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<a href="Bio-module.html">Package Bio</a> ::
Module Seq
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<h1 class="epydoc">Source Code for <a href="Bio.Seq-module.html">Module Bio.Seq</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000-2002 Brad Chapman.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright 2004-2005 by M de Hoon.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright 2007 by Peter Cock.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># All rights reserved.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">array</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt id="link-0" 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-0', 'Alphabet', 'link-0');">Alphabet</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-1" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-0');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" 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-2', 'IUPAC', 'link-2');">IUPAC</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name" 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-op">.</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 class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_dna_complement=Bio.Data.IUPACData-module.html#ambiguous_dna_complement"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-5', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Variable Bio.Data.IUPACData.ambiguous_rna_complement=Bio.Data.IUPACData-module.html#ambiguous_rna_complement"><a title="Bio.Data.IUPACData.ambiguous_rna_complement" class="py-name" href="#" onclick="return doclink('link-6', 'ambiguous_rna_complement', 'link-6');">ambiguous_rna_complement</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-7');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-8', 'Data', 'link-3');">Data</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" 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-9', 'CodonTable', 'link-9');">CodonTable</a></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> </tt>
<a name="Seq"></a><div id="Seq-def"><a name="L15"></a><tt class="py-lineno"> 15</tt> <a class="py-toggle" href="#" id="Seq-toggle" onclick="return toggle('Seq');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html">Seq</a><tt class="py-op">:</tt> </tt>
</div><div id="Seq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Seq-expanded"><a name="Seq.__init__"></a><div id="Seq.__init__-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="Seq.__init__-toggle" onclick="return toggle('Seq.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-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">data</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-10', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Variable Bio.Alphabet.generic_alphabet=Bio.Alphabet-module.html#generic_alphabet"><a title="Bio.Alphabet.generic_alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'generic_alphabet', 'link-11');">generic_alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Seq.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__init__-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-comment"># Enforce string storage</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-12', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-13', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-14" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-14', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-comment"># must use a string</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt id="link-15" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-15', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-16', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-17" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-17', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">u""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># but can be a unicode string</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-18', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-19', 'data', 'link-13');">data</a></tt> <tt class="py-comment"># Seq API requirement</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Variable Bio.Prosite.Pattern.Prosite.alphabet=Bio.Prosite.Pattern.Prosite-class.html#alphabet,Function Bio.Std.alphabet()=Bio.Std-module.html#alphabet"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-20', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-21', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-comment"># Seq API requirement</tt> </tt>
</div><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="Seq.__repr__"></a><div id="Seq.__repr__-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="Seq.__repr__-toggle" onclick="return toggle('Seq.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#__repr__">__repr__</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="Seq.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__repr__-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a (truncated) representation of the sequence for debugging."""</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">60</tt> <tt class="py-op">:</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> <tt class="py-comment">#Shows the last three letters as it is often useful to see if there</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#is a stop codon at the end of a sequence.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Note total length is 54+3+3=60</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-string">"%s('%s...%s', %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-22', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">54</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-23', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-24', 'alphabet', 'link-20');">alphabet</a></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 class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s(%s, %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-25', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-26', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="Seq.__str__"></a><div id="Seq.__str__-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="Seq.__str__-toggle" onclick="return toggle('Seq.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-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="Seq.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__str__-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the full sequence as a python string.</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> Note that Biopython 1.44 and earlier would give a truncated</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> version of repr(my_seq) for str(my_seq). If you are writing code</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> which need to be backwards compatible with old Biopython, you</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> should continue to use my_seq.tostring() rather than str(my_seq)</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</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-27" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-27', 'data', 'link-13');">data</a></tt> </tt>
</div><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-comment"># I don't think I like this method...</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## def __cmp__(self, other):</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">## if isinstance(other, Seq):</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">## return cmp(self.data, other.data)</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">## else:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return cmp(self.data, other)</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="Seq.__len__"></a><div id="Seq.__len__-def"><a name="L54"></a><tt class="py-lineno"> 54</tt> <a class="py-toggle" href="#" id="Seq.__len__-toggle" onclick="return toggle('Seq.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-28', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># Seq API requirement</tt> </tt>
</div><a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="Seq.__getitem__"></a><div id="Seq.__getitem__-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="Seq.__getitem__-toggle" onclick="return toggle('Seq.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-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">index</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-comment"># Seq API requirement</tt> </tt>
</div><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment">#Note since Python 2.0, __getslice__ is deprecated</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#and __getitem__ is used instead.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#See http://docs.python.org/ref/sequence-methods.html</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-29', 'index', 'link-29');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-comment">#Return a single letter as a string</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-30', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-31" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-31', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-comment">#Return the (sub)sequence as another Seq object</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-32" class="py-name" targets="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html,Class Martel.Expression.Seq=Martel.Expression.Seq-class.html,Function Martel.Seq()=Martel-module.html#Seq"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-32', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-33', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-34" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-34', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-35', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="Seq.__add__"></a><div id="Seq.__add__-def"><a name="L67"></a><tt class="py-lineno"> 67</tt> <a class="py-toggle" href="#" id="Seq.__add__-toggle" onclick="return toggle('Seq.__add__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#__add__">__add__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Seq.__add__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__add__-expanded"><a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-36" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-36', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-37" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-37', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">' '</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-38', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">other</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-39', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-40', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method Bio.Alphabet.Alphabet.contains()=Bio.Alphabet.Alphabet-class.html#contains,Method Bio.Alphabet.AlphabetEncoder.contains()=Bio.Alphabet.AlphabetEncoder-class.html#contains,Method Bio.Alphabet.Gapped.contains()=Bio.Alphabet.Gapped-class.html#contains,Method Bio.Alphabet.HasStopCodon.contains()=Bio.Alphabet.HasStopCodon-class.html#contains,Method Bio.Pathway.Rep.HashSet.HashSet.contains()=Bio.Pathway.Rep.HashSet.HashSet-class.html#contains,Method Bio.biblio.Biblio.contains()=Bio.biblio.Biblio-class.html#contains"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-41', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-42', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-43', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-44" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-44', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-45', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-46', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-47', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-48', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-49', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-50', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-51', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"incompatable alphabets"</tt><tt class="py-op">,</tt> <tt class="py-name">str</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.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-52', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-53', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="Seq.__radd__"></a><div id="Seq.__radd__-def"><a name="L78"></a><tt class="py-lineno"> 78</tt> <a class="py-toggle" href="#" id="Seq.__radd__-toggle" onclick="return toggle('Seq.__radd__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#__radd__">__radd__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Seq.__radd__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__radd__-expanded"><a name="L79"></a><tt class="py-lineno"> 79</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-54" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-54', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-55', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-56', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-57', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-58', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-59', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-60', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-61', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-62', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-63', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-64', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-65', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"incompatable alphabets"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-66', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</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">str</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-67', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="Seq.tostring"></a><div id="Seq.tostring-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="Seq.tostring-toggle" onclick="return toggle('Seq.tostring');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#tostring">tostring</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># Seq API requirement</tt> </tt>
