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        <a href="Bio-module.html">Package&nbsp;Bio</a> ::
        <a href="Bio.Alphabet-module.html">Package&nbsp;Alphabet</a> ::
        Module&nbsp;IUPAC
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<h1 class="epydoc">Source Code for <a href="Bio.Alphabet.IUPAC-module.html">Module Bio.Alphabet.IUPAC</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Define the IUPAC Alphabets you know and love</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></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-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="L4"></a><tt class="py-lineno">  4</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" targets="Package Bio.Data=Bio.Data-module.html"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-3', 'Data', 'link-3');">Data</a></tt> <tt class="py-keyword">import</tt> <tt id="link-4" 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-4', 'IUPACData', 'link-4');">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 class="py-comment">##################### Protein</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"># From the IUPAC definition at:</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html#AA21</tt> </tt>
<a name="IUPACProtein"></a><div id="IUPACProtein-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="IUPACProtein-toggle" onclick="return toggle('IUPACProtein');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.IUPACProtein-class.html">IUPACProtein</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IUPACProtein-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IUPACProtein-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line">    <tt id="link-5" 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-5', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-6', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Variable Bio.Data.IUPACData.protein_letters=Bio.Data.IUPACData-module.html#protein_letters"><a title="Bio.Data.IUPACData.protein_letters" class="py-name" href="#" onclick="return doclink('link-7', 'protein_letters', 'link-7');">protein_letters</a></tt> </tt>
</div><a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt id="link-8" 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-8', 'protein', 'link-8');">protein</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name" targets="Class Bio.Alphabet.IUPAC.IUPACProtein=Bio.Alphabet.IUPAC.IUPACProtein-class.html"><a title="Bio.Alphabet.IUPAC.IUPACProtein" class="py-name" href="#" onclick="return doclink('link-9', 'IUPACProtein', 'link-9');">IUPACProtein</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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"># This could be considered the base class for the standard IUPAC</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># protein, except that some encodings will use "X" to mean "unknown</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># character", which causes a collision.  If you use X for</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># selenocysteines, then you'll need a new alphabet.</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="ExtendedIUPACProtein"></a><div id="ExtendedIUPACProtein-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="ExtendedIUPACProtein-toggle" onclick="return toggle('ExtendedIUPACProtein');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html">ExtendedIUPACProtein</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">ProteinAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExtendedIUPACProtein-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExtendedIUPACProtein-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">    <tt id="link-10" 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-10', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-11', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Variable Bio.Data.IUPACData.extended_protein_letters=Bio.Data.IUPACData-module.html#extended_protein_letters"><a title="Bio.Data.IUPACData.extended_protein_letters" class="py-name" href="#" onclick="return doclink('link-12', 'extended_protein_letters', 'link-12');">extended_protein_letters</a></tt> </tt>
</div><a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">    <tt class="py-comment"># B = "Asx";  aspartic acid or asparagine</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># X = "Sec";  selenocysteine  Note: IUPAC is moving to use 'U' for this</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment"># Z = "Glx";  glutamic acid or glutamine (or substances such as</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#         4-carboxyglutamic acid and 5-oxoproline that yield glutamic</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#         acid on acid hydrolysis of peptides)</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line"><tt id="link-13" 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-13', 'extended_protein', 'link-13');">extended_protein</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Class Bio.Alphabet.IUPAC.ExtendedIUPACProtein=Bio.Alphabet.IUPAC.ExtendedIUPACProtein-class.html"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACProtein" class="py-name" href="#" onclick="return doclink('link-14', 'ExtendedIUPACProtein', 'link-14');">ExtendedIUPACProtein</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line"><tt class="py-comment">##################### DNA</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"><tt class="py-comment"># The next two are the IUPAC definitions, from:</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#   http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html</tt> </tt>
