB.SecondaryTable.keys Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys Bio.Prosite.ExPASyDictionary.keys Bio.Prosite.Prodoc.ExPASyDictionary.keys Bio.PubMed.Dictionary.keys Bio.SwissProt.SProt.Dictionary.keys Bio.SwissProt.SProt.ExPASyDictionary.keys Bio.config.Registry.Registry.keys BioSQL.BioSeqDatabase.BioSeqDatabase.keys BioSQL.BioSeqDatabase.DBServer.keys Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-381', 'keys', 'link-72');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt> <a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-382" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_id Bio.Translate.ambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-382', 'ambiguous_rna_by_id', 'link-338');">ambiguous_rna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-383" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-383', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-384" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-384', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GUU"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-385" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_id Bio.Translate.ambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-385', 'ambiguous_rna_by_id', 'link-338');">ambiguous_rna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-386" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-386', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-387" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-387', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GUN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-388" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_rna_by_id Bio.Translate.ambiguous_rna_by_id" class="py-name" href="#" onclick="return doclink('link-388', 'ambiguous_rna_by_id', 'link-338');">ambiguous_rna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-389" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-389', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-390" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-390', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"UUN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> <tt class="py-comment">#F or L</tt> </tt> <a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> </tt> <a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-391" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_id Bio.Translate.ambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-391', 'ambiguous_dna_by_id', 'link-308');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-392" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-392', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-393" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-393', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GTT"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-394" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_id Bio.Translate.ambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-394', 'ambiguous_dna_by_id', 'link-308');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-395" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-395', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-396" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-396', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"TTN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> <tt class="py-comment">#F or L</tt> </tt> <a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-397" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_dna_by_id Bio.Translate.ambiguous_dna_by_id" class="py-name" href="#" onclick="return doclink('link-397', 'ambiguous_dna_by_id', 'link-308');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-398" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-398', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-399" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-399', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GTN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> </tt> <a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-400" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-400', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-401" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-401', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-402" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-402', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">.</tt><tt id="link-403" 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-403', 'get', 'link-255');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"TTN"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> </tt> <a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-404" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-404', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-405" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-405', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-406" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-406', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"ACN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"T"</tt> </tt> <a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-407" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-407', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-408" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-408', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-409" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-409', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GUU"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-410" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-410', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-411" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-411', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-412" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-412', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GUN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-413" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-413', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-414" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-414', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-415" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-415', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"UUN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> <tt class="py-comment">#F or L</tt> </tt> <a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-416" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-416', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-417" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-417', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-418" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-418', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GTT"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-419" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-419', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-420" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-420', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-421" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-421', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"TTN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> <tt class="py-comment">#F or L</tt> </tt> <a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-422" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-422', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-423" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-423', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-424" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-424', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"GTN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"V"</tt> </tt> <a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"> <tt class="py-comment">#And finally something evil, an RNA-DNA mixture:</tt> </tt> <a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt id="link-425" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-425', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-426" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-426', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-427" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-427', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"UTN"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"X"</tt> <tt class="py-comment">#F or L</tt> </tt> <a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-428" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-428', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-429" class="py-name"><a title="Bio.Data.CodonTable.id Bio.Encodings.IUPACEncoding.id Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-429', 'id', 'link-46');">id</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-430" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-430', 'forward_table', 'link-24');">forward_table</a></tt><tt class="py-op">[</tt><tt class="py-string">"UTU"</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"F"</tt> </tt> <a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"> </tt> <a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"><tt class="py-keyword">assert</tt> <tt id="link-431" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-431', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</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-432" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-432', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">==</tt> <tt id="link-433" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-433', 'ambiguous_generic_by_name', 'link-14');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt class="py-string">"Standard"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-434" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-434', 'stop_codons', 'link-27');">stop_codons</a></tt> </tt> <a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"><tt class="py-keyword">assert</tt> <tt id="link-435" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-435', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-436" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-436', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">==</tt> <tt id="link-437" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-437', 'ambiguous_generic_by_name', 'link-14');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt class="py-string">"SGC3"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-438" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-438', 'stop_codons', 'link-27');">stop_codons</a></tt> </tt> <a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"><tt class="py-keyword">assert</tt> <tt id="link-439" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-439', 'ambiguous_generic_by_id', 'link-15');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt class="py-number">15</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-440" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-440', 'stop_codons', 'link-27');">stop_codons</a></tt> <tt class="py-op">==</tt> <tt id="link-441" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-441', 'ambiguous_generic_by_name', 'link-14');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt class="py-string">'Blepharisma Macronuclear'</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-442" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.stop_codons" class="py-name" href="#" onclick="return doclink('link-442', 'stop_codons', 'link-27');">stop_codons</a></tt> </tt> <a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"><tt class="py-keyword">del</tt> <tt class="py-name">_merged_values</tt> </tt> <a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"><tt class="py-keyword">del</tt> <tt id="link-443" class="py-name"><a title="Bio.Translate.key" class="py-name" href="#" onclick="return doclink('link-443', 'key', 'link-77');">key</a></tt><tt class="py-op">,</tt> <tt class="py-name">val</tt> </tt> <a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> </tt><script type="text/javascript"> <!-- expandto(location.href); // --> </script> </pre> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 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