</div><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the full sequence as a python string.</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> Although not formally deprecated, you are now encouraged to use</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> str(my_seq) instead of my_seq.tostring()."""</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</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-68" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-68', 'data', 'link-13');">data</a></tt> </tt>
</div><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="Seq.tomutable"></a><div id="Seq.tomutable-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="Seq.tomutable-toggle" onclick="return toggle('Seq.tomutable');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#tomutable">tomutable</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># Needed? Or use a function?</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-69" class="py-name" targets="Class Bio.Seq.MutableSeq=Bio.Seq.MutableSeq-class.html"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-69', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-70" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-70', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-71', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> </tt>
<a name="Seq.count"></a><div id="Seq.count-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="Seq.count-toggle" onclick="return toggle('Seq.count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#count">count</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sub</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</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="Seq.count-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.count-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-docstring">"""Count method, like that of a python string.</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> Return an integer, the number of occurrences of substring</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> argument sub in the (sub)sequence given by [start:end].</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Optional arguments start and end are interpreted as in slice</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> notation.</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> sub - a string or another Seq object to look for</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> start - optional integer, slice start</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> end - optional integer, slice end</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> from Bio.Seq import Seq</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> my_seq = Seq("AAAATGA")</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> print my_seq.count("A")</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> print my_seq.count("ATG")</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> print my_seq.count(Seq("AT"))</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> print my_seq.count("AT", 2, -1)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment">#Assume sub is a Seq or MutableSeq object, so pass</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#it to the string's count method as a string.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#TODO - Should we check the alphabet?</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-72" class="py-name" targets="Method Bio.EUtils.DBIdsClient.DBIdsClient.search()=Bio.EUtils.DBIdsClient.DBIdsClient-class.html#search,Method Bio.EUtils.HistoryClient.HistoryClient.search()=Bio.EUtils.HistoryClient.HistoryClient-class.html#search,Method Bio.KDTree.KDTree.KDTree.search()=Bio.KDTree.KDTree.KDTree-class.html#search,Method Bio.PDB.NeighborSearch.NeighborSearch.search()=Bio.PDB.NeighborSearch.NeighborSearch-class.html#search,Method Bio.Prosite.Pattern.Prosite.search()=Bio.Prosite.Pattern.Prosite-class.html#search,Class Method Bio.Restriction.Restriction.AbstractCut.search()=Bio.Restriction.Restriction.AbstractCut-class.html#search,Method Bio.Restriction.Restriction.RestrictionBatch.search()=Bio.Restriction.Restriction.RestrictionBatch-class.html#search,Function Bio.SCOP.search()=Bio.SCOP-module.html#search,Module Bio.builders.Search.search=Bio.builders.Search.search-module.html,Module Bio.formatdefs.search=Bio.formatdefs.search-module.html,Variable Bio.formatdefs.search.search=Bio.formatdefs.search-module.html#search"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-72', 'search', 'link-72');">search</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sub</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.Crystal.Crystal.tostring()=Bio.Crystal.Crystal-class.html#tostring,Method Bio.EUtils.POM.ElementNode.tostring()=Bio.EUtils.POM.ElementNode-class.html#tostring,Method Bio.Prosite.Pattern.Prosite.tostring()=Bio.Prosite.Pattern.Prosite-class.html#tostring,Method Bio.Seq.MutableSeq.tostring()=Bio.Seq.MutableSeq-class.html#tostring,Method Bio.Seq.Seq.tostring()=Bio.Seq.Seq-class.html#tostring,Method BioSQL.BioSeq.DBSeq.tostring()=BioSQL.BioSeq.DBSeq-class.html#tostring"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-73', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">AttributeError</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment">#Assume sub is a string.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-74" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-74', 'search', 'link-72');">search</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sub</tt> </tt>
<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 class="py-comment">#TODO - More elegant way of doing this splice notation</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-75" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-75', 'start', 'link-75');">start</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-76" class="py-name" targets="Method Bio.GFF.easy.Location.end()=Bio.GFF.easy.Location-class.html#end,Method Bio.Prosite.Pattern.PrositeMatch.end()=Bio.Prosite.Pattern.PrositeMatch-class.html#end,Variable Bio.expressions.blocks.end=Bio.expressions.blocks-module.html#end,Variable Bio.expressions.embl.embl65.end=Bio.expressions.embl.embl65-module.html#end,Variable Bio.expressions.swissprot.sprot38.end=Bio.expressions.swissprot.sprot38-module.html#end,Method Martel.LAX.LAX.end()=Martel.LAX.LAX-class.html#end,Variable Martel.test.test_swissprot38.end=Martel.test.test_swissprot38-module.html#end,Variable Martel.test.testformats.swissprot38.end=Martel.test.testformats.swissprot38-module.html#end"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-76', 'end', 'link-76');">end</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</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-77" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-77', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-78" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-78', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-79', 'search', 'link-72');">search</a></tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-80" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-80', 'end', 'link-76');">end</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</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-81" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-81', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-82', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-83', 'search', 'link-72');">search</a></tt><tt class="py-op">,</tt> <tt id="link-84" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-84', 'start', 'link-75');">start</a></tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</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-85" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-85', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-86', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-87" class="py-name"><a title="Bio.EUtils.DBIdsClient.DBIdsClient.search
Bio.EUtils.HistoryClient.HistoryClient.search
Bio.KDTree.KDTree.KDTree.search
Bio.PDB.NeighborSearch.NeighborSearch.search
Bio.Prosite.Pattern.Prosite.search
Bio.Restriction.Restriction.AbstractCut.search
Bio.Restriction.Restriction.RestrictionBatch.search
Bio.SCOP.search
Bio.builders.Search.search
Bio.formatdefs.search
Bio.formatdefs.search.search" class="py-name" href="#" onclick="return doclink('link-87', 'search', 'link-72');">search</a></tt><tt class="py-op">,</tt> <tt id="link-88" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-88', 'start', 'link-75');">start</a></tt><tt class="py-op">,</tt> <tt id="link-89" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-89', 'end', 'link-76');">end</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="Seq.__maketrans"></a><div id="Seq.__maketrans-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="Seq.__maketrans-toggle" onclick="return toggle('Seq.__maketrans');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#__maketrans">__maketrans</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="Seq.__maketrans-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.__maketrans-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-docstring">"""Seq.__maketrans(alphabet) -> translation table.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> Return a translation table for use with complement()</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> and reverse_complement().</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> Compatible with lower case and upper case sequences.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> alphabet is a dictionary as implement in Data.IUPACData</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> For internal use only.</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-name">before</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-90" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-90', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-91" 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-91', 'keys', 'link-91');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</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">after</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-92" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-92', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-93" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.EUtils.MultiDict._BaseMultiDict.values()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#values,Method Bio.GenBank.NCBIDictionary.values()=Bio.GenBank.NCBIDictionary-class.html#values,Method Bio.Mindy.BaseDB.DictLookup.values()=Bio.Mindy.BaseDB.DictLookup-class.html#values,Method Bio.Prosite.ExPASyDictionary.values()=Bio.Prosite.ExPASyDictionary-class.html#values,Method Bio.Prosite.Prodoc.ExPASyDictionary.values()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#values,Method Bio.PubMed.Dictionary.values()=Bio.PubMed.Dictionary-class.html#values,Method Bio.SwissProt.SProt.ExPASyDictionary.values()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#values,Method Bio.config.Registry.Registry.values()=Bio.config.Registry.Registry-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values,Method Martel.Parser.MartelAttributeList.values()=Martel.Parser.MartelAttributeList-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-93', 'values', 'link-93');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">before</tt> <tt class="py-op">=</tt> <tt class="py-name">before</tt> <tt class="py-op">+</tt> <tt class="py-name">before</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-name">after</tt> <tt class="py-op">=</tt> <tt class="py-name">after</tt> <tt class="py-op">+</tt> <tt class="py-name">after</tt><tt class="py-op">.</tt><tt class="py-name">lower</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-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">maketrans</tt><tt class="py-op">(</tt><tt class="py-name">before</tt><tt class="py-op">,</tt> <tt class="py-name">after</tt><tt class="py-op">)</tt> </tt>
</div><a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> </tt>