<a name="IUPACAmbiguousDNA"></a><div id="IUPACAmbiguousDNA-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="IUPACAmbiguousDNA-toggle" onclick="return toggle('IUPACAmbiguousDNA');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html">IUPACAmbiguousDNA</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">DNAAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IUPACAmbiguousDNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IUPACAmbiguousDNA-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt id="link-15" 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-15', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-16', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_dna_letters=Bio.Data.IUPACData-module.html#ambiguous_dna_letters"><a title="Bio.Data.IUPACData.ambiguous_dna_letters" class="py-name" href="#" onclick="return doclink('link-17', 'ambiguous_dna_letters', 'link-17');">ambiguous_dna_letters</a></tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"><tt id="link-18" 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-18', 'ambiguous_dna', 'link-18');">ambiguous_dna</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Class Bio.Alphabet.IUPAC.IUPACAmbiguousDNA=Bio.Alphabet.IUPAC.IUPACAmbiguousDNA-class.html"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousDNA" class="py-name" href="#" onclick="return doclink('link-19', 'IUPACAmbiguousDNA', 'link-19');">IUPACAmbiguousDNA</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line"> </tt>
<a name="IUPACUnambiguousDNA"></a><div id="IUPACUnambiguousDNA-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="IUPACUnambiguousDNA-toggle" onclick="return toggle('IUPACUnambiguousDNA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html">IUPACUnambiguousDNA</a><tt class="py-op">(</tt><tt class="py-base-class">IUPACAmbiguousDNA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IUPACUnambiguousDNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IUPACUnambiguousDNA-expanded"><a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt id="link-20" 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-20', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-21', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Variable Bio.Data.IUPACData.unambiguous_dna_letters=Bio.Data.IUPACData-module.html#unambiguous_dna_letters"><a title="Bio.Data.IUPACData.unambiguous_dna_letters" class="py-name" href="#" onclick="return doclink('link-22', 'unambiguous_dna_letters', 'link-22');">unambiguous_dna_letters</a></tt> </tt>
</div><a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt id="link-23" 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-23', 'unambiguous_dna', 'link-23');">unambiguous_dna</a></tt> <tt class="py-op">=</tt> <tt id="link-24" class="py-name" targets="Class Bio.Alphabet.IUPAC.IUPACUnambiguousDNA=Bio.Alphabet.IUPAC.IUPACUnambiguousDNA-class.html"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousDNA" class="py-name" href="#" onclick="return doclink('link-24', 'IUPACUnambiguousDNA', 'link-24');">IUPACUnambiguousDNA</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-comment"># Also from the URL, but not part of the standard</tt> </tt>
<a name="ExtendedIUPACDNA"></a><div id="ExtendedIUPACDNA-def"><a name="L46"></a><tt class="py-lineno"> 46</tt> <a class="py-toggle" href="#" id="ExtendedIUPACDNA-toggle" onclick="return toggle('ExtendedIUPACDNA');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html">ExtendedIUPACDNA</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">DNAAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ExtendedIUPACDNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ExtendedIUPACDNA-expanded"><a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">    <tt id="link-25" 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-25', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-26" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-26', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-27" class="py-name" targets="Variable Bio.Data.IUPACData.extended_dna_letters=Bio.Data.IUPACData-module.html#extended_dna_letters"><a title="Bio.Data.IUPACData.extended_dna_letters" class="py-name" href="#" onclick="return doclink('link-27', 'extended_dna_letters', 'link-27');">extended_dna_letters</a></tt> </tt>
</div><a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line">    <tt class="py-comment">#   B == 5-bromouridine</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#   D == 5,6-dihydrouridine</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#   S == thiouridine</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-comment">#   W == wyosine</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt id="link-28" class="py-name" targets="Variable Bio.Alphabet.IUPAC.extended_dna=Bio.Alphabet.IUPAC-module.html#extended_dna"><a title="Bio.Alphabet.IUPAC.extended_dna" class="py-name" href="#" onclick="return doclink('link-28', 'extended_dna', 'link-28');">extended_dna</a></tt> <tt class="py-op">=</tt> <tt id="link-29" class="py-name" targets="Class Bio.Alphabet.IUPAC.ExtendedIUPACDNA=Bio.Alphabet.IUPAC.ExtendedIUPACDNA-class.html"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACDNA" class="py-name" href="#" onclick="return doclink('link-29', 'ExtendedIUPACDNA', 'link-29');">ExtendedIUPACDNA</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-comment">##################### RNA</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="IUPACAmbiguousRNA"></a><div id="IUPACAmbiguousRNA-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="IUPACAmbiguousRNA-toggle" onclick="return toggle('IUPACAmbiguousRNA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html">IUPACAmbiguousRNA</a><tt class="py-op">(</tt><tt class="py-base-class">Alphabet</tt><tt class="py-op">.</tt><tt class="py-base-class">RNAAlphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IUPACAmbiguousRNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IUPACAmbiguousRNA-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt id="link-30" 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-30', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-31" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-31', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_rna_letters=Bio.Data.IUPACData-module.html#ambiguous_rna_letters"><a title="Bio.Data.IUPACData.ambiguous_rna_letters" class="py-name" href="#" onclick="return doclink('link-32', 'ambiguous_rna_letters', 'link-32');">ambiguous_rna_letters</a></tt> </tt>
</div><a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt id="link-33" 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-33', 'ambiguous_rna', 'link-33');">ambiguous_rna</a></tt> <tt class="py-op">=</tt> <tt id="link-34" class="py-name" targets="Class Bio.Alphabet.IUPAC.IUPACAmbiguousRNA=Bio.Alphabet.IUPAC.IUPACAmbiguousRNA-class.html"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousRNA" class="py-name" href="#" onclick="return doclink('link-34', 'IUPACAmbiguousRNA', 'link-34');">IUPACAmbiguousRNA</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"> </tt>
<a name="IUPACUnambiguousRNA"></a><div id="IUPACUnambiguousRNA-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="IUPACUnambiguousRNA-toggle" onclick="return toggle('IUPACUnambiguousRNA');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html">IUPACUnambiguousRNA</a><tt class="py-op">(</tt><tt class="py-base-class">IUPACAmbiguousRNA</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="IUPACUnambiguousRNA-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="IUPACUnambiguousRNA-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line">    <tt id="link-35" 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-35', 'letters', 'link-5');">letters</a></tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-36', 'IUPACData', 'link-4');">IUPACData</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Variable Bio.Data.IUPACData.unambiguous_rna_letters=Bio.Data.IUPACData-module.html#unambiguous_rna_letters"><a title="Bio.Data.IUPACData.unambiguous_rna_letters" class="py-name" href="#" onclick="return doclink('link-37', 'unambiguous_rna_letters', 'link-37');">unambiguous_rna_letters</a></tt> </tt>
</div><a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt id="link-38" 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-38', 'unambiguous_rna', 'link-38');">unambiguous_rna</a></tt> <tt class="py-op">=</tt> <tt id="link-39" class="py-name" targets="Class Bio.Alphabet.IUPAC.IUPACUnambiguousRNA=Bio.Alphabet.IUPAC.IUPACUnambiguousRNA-class.html"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousRNA" class="py-name" href="#" onclick="return doclink('link-39', 'IUPACUnambiguousRNA', 'link-39');">IUPACUnambiguousRNA</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>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-comment"># are there extended forms?</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#class ExtendedIUPACRNA(Alphabet.RNAAlphabet):</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">#    letters = extended_rna_letters</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    #   B == 5-bromouridine</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    #   D == 5,6-dihydrouridine</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    #   S == thiouridine</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#    #   W == wyosine</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line"><tt class="py-comment"># We need to load the property resolution information, but we need to</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># wait until after the systems have been loaded. (There's a nasty loop</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># where, eg, translation objects need an alphabet, which need to be</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># assocated with translators.)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-40" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-40', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Module Bio.PropertyManager=Bio.PropertyManager-module.html,Class Bio.PropertyManager.PropertyManager=Bio.PropertyManager.PropertyManager-class.html"><a title="Bio.PropertyManager
Bio.PropertyManager.PropertyManager" class="py-name" href="#" onclick="return doclink('link-41', 'PropertyManager', 'link-41');">PropertyManager</a></tt> <tt class="py-keyword">import</tt> <tt id="link-42" class="py-name" targets="Variable Bio.PropertyManager.default_manager=Bio.PropertyManager-module.html#default_manager"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-42', 'default_manager', 'link-42');">default_manager</a></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"> </tt>
<a name="_bootstrap"></a><div id="_bootstrap-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="_bootstrap-toggle" onclick="return toggle('_bootstrap');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Alphabet.IUPAC-module.html#_bootstrap">_bootstrap</a><tt class="py-op">(</tt><tt class="py-param">manager</tt><tt class="py-op">,</tt> <tt class="py-param">klass</tt><tt class="py-op">,</tt> <tt class="py-param">property</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_bootstrap-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_bootstrap-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">manager</tt> <tt class="py-keyword">is</tt> <tt id="link-43" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-43', 'default_manager', 'link-42');">default_manager</a></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">    <tt class="py-keyword">del</tt> <tt id="link-44" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-44', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-45" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACProtein" class="py-name" href="#" onclick="return doclink('link-45', 'IUPACProtein', 'link-9');">IUPACProtein</a></tt><tt class="py-op">]</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">    <tt class="py-keyword">del</tt> <tt id="link-46" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-46', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-47" class="py-name"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACProtein" class="py-name" href="#" onclick="return doclink('link-47', 'ExtendedIUPACProtein', 'link-14');">ExtendedIUPACProtein</a></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">del</tt> <tt id="link-48" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-48', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-49" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousDNA" class="py-name" href="#" onclick="return doclink('link-49', 'IUPACAmbiguousDNA', 'link-19');">IUPACAmbiguousDNA</a></tt><tt class="py-op">]</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">    <tt class="py-keyword">del</tt> <tt id="link-50" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-50', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-51" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousDNA" class="py-name" href="#" onclick="return doclink('link-51', 'IUPACUnambiguousDNA', 'link-24');">IUPACUnambiguousDNA</a></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">del</tt> <tt id="link-52" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-52', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-53" class="py-name"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACDNA" class="py-name" href="#" onclick="return doclink('link-53', 'ExtendedIUPACDNA', 'link-29');">ExtendedIUPACDNA</a></tt><tt class="py-op">]</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-keyword">del</tt> <tt id="link-54" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-54', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-55" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousRNA" class="py-name" href="#" onclick="return doclink('link-55', 'IUPACAmbiguousRNA', 'link-34');">IUPACAmbiguousRNA</a></tt><tt class="py-op">]</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">    <tt class="py-keyword">del</tt> <tt id="link-56" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-56', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-57" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousRNA" class="py-name" href="#" onclick="return doclink('link-57', 'IUPACUnambiguousRNA', 'link-39');">IUPACUnambiguousRNA</a></tt><tt class="py-op">]</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt class="py-keyword">from</tt> <tt id="link-58" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-58', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Package Bio.Encodings=Bio.Encodings-module.html"><a title="Bio.Encodings" class="py-name" href="#" onclick="return doclink('link-59', 'Encodings', 'link-59');">Encodings</a></tt> <tt class="py-keyword">import</tt> <tt id="link-60" class="py-name" targets="Module Bio.Encodings.IUPACEncoding=Bio.Encodings.IUPACEncoding-module.html"><a title="Bio.Encodings.IUPACEncoding" class="py-name" href="#" onclick="return doclink('link-60', 'IUPACEncoding', 'link-60');">IUPACEncoding</a></tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">manager</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name" targets="Method Bio.PropertyManager.PropertyManager.resolve_class()=Bio.PropertyManager.PropertyManager-class.html#resolve_class"><a title="Bio.PropertyManager.PropertyManager.resolve_class" class="py-name" href="#" onclick="return doclink('link-61', 'resolve_class', 'link-61');">resolve_class</a></tt><tt class="py-op">(</tt><tt class="py-name">klass</tt><tt class="py-op">,</tt> <tt id="link-62" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.property=Bio.Encodings.IUPACEncoding-module.html#property"><a title="Bio.Encodings.IUPACEncoding.property" class="py-name" href="#" onclick="return doclink('link-62', 'property', 'link-62');">property</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line"><tt id="link-63" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-63', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-64" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACProtein" class="py-name" href="#" onclick="return doclink('link-64', 'IUPACProtein', 'link-9');">IUPACProtein</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-65" class="py-name" targets="Function Bio.Alphabet.IUPAC._bootstrap()=Bio.Alphabet.IUPAC-module.html#_bootstrap"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-65', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line"><tt id="link-66" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-66', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-67" class="py-name"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACProtein" class="py-name" href="#" onclick="return doclink('link-67', 'ExtendedIUPACProtein', 'link-14');">ExtendedIUPACProtein</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-68', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt id="link-69" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-69', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-70" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousDNA" class="py-name" href="#" onclick="return doclink('link-70', 'IUPACAmbiguousDNA', 'link-19');">IUPACAmbiguousDNA</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-71" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-71', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt id="link-72" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-72', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-73" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousDNA" class="py-name" href="#" onclick="return doclink('link-73', 'IUPACUnambiguousDNA', 'link-24');">IUPACUnambiguousDNA</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-74', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt id="link-75" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-75', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-76" class="py-name"><a title="Bio.Alphabet.IUPAC.ExtendedIUPACDNA" class="py-name" href="#" onclick="return doclink('link-76', 'ExtendedIUPACDNA', 'link-29');">ExtendedIUPACDNA</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-77" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-77', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt id="link-78" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-78', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-79" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACAmbiguousRNA" class="py-name" href="#" onclick="return doclink('link-79', 'IUPACAmbiguousRNA', 'link-34');">IUPACAmbiguousRNA</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-80" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-80', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt id="link-81" class="py-name"><a title="Bio.PropertyManager.default_manager" class="py-name" href="#" onclick="return doclink('link-81', 'default_manager', 'link-42');">default_manager</a></tt><tt class="py-op">.</tt><tt class="py-name">class_resolver</tt><tt class="py-op">[</tt><tt id="link-82" class="py-name"><a title="Bio.Alphabet.IUPAC.IUPACUnambiguousRNA" class="py-name" href="#" onclick="return doclink('link-82', 'IUPACUnambiguousRNA', 'link-39');">IUPACUnambiguousRNA</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name"><a title="Bio.Alphabet.IUPAC._bootstrap" class="py-name" href="#" onclick="return doclink('link-83', '_bootstrap', 'link-65');">_bootstrap</a></tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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