<a name="Seq.complement"></a><div id="Seq.complement-def"><a name="L153"></a><tt class="py-lineno">153</tt> <a class="py-toggle" href="#" id="Seq.complement-toggle" onclick="return toggle('Seq.complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#complement">complement</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="Seq.complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.complement-expanded"><a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the complement sequence. New Seq object.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</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-94" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-94', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-95" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-95', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-96" class="py-name" targets="Class Bio.Alphabet.ProteinAlphabet=Bio.Alphabet.ProteinAlphabet-class.html"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-96', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins do not have complements!"</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</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-97" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-97', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-98" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-98', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-99" 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-99', 'DNAAlphabet', 'link-99');">DNAAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt id="link-100" class="py-name" targets="Variable Bio.EUtils.setup.d=Bio.EUtils.setup-module.html#d"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-100', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-101', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-102', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-103" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-103', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Class Bio.Alphabet.RNAAlphabet=Bio.Alphabet.RNAAlphabet-class.html"><a title="Bio.Alphabet.RNAAlphabet" class="py-name" href="#" onclick="return doclink('link-104', 'RNAAlphabet', 'link-104');">RNAAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-105', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-106" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_complement" class="py-name" href="#" onclick="return doclink('link-106', 'ambiguous_rna_complement', 'link-6');">ambiguous_rna_complement</a></tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-string">'U'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-107" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-107', 'data', 'link-13');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-108" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-108', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_complement" class="py-name" href="#" onclick="return doclink('link-109', 'ambiguous_rna_complement', 'link-6');">ambiguous_rna_complement</a></tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt id="link-110" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-110', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-111" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-111', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">ttable</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name" targets="Method Bio.Seq.Seq.__maketrans()=Bio.Seq.Seq-class.html#__maketrans"><a title="Bio.Seq.Seq.__maketrans" class="py-name" href="#" onclick="return doclink('link-112', '__maketrans', 'link-112');">__maketrans</a></tt><tt class="py-op">(</tt><tt id="link-113" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-113', 'd', 'link-100');">d</a></tt><tt class="py-op">)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment">#Much faster on really long sequences than the previous loop based one.</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#thx to Michael Palmer, University of Waterloo</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-114" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-114', 's', 'link-114');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-115', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Method Bio.GFF.Feature.translate()=Bio.GFF.Feature-class.html#translate,Method Bio.GFF.FeatureAggregate.translate()=Bio.GFF.FeatureAggregate-class.html#translate,Function Bio.Seq.translate()=Bio.Seq-module.html#translate,Function Bio.SeqUtils.translate()=Bio.SeqUtils-module.html#translate,Method Bio.Translate.Translator.translate()=Bio.Translate.Translator-class.html#translate,Function Bio.utils.translate()=Bio.utils-module.html#translate"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-116', 'translate', 'link-116');">translate</a></tt><tt class="py-op">(</tt><tt class="py-name">ttable</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-117" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-117', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-118" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-118', 's', 'link-114');">s</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-119', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="Seq.reverse_complement"></a><div id="Seq.reverse_complement-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="Seq.reverse_complement-toggle" onclick="return toggle('Seq.reverse_complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.Seq-class.html#reverse_complement">reverse_complement</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="Seq.reverse_complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Seq.reverse_complement-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the reverse complement sequence. New Seq object.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-comment">#Use -1 stride to reverse the complement</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-120" class="py-name" targets="Method Bio.Seq.MutableSeq.complement()=Bio.Seq.MutableSeq-class.html#complement,Method Bio.Seq.Seq.complement()=Bio.Seq.Seq-class.html#complement"><a title="Bio.Seq.MutableSeq.complement
Bio.Seq.Seq.complement" class="py-name" href="#" onclick="return doclink('link-120', 'complement', 'link-120');">complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> </tt>
<a name="MutableSeq"></a><div id="MutableSeq-def"><a name="L178"></a><tt class="py-lineno">178</tt> <a class="py-toggle" href="#" id="MutableSeq-toggle" onclick="return toggle('MutableSeq');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html">MutableSeq</a><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="MutableSeq-expanded"><a name="MutableSeq.__init__"></a><div id="MutableSeq.__init__-def"><a name="L179"></a><tt class="py-lineno">179</tt> <a class="py-toggle" href="#" id="MutableSeq.__init__-toggle" onclick="return toggle('MutableSeq.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-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">data</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-121" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-121', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Alphabet.generic_alphabet" class="py-name" href="#" onclick="return doclink('link-122', 'generic_alphabet', 'link-11');">generic_alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__init__-expanded"><a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-123" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-123', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt id="link-124" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-124', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-125" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-125', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-126', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-string">"c"</tt><tt class="py-op">,</tt> <tt id="link-127" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-127', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-128', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-129" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-129', 'data', 'link-13');">data</a></tt> <tt class="py-comment"># assumes the input is an array</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-130', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-131" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-131', 'alphabet', 'link-20');">alphabet</a></tt> </tt>
</div><a name="MutableSeq.__repr__"></a><div id="MutableSeq.__repr__-def"><a name="L185"></a><tt class="py-lineno">185</tt> <a class="py-toggle" href="#" id="MutableSeq.__repr__-toggle" onclick="return toggle('MutableSeq.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__repr__">__repr__</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="MutableSeq.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__repr__-expanded"><a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a (truncated) representation of the sequence for debugging."""</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">60</tt> <tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-comment">#Shows the last three letters as it is often useful to see if there</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">#is a stop codon at the end of a sequence.</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">#Note total length is 54+3+3=60</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-string">"%s('%s...%s', %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">54</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-132', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s('%s', %s)"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">.</tt><tt class="py-name">__name__</tt><tt class="py-op">,</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-133', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__str__"></a><div id="MutableSeq.__str__-def"><a name="L199"></a><tt class="py-lineno">199</tt> <a class="py-toggle" href="#" id="MutableSeq.__str__-toggle" onclick="return toggle('MutableSeq.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-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="MutableSeq.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__str__-expanded"><a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the full sequence as a python string.</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> Note that Biopython 1.44 and earlier would give a truncated</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> version of repr(my_seq) for str(my_seq). If you are writing code</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"> which need to be backwards compatible with old Biopython, you</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> should continue to use my_seq.tostring() rather than str(my_seq).</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-134', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__cmp__"></a><div id="MutableSeq.__cmp__-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="MutableSeq.__cmp__-toggle" onclick="return toggle('MutableSeq.__cmp__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__cmp__">__cmp__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__cmp__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__cmp__-expanded"><a name="L210"></a><tt class="py-lineno">210</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">other</tt><tt class="py-op">,</tt> <tt id="link-135" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-135', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt id="link-136" 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-136', 'x', 'link-136');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-137', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-138', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-139" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-139', 'x', 'link-136');">x</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-140', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-141', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-142" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-142', 'x', 'link-136');">x</a></tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-143" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-143', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-144" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-144', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-145', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-146" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-146', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">,</tt> <tt id="link-147" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-147', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt id="link-148" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-148', 'x', 'link-136');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-149" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-149', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-150" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-150', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-151" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-151', 'x', 'link-136');">x</a></tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-152" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-152', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-153', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-154" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-154', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-155" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-155', 'x', 'link-136');">x</a></tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">cmp</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-156" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-156', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">)</tt> </tt>
</div><a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__len__"></a><div id="MutableSeq.__len__-def"><a name="L225"></a><tt class="py-lineno">225</tt> <a class="py-toggle" href="#" id="MutableSeq.__len__-toggle" onclick="return toggle('MutableSeq.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-157" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-157', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__getitem__"></a><div id="MutableSeq.__getitem__-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="MutableSeq.__getitem__-toggle" onclick="return toggle('MutableSeq.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-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">index</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__getitem__-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-comment">#Note since Python 2.0, __getslice__ is deprecated</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">#and __getitem__ is used instead.</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">#See http://docs.python.org/ref/sequence-methods.html</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-158" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-158', 'index', 'link-29');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-comment">#Return a single letter as a string</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-159" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-159', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-160" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-160', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-comment">#Return the (sub)sequence as another Seq object</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-161" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-161', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-162" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-162', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-163" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-163', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-164', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__setitem__"></a><div id="MutableSeq.__setitem__-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="MutableSeq.__setitem__-toggle" onclick="return toggle('MutableSeq.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__setitem__-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-comment">#Note since Python 2.0, __setslice__ is deprecated</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">#and __setitem__ is used instead.</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">#See http://docs.python.org/ref/sequence-methods.html</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-165', 'index', 'link-29');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-comment">#Replacing a single letter with a new string</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-166" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-166', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-167" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-167', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-168" class="py-name" targets="Variable Bio.Translate.value=Bio.Translate-module.html#value"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-168', 'value', 'link-168');">value</a></tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment">#Replacing a sub-sequence</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-169" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-169', 'value', 'link-168');">value</a></tt><tt class="py-op">,</tt> <tt id="link-170" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-170', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-171" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-171', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-172" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-172', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-173" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-173', 'value', 'link-168');">value</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-174', 'data', 'link-13');">data</a></tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-175" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-175', 'value', 'link-168');">value</a></tt><tt class="py-op">,</tt> <tt id="link-176" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-176', 'type', 'link-12');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-177" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-177', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-178" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-178', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-179" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-179', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-180" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-180', 'value', 'link-168');">value</a></tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-181" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-181', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-182" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-182', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-string">"c"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-183" class="py-name"><a title="Bio.Translate.value" class="py-name" href="#" onclick="return doclink('link-183', 'value', 'link-168');">value</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__delitem__"></a><div id="MutableSeq.__delitem__-def"><a name="L254"></a><tt class="py-lineno">254</tt> <a class="py-toggle" href="#" id="MutableSeq.__delitem__-toggle" onclick="return toggle('MutableSeq.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__delitem__">__delitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__delitem__-expanded"><a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-comment">#Note since Python 2.0, __delslice__ is deprecated</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">#and __delitem__ is used instead.</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">#See http://docs.python.org/ref/sequence-methods.html</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-comment">#Could be deleting a single letter, or a slice</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-184" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-184', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-185" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-185', 'index', 'link-29');">index</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.__add__"></a><div id="MutableSeq.__add__-def"><a name="L262"></a><tt class="py-lineno">262</tt> <a class="py-toggle" href="#" id="MutableSeq.__add__-toggle" onclick="return toggle('MutableSeq.__add__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__add__">__add__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__add__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__add__-expanded"><a name="L263"></a><tt class="py-lineno">263</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-186" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-186', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-187" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-187', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-188" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-188', 'alphabet', 'link-20');">alphabet</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-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-189" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-189', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-190" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-190', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-191', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-192" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-192', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-193" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-193', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-194" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-194', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-195" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-195', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-196" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-196', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-197" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-197', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"incompatable alphabets"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-198" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-198', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-199" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-199', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="MutableSeq.__radd__"></a><div id="MutableSeq.__radd__-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="MutableSeq.__radd__-toggle" onclick="return toggle('MutableSeq.__radd__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#__radd__">__radd__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.__radd__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.__radd__-expanded"><a name="L271"></a><tt class="py-lineno">271</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-200" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-200', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-201" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-201', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-202', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-203" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-203', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-204" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-204', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-205', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-206" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-206', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">.</tt><tt id="link-207" class="py-name"><a title="Bio.Alphabet.Alphabet.contains
Bio.Alphabet.AlphabetEncoder.contains
Bio.Alphabet.Gapped.contains
Bio.Alphabet.HasStopCodon.contains
Bio.Pathway.Rep.HashSet.HashSet.contains
Bio.biblio.Biblio.contains" class="py-name" href="#" onclick="return doclink('link-207', 'contains', 'link-41');">contains</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-208" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-208', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-209', 'data', 'link-13');">data</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-210" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-210', 'data', 'link-13');">data</a></tt><tt class="py-op">,</tt> <tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-211" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-211', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-string">"incompatable alphabets"</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-212" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-212', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">other</tt><tt class="py-op">.</tt><tt id="link-213" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-213', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.append"></a><div id="MutableSeq.append-def"><a name="L279"></a><tt class="py-lineno">279</tt> <a class="py-toggle" href="#" id="MutableSeq.append-toggle" onclick="return toggle('MutableSeq.append');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.append-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.append-expanded"><a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-214" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-214', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-215" 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-215', 'append', 'link-215');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
</div><a name="MutableSeq.insert"></a><div id="MutableSeq.insert-def"><a name="L281"></a><tt class="py-lineno">281</tt> <a class="py-toggle" href="#" id="MutableSeq.insert-toggle" onclick="return toggle('MutableSeq.insert');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#insert">insert</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt><tt class="py-op">,</tt> <tt class="py-param">c</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.insert-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.insert-expanded"><a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-216" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-216', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-217" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-217', 'insert', 'link-217');">insert</a></tt><tt class="py-op">(</tt><tt id="link-218" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-218', 'i', 'link-218');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
</div><a name="MutableSeq.pop"></a><div id="MutableSeq.pop-def"><a name="L283"></a><tt class="py-lineno">283</tt> <a class="py-toggle" href="#" id="MutableSeq.pop-toggle" onclick="return toggle('MutableSeq.pop');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#pop">pop</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">i</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.pop-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.pop-expanded"><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-219" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-219', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-220" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-220', 'i', 'link-218');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-221', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-222" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-222', 'i', 'link-218');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">c</tt> </tt>
</div><a name="MutableSeq.remove"></a><div id="MutableSeq.remove-def"><a name="L287"></a><tt class="py-lineno">287</tt> <a class="py-toggle" href="#" id="MutableSeq.remove-toggle" onclick="return toggle('MutableSeq.remove');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#remove">remove</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.remove-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.remove-expanded"><a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-223" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-223', 'i', 'link-218');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-224" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-224', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</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-225" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-225', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-226" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-226', 'i', 'link-218');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt id="link-227" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-227', 'item', 'link-227');">item</a></tt><tt class="py-op">:</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-228" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-228', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-229" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-229', 'i', 'link-218');">i</a></tt><tt class="py-op">]</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"MutableSeq.remove(x): x not in list"</tt> </tt>
</div><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.count"></a><div id="MutableSeq.count-def"><a name="L294"></a><tt class="py-lineno">294</tt> <a class="py-toggle" href="#" id="MutableSeq.count-toggle" onclick="return toggle('MutableSeq.count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#count">count</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">sub</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</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="MutableSeq.count-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.count-expanded"><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-docstring">"""Count method, like that of a python string.</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> Return an integer, the number of occurrences of substring</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> argument sub in the (sub)sequence given by [start:end].</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> Optional arguments start and end are interpreted as in slice</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> notation.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> sub - a string or another Seq object to look for</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> start - optional integer, slice start</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> end - optional integer, slice end</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"> from Bio.Seq import MutableSeq</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> my_mseq = MutableSeq("AAAATGA")</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> print my_mseq.count("A")</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-docstring"> print my_mseq.count("ATG")</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-docstring"> print my_mseq.count(Seq("AT"))</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-docstring"> print my_mseq.count("AT", 2, -1)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">sub</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="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-comment">#Try and be efficient and work directly from the array.</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-comment">#Assume item is a single letter Seq/MutableSeq</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#TODO - Should we check the alphabet?</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">letter</tt> <tt class="py-op">=</tt> <tt class="py-name">sub</tt><tt class="py-op">.</tt><tt id="link-230" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-230', 'tostring', 'link-73');">tostring</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-keyword">except</tt> <tt class="py-name">AttributeError</tt> <tt class="py-op">:</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">letter</tt> <tt class="py-op">=</tt> <tt class="py-name">sub</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt id="link-231" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-231', 'count', 'link-78');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-comment">#TODO - More elegant way of doing this splice notation</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-232" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-232', 'start', 'link-75');">start</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt id="link-233" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-233', 'end', 'link-76');">end</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</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">self</tt><tt class="py-op">.</tt><tt id="link-234" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-234', 'data', 'link-13');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">letter</tt><tt class="py-op">:</tt> <tt id="link-235" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-235', 'count', 'link-78');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-236" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-236', 'end', 'link-76');">end</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</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">self</tt><tt class="py-op">.</tt><tt id="link-237" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-237', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-238" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-238', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">letter</tt><tt class="py-op">:</tt> <tt id="link-239" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-239', 'count', 'link-78');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</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">self</tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-240', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-241" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-241', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt id="link-242" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-242', 'end', 'link-76');">end</a></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 class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">letter</tt><tt class="py-op">:</tt> <tt id="link-243" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-243', 'count', 'link-78');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-244" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-244', 'count', 'link-78');">count</a></tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Can we do this more efficiently?</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#We could use the self.tostring().count(...) method</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-245" class="py-name" targets="Method Bio.Seq.MutableSeq.toseq()=Bio.Seq.MutableSeq-class.html#toseq"><a title="Bio.Seq.MutableSeq.toseq" class="py-name" href="#" onclick="return doclink('link-245', 'toseq', 'link-245');">toseq</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-246', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">sub</tt><tt class="py-op">,</tt> <tt id="link-247" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-247', 'start', 'link-75');">start</a></tt><tt class="py-op">,</tt> <tt id="link-248" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-248', 'end', 'link-76');">end</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.index"></a><div id="MutableSeq.index-def"><a name="L340"></a><tt class="py-lineno">340</tt> <a class="py-toggle" href="#" id="MutableSeq.index-toggle" onclick="return toggle('MutableSeq.index');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#index">index</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">item</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.index-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.index-expanded"><a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-249" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-249', 'i', 'link-218');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-250" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-250', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-251" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-251', 'data', 'link-13');">data</a></tt><tt class="py-op">[</tt><tt id="link-252" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-252', 'i', 'link-218');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt id="link-253" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-253', 'item', 'link-227');">item</a></tt><tt class="py-op">:</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-254" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-254', 'i', 'link-218');">i</a></tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"MutableSeq.index(x): x not in list"</tt> </tt>
</div><a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.reverse"></a><div id="MutableSeq.reverse-def"><a name="L346"></a><tt class="py-lineno">346</tt> <a class="py-toggle" href="#" id="MutableSeq.reverse-toggle" onclick="return toggle('MutableSeq.reverse');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#reverse">reverse</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="MutableSeq.reverse-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.reverse-expanded"><a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-docstring">"""Modify the MutableSequence to reverse itself.</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"><tt class="py-docstring"> No return value"""</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-255" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-255', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-256" class="py-name" targets="Method Bio.GFF.easy.Location.reverse()=Bio.GFF.easy.Location-class.html#reverse,Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse,Function Bio.SeqUtils.reverse()=Bio.SeqUtils-module.html#reverse"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-256', 'reverse', 'link-256');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.complement"></a><div id="MutableSeq.complement-def"><a name="L352"></a><tt class="py-lineno">352</tt> <a class="py-toggle" href="#" id="MutableSeq.complement-toggle" onclick="return toggle('MutableSeq.complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#complement">complement</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="MutableSeq.complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.complement-expanded"><a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-docstring">"""Modify the MutableSequence to take on its complement.</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-docstring"> No return value"""</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</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-257" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-257', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-258" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-258', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-259" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-259', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins do not have complements!"</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</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-260" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-260', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-261" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-261', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-262" 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-262', 'ambiguous_dna', 'link-262');">ambiguous_dna</a></tt><tt class="py-op">,</tt> <tt id="link-263" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-263', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-264" 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-264', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt id="link-265" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-265', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-266" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-266', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-267" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-267', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-268" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-268', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-269" 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-269', 'ambiguous_rna', 'link-269');">ambiguous_rna</a></tt><tt class="py-op">,</tt> <tt id="link-270" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-270', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-271" 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-271', 'unambiguous_rna', 'link-271');">unambiguous_rna</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt id="link-272" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-272', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-273" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_complement" class="py-name" href="#" onclick="return doclink('link-273', 'ambiguous_rna_complement', 'link-6');">ambiguous_rna_complement</a></tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-string">'U'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-274" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-274', 'data', 'link-13');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt id="link-275" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-275', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-276" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_complement" class="py-name" href="#" onclick="return doclink('link-276', 'ambiguous_rna_complement', 'link-6');">ambiguous_rna_complement</a></tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt id="link-277" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-277', 'd', 'link-100');">d</a></tt> <tt class="py-op">=</tt> <tt id="link-278" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-278', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-279" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-279', 'x', 'link-136');">x</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">y</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-280" class="py-name"><a title="Bio.MarkovModel.x
Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-280', 'x', 'link-136');">x</a></tt><tt class="py-op">,</tt><tt class="py-name">y</tt> <tt class="py-keyword">in</tt> <tt id="link-281" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-281', 'd', 'link-100');">d</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 class="py-op">)</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt id="link-282" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-282', 'd', 'link-100');">d</a></tt><tt class="py-op">.</tt><tt id="link-283" class="py-name" targets="Method Bio.GenBank.NCBIDictionary.update()=Bio.GenBank.NCBIDictionary-class.html#update,Method Bio.Index._InMemoryIndex.update()=Bio.Index._InMemoryIndex-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.InputLayer-class.html#update,Method Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update()=Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer-class.html#update,Method Bio.Prosite.ExPASyDictionary.update()=Bio.Prosite.ExPASyDictionary-class.html#update,Method Bio.Prosite.Prodoc.ExPASyDictionary.update()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#update,Method Bio.PubMed.Dictionary.update()=Bio.PubMed.Dictionary-class.html#update,Method Bio.Restriction._Update.Update.RebaseUpdate.update()=Bio.Restriction._Update.Update.RebaseUpdate-class.html#update,Method Bio.SwissProt.SProt.ExPASyDictionary.update()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#update"><a title="Bio.GenBank.NCBIDictionary.update
Bio.Index._InMemoryIndex.update
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.update
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.update
Bio.Prosite.ExPASyDictionary.update
Bio.Prosite.Prodoc.ExPASyDictionary.update
Bio.PubMed.Dictionary.update
Bio.Restriction._Update.Update.RebaseUpdate.update
Bio.SwissProt.SProt.ExPASyDictionary.update" class="py-name" href="#" onclick="return doclink('link-283', 'update', 'link-283');">update</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-284" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-284', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-285" class="py-name" targets="Method Bio.GFF.FeatureAggregate.map()=Bio.GFF.FeatureAggregate-class.html#map"><a title="Bio.GFF.FeatureAggregate.map" class="py-name" href="#" onclick="return doclink('link-285', 'map', 'link-285');">map</a></tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">c</tt><tt class="py-op">:</tt> <tt id="link-286" class="py-name"><a title="Bio.EUtils.setup.d" class="py-name" href="#" onclick="return doclink('link-286', 'd', 'link-100');">d</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-name">self</tt><tt class="py-op">.</tt><tt id="link-287" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-287', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-288" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-288', 'data', 'link-13');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">.</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-string">'c'</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-289" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-289', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.reverse_complement"></a><div id="MutableSeq.reverse_complement-def"><a name="L371"></a><tt class="py-lineno">371</tt> <a class="py-toggle" href="#" id="MutableSeq.reverse_complement-toggle" onclick="return toggle('MutableSeq.reverse_complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#reverse_complement">reverse_complement</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="MutableSeq.reverse_complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.reverse_complement-expanded"><a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-docstring">"""Modify the MutableSequence to take on its reverse complement.</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-docstring"> No return value"""</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</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-290" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-290', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-291" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-291', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-292" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-292', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins do not have complements!"</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-293" class="py-name"><a title="Bio.Seq.MutableSeq.complement
Bio.Seq.Seq.complement" class="py-name" href="#" onclick="return doclink('link-293', 'complement', 'link-120');">complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-294" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-294', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-295" class="py-name"><a title="Bio.GFF.easy.Location.reverse
Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse
Bio.SeqUtils.reverse" class="py-name" href="#" onclick="return doclink('link-295', 'reverse', 'link-256');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-comment">## Sorting a sequence makes no sense.</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># def sort(self, *args): self.data.sort(*args)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="MutableSeq.extend"></a><div id="MutableSeq.extend-def"><a name="L383"></a><tt class="py-lineno">383</tt> <a class="py-toggle" href="#" id="MutableSeq.extend-toggle" onclick="return toggle('MutableSeq.extend');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#extend">extend</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">other</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="MutableSeq.extend-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.extend-expanded"><a name="L384"></a><tt class="py-lineno">384</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">other</tt><tt class="py-op">,</tt> <tt id="link-296" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-296', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</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">other</tt><tt class="py-op">.</tt><tt id="link-297" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-297', 'data', 'link-13');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-298" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-298', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-299" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-299', 'append', 'link-215');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-name">other</tt><tt class="py-op">:</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-300" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-300', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt id="link-301" 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-301', 'append', 'link-215');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">c</tt><tt class="py-op">)</tt> </tt>
</div><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.tostring"></a><div id="MutableSeq.tostring-def"><a name="L391"></a><tt class="py-lineno">391</tt> <a class="py-toggle" href="#" id="MutableSeq.tostring-toggle" onclick="return toggle('MutableSeq.tostring');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#tostring">tostring</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="MutableSeq.tostring-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.tostring-expanded"><a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the full sequence as a python string.</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> Although not formally deprecated, you are now encouraged to use</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> str(my_seq) instead of my_seq.tostring()."""</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-302" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-302', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> </tt>
<a name="MutableSeq.toseq"></a><div id="MutableSeq.toseq-def"><a name="L398"></a><tt class="py-lineno">398</tt> <a class="py-toggle" href="#" id="MutableSeq.toseq-toggle" onclick="return toggle('MutableSeq.toseq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq.MutableSeq-class.html#toseq">toseq</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="MutableSeq.toseq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="MutableSeq.toseq-expanded"><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the full sequence as a new immutable Seq object"""</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-303" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-303', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-304" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-304', 'data', 'link-13');">data</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-305" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-305', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-comment"># The transcribe, backward_transcribe, and translate functions are</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># user-friendly versions of the corresponding functions in Bio.Transcribe</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># and Bio.Translate. The functions work both on Seq objects, and on strings.</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="transcribe"></a><div id="transcribe-def"><a name="L407"></a><tt class="py-lineno">407</tt> <a class="py-toggle" href="#" id="transcribe-toggle" onclick="return toggle('transcribe');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq-module.html#transcribe">transcribe</a><tt class="py-op">(</tt><tt class="py-param">dna</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="transcribe-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="transcribe-expanded"><a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-docstring">"""Transcribes a DNA sequence into RNA.</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"> If given a string, returns a new string object.</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-docstring"> Given a Seq or MutableSeq, returns a new Seq object with the same alphabet.</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</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">dna</tt><tt class="py-op">,</tt> <tt id="link-306" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-306', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">,</tt> <tt id="link-307" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-307', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</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">dna</tt><tt class="py-op">.</tt><tt id="link-308" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-308', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-309" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-309', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-310" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-310', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins cannot be transcribed!"</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Raise an error if already is RNA alphabet?</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">rna</tt> <tt class="py-op">=</tt> <tt class="py-name">dna</tt><tt class="py-op">.</tt><tt id="link-311" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-311', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'T'</tt><tt class="py-op">,</tt><tt class="py-string">'U'</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'t'</tt><tt class="py-op">,</tt><tt class="py-string">'u'</tt><tt class="py-op">)</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">dna</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-312', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-313" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-313', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-314" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-314', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt id="link-315" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-315', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-316" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-316', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-317" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_rna" class="py-name" href="#" onclick="return doclink('link-317', 'unambiguous_rna', 'link-271');">unambiguous_rna</a></tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">dna</tt><tt class="py-op">.</tt><tt id="link-318" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-318', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-319" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-319', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-320" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-320', 'ambiguous_dna', 'link-262');">ambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt id="link-321" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-321', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-322" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-322', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-323" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_rna" class="py-name" href="#" onclick="return doclink('link-323', 'ambiguous_rna', 'link-269');">ambiguous_rna</a></tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt id="link-324" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-324', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-325" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-325', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-326" class="py-name" targets="Variable Bio.Alphabet.generic_rna=Bio.Alphabet-module.html#generic_rna"><a title="Bio.Alphabet.generic_rna" class="py-name" href="#" onclick="return doclink('link-326', 'generic_rna', 'link-326');">generic_rna</a></tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-327" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-327', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">rna</tt><tt class="py-op">,</tt> <tt id="link-328" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-328', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">rna</tt> <tt class="py-op">=</tt> <tt class="py-name">dna</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 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="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rna</tt> </tt>
</div><a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="back_transcribe"></a><div id="back_transcribe-def"><a name="L430"></a><tt class="py-lineno">430</tt> <a class="py-toggle" href="#" id="back_transcribe-toggle" onclick="return toggle('back_transcribe');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq-module.html#back_transcribe">back_transcribe</a><tt class="py-op">(</tt><tt class="py-param">rna</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="back_transcribe-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="back_transcribe-expanded"><a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-docstring">"""Back-transcribes an RNA sequence into DNA.</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-docstring"> If given a string, returns a new string object.</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"><tt class="py-docstring"> Given a Seq or MutableSeq, returns a new Seq object with the same alphabet.</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">rna</tt><tt class="py-op">,</tt> <tt id="link-329" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-329', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">rna</tt><tt class="py-op">,</tt> <tt id="link-330" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-330', 'MutableSeq', 'link-69');">MutableSeq</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-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">rna</tt><tt class="py-op">.</tt><tt id="link-331" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-331', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <tt id="link-332" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-332', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-333" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-333', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins cannot be (back)transcribed!"</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Raise an error if already is DNA alphabet?</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt class="py-name">rna</tt><tt class="py-op">.</tt><tt id="link-334" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-334', 'data', 'link-13');">data</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'U'</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-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'u'</tt><tt class="py-op">,</tt><tt class="py-string">'t'</tt><tt class="py-op">)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rna</tt><tt class="py-op">.</tt><tt id="link-335" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-335', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-336" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-336', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-337" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_rna" class="py-name" href="#" onclick="return doclink('link-337', 'unambiguous_rna', 'link-271');">unambiguous_rna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt id="link-338" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-338', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-339" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-339', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-340" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-340', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">rna</tt><tt class="py-op">.</tt><tt id="link-341" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-341', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-342" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-342', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-343" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_rna" class="py-name" href="#" onclick="return doclink('link-343', 'ambiguous_rna', 'link-269');">ambiguous_rna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt id="link-344" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-344', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-345" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-345', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-346" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-346', 'ambiguous_dna', 'link-262');">ambiguous_dna</a></tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt id="link-347" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-347', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-348" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-348', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-349" class="py-name" targets="Variable Bio.Alphabet.generic_dna=Bio.Alphabet-module.html#generic_dna"><a title="Bio.Alphabet.generic_dna" class="py-name" href="#" onclick="return doclink('link-349', 'generic_dna', 'link-349');">generic_dna</a></tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-350" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-350', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">dna</tt><tt class="py-op">,</tt> <tt id="link-351" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-351', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">dna</tt> <tt class="py-op">=</tt> <tt class="py-name">rna</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'U'</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-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">'u'</tt><tt class="py-op">,</tt><tt class="py-string">'t'</tt><tt class="py-op">)</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">dna</tt> </tt>
</div><a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> </tt>
<a name="translate"></a><div id="translate-def"><a name="L453"></a><tt class="py-lineno">453</tt> <a class="py-toggle" href="#" id="translate-toggle" onclick="return toggle('translate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq-module.html#translate">translate</a><tt class="py-op">(</tt><tt class="py-param">sequence</tt><tt class="py-op">,</tt> <tt class="py-param">table</tt> <tt class="py-op">=</tt> <tt class="py-string">"Standard"</tt><tt class="py-op">,</tt> <tt class="py-param">stop_symbol</tt> <tt class="py-op">=</tt> <tt class="py-string">"*"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="translate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="translate-expanded"><a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-docstring">"""Translate a nucleotide sequence into amino acids.</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"><tt class="py-docstring"> If given a string, returns a new string object.</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"> Given a Seq or MutableSeq, returns a Seq object.</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> table - Which codon table to use? This can be either a name</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> (string) or an identifier (integer)</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"><tt class="py-docstring"> NOTE - Does NOT support ambiguous nucleotide sequences which</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"><tt class="py-docstring"> could code for a stop codon. This will throw a TranslationError.</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"><tt class="py-docstring"> NOTE - Does NOT support gapped sequences.</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"><tt class="py-docstring"> It will however translate either DNA or RNA."""</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt id="link-352" 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-352', 'id', 'link-352');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt id="link-353" 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-353', 'table', 'link-353');">table</a></tt><tt class="py-op">)</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt id="link-354" 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-354', 'id', 'link-352');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-355" class="py-name" targets="Method Bio.AlignAce.Parser.AlignAceConsumer.sequence()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#sequence,Variable Bio.Emboss.primer3_format.sequence=Bio.Emboss.primer3_format-module.html#sequence,Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.IntelliGenetics._RecordConsumer.sequence()=Bio.IntelliGenetics._RecordConsumer-class.html#sequence,Method Bio.Rebase._RecordConsumer.sequence()=Bio.Rebase._RecordConsumer-class.html#sequence,Function Bio.Std.sequence()=Bio.Std-module.html#sequence,Module Bio.builders.SeqRecord.sequence=Bio.builders.SeqRecord.sequence-module.html,Variable Bio.expressions.fasta.sequence=Bio.expressions.fasta-module.html#sequence,Variable Bio.expressions.genbank.sequence=Bio.expressions.genbank-module.html#sequence,Variable Bio.expressions.swissprot.sprot38.sequence=Bio.expressions.swissprot.sprot38-module.html#sequence,Module Bio.formatdefs.sequence=Bio.formatdefs.sequence-module.html,Variable Bio.formatdefs.sequence.sequence=Bio.formatdefs.sequence-module.html#sequence,Variable Martel.test.test_swissprot38.sequence=Martel.test.test_swissprot38-module.html#sequence,Variable Martel.test.testformats.swissprot38.sequence=Martel.test.testformats.swissprot38-module.html#sequence"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-355', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-356" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-356', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-357" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-357', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-358" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-358', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-359" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-359', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-360" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-360', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">,</tt> <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-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-362" class="py-name"><a title="Bio.Alphabet.ProteinAlphabet" class="py-name" href="#" onclick="return doclink('link-362', 'ProteinAlphabet', 'link-96');">ProteinAlphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">,</tt> <tt class="py-string">"Proteins cannot be translated!"</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-363" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-363', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-364" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-364', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-365" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-365', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-366" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-366', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-367" 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-367', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt id="link-368" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-368', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-369" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-369', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-370" 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-370', 'unambiguous_dna_by_name', 'link-370');">unambiguous_dna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-371" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-371', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt id="link-372" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-372', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-373" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-373', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-374" 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-374', 'unambiguous_dna_by_id', 'link-374');">unambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-375" 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-375', 'id', 'link-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-376" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-376', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-377" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-377', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-378" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-378', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_dna" class="py-name" href="#" onclick="return doclink('link-379', 'ambiguous_dna', 'link-262');">ambiguous_dna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-380" 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-380', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt id="link-381" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-381', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-382" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-382', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-383" 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-383', 'ambiguous_dna_by_name', 'link-383');">ambiguous_dna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-384" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-384', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt id="link-385" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-385', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-386" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-386', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-387" 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-387', 'ambiguous_dna_by_id', 'link-387');">ambiguous_dna_by_id</a></tt><tt class="py-op">[</tt><tt id="link-388" 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-388', 'id', 'link-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-389" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-389', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-390" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-390', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-391" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-391', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-392" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_rna" class="py-name" href="#" onclick="return doclink('link-392', 'unambiguous_rna', 'link-271');">unambiguous_rna</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-keyword">if</tt> <tt id="link-393" 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-393', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt id="link-394" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-394', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-395" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-395', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-396" 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-396', 'unambiguous_rna_by_name', 'link-396');">unambiguous_rna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-397" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-397', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> <tt id="link-398" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-398', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-399" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-399', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-400" 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-400', 'unambiguous_rna_by_id', 'link-400');">unambiguous_rna_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-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-402" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-402', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-403" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-403', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">==</tt><tt id="link-404" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-404', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-405" class="py-name"><a title="Bio.Alphabet.IUPAC.ambiguous_rna" class="py-name" href="#" onclick="return doclink('link-405', 'ambiguous_rna', 'link-269');">ambiguous_rna</a></tt><tt class="py-op">:</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-406" 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-406', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt id="link-407" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-407', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-408" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-408', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-409" 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-409', 'ambiguous_rna_by_name', 'link-409');">ambiguous_rna_by_name</a></tt><tt class="py-op">[</tt><tt id="link-410" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-410', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt id="link-411" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-411', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-412" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-412', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-413" 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-413', 'ambiguous_rna_by_id', 'link-413');">ambiguous_rna_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-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-415" 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-415', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"> <tt id="link-416" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-416', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-417" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-417', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-418" 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-418', 'ambiguous_generic_by_name', 'link-418');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt id="link-419" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-419', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt id="link-420" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-420', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-421" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-421', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-422" 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-422', 'ambiguous_generic_by_id', 'link-422');">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-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt id="link-424" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-424', 'sequence', 'link-355');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-425" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-425', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-426" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-426', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</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 id="link-427" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-427', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt id="link-428" 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-428', 'get', 'link-428');">get</a></tt> <tt class="py-op">=</tt> <tt id="link-429" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-429', 'table', 'link-353');">table</a></tt><tt class="py-op">.</tt><tt id="link-430" 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-430', 'forward_table', 'link-430');">forward_table</a></tt><tt class="py-op">.</tt><tt id="link-431" 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-431', 'get', 'link-428');">get</a></tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt id="link-432" 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-432', 'protein', 'link-432');">protein</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-433" 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-433', 'get', 'link-428');">get</a></tt><tt class="py-op">(</tt><tt id="link-434" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-434', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-435" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-435', 'i', 'link-218');">i</a></tt><tt class="py-op">:</tt><tt id="link-436" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-436', 'i', 'link-218');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">stop_symbol</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-437" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-437', 'i', 'link-218');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-438" class="py-name" targets="Method Bio.GFF.Feature.xrange()=Bio.GFF.Feature-class.html#xrange"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-438', 'xrange', 'link-438');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">n</tt><tt class="py-op">%</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt id="link-439" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-439', 'protein', 'link-432');">protein</a></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-440" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-440', 'protein', 'link-432');">protein</a></tt><tt class="py-op">)</tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">stop_symbol</tt> <tt class="py-keyword">in</tt> <tt id="link-441" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-441', 'protein', 'link-432');">protein</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt id="link-442" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-442', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-443" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-443', 'Alphabet', 'link-0');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-444" class="py-name" targets="Class Bio.Alphabet.HasStopCodon=Bio.Alphabet.HasStopCodon-class.html"><a title="Bio.Alphabet.HasStopCodon" class="py-name" href="#" onclick="return doclink('link-444', 'HasStopCodon', 'link-444');">HasStopCodon</a></tt><tt class="py-op">(</tt><tt id="link-445" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-445', 'table', 'link-353');">table</a></tt><tt class="py-op">.</tt><tt id="link-446" 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-446', 'protein_alphabet', 'link-446');">protein_alphabet</a></tt><tt class="py-op">,</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">stop_symbol</tt> <tt class="py-op">=</tt> <tt class="py-name">stop_symbol</tt><tt class="py-op">)</tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt id="link-447" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-447', 'alphabet', 'link-20');">alphabet</a></tt> <tt class="py-op">=</tt> <tt id="link-448" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-448', 'table', 'link-353');">table</a></tt><tt class="py-op">.</tt><tt id="link-449" 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-449', 'protein_alphabet', 'link-446');">protein_alphabet</a></tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-450" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-450', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-451" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-451', 'protein', 'link-432');">protein</a></tt><tt class="py-op">,</tt> <tt id="link-452" class="py-name"><a title="Bio.Prosite.Pattern.Prosite.alphabet
Bio.Std.alphabet" class="py-name" href="#" onclick="return doclink('link-452', 'alphabet', 'link-20');">alphabet</a></tt><tt class="py-op">)</tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-453" 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-453', 'id', 'link-352');">id</a></tt><tt class="py-op">==</tt><tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"> <tt id="link-454" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-454', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-455" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-455', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-456" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_name" class="py-name" href="#" onclick="return doclink('link-456', 'ambiguous_generic_by_name', 'link-418');">ambiguous_generic_by_name</a></tt><tt class="py-op">[</tt><tt id="link-457" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-457', 'table', 'link-353');">table</a></tt><tt class="py-op">]</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"> <tt id="link-458" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-458', 'table', 'link-353');">table</a></tt> <tt class="py-op">=</tt> <tt id="link-459" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-459', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-460" class="py-name"><a title="Bio.Data.CodonTable.ambiguous_generic_by_id" class="py-name" href="#" onclick="return doclink('link-460', 'ambiguous_generic_by_id', 'link-422');">ambiguous_generic_by_id</a></tt><tt class="py-op">[</tt><tt id="link-461" 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-461', 'id', 'link-352');">id</a></tt><tt class="py-op">]</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"> <tt id="link-462" 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-462', 'get', 'link-428');">get</a></tt> <tt class="py-op">=</tt> <tt id="link-463" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-463', 'table', 'link-353');">table</a></tt><tt class="py-op">.</tt><tt id="link-464" class="py-name"><a title="Bio.Data.CodonTable.CodonTable.forward_table" class="py-name" href="#" onclick="return doclink('link-464', 'forward_table', 'link-430');">forward_table</a></tt><tt class="py-op">.</tt><tt id="link-465" 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-465', 'get', 'link-428');">get</a></tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"> <tt id="link-466" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-466', 'sequence', 'link-355');">sequence</a></tt> <tt class="py-op">=</tt> <tt id="link-467" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-467', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt class="py-name">upper</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</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 id="link-468" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-468', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">)</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"> <tt id="link-469" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-469', 'protein', 'link-432');">protein</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt id="link-470" 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-470', 'get', 'link-428');">get</a></tt><tt class="py-op">(</tt><tt id="link-471" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-471', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">[</tt><tt id="link-472" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-472', 'i', 'link-218');">i</a></tt><tt class="py-op">:</tt><tt id="link-473" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-473', 'i', 'link-218');">i</a></tt><tt class="py-op">+</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">stop_symbol</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt id="link-474" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-474', 'i', 'link-218');">i</a></tt> <tt class="py-keyword">in</tt> <tt id="link-475" class="py-name"><a title="Bio.GFF.Feature.xrange" class="py-name" href="#" onclick="return doclink('link-475', 'xrange', 'link-438');">xrange</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">n</tt><tt class="py-op">-</tt><tt class="py-name">n</tt><tt class="py-op">%</tt><tt class="py-number">3</tt><tt class="py-op">,</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"> <tt id="link-476" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-476', 'protein', 'link-432');">protein</a></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-477" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-477', 'protein', 'link-432');">protein</a></tt><tt class="py-op">)</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-478" class="py-name"><a title="Bio.Alphabet.IUPAC.protein" class="py-name" href="#" onclick="return doclink('link-478', 'protein', 'link-432');">protein</a></tt> </tt>
</div><a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"> </tt>
<a name="reverse_complement"></a><div id="reverse_complement-def"><a name="L524"></a><tt class="py-lineno">524</tt> <a class="py-toggle" href="#" id="reverse_complement-toggle" onclick="return toggle('reverse_complement');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Seq-module.html#reverse_complement">reverse_complement</a><tt class="py-op">(</tt><tt class="py-param">sequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="reverse_complement-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="reverse_complement-expanded"><a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the reverse complement sequence of a nucleotide string.</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"><tt class="py-docstring"> If given a string, returns a new string object.</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"><tt class="py-docstring"> Given a Seq or a MutableSeq, returns a new Seq object with the same alphabet.</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"><tt class="py-docstring"> Supports unambiguous nucleotide sequences</tt> </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-479" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-479', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-480" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-480', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-comment">#Return a Seq</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-481" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-481', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-482" class="py-name" targets="Method Bio.Seq.MutableSeq.reverse_complement()=Bio.Seq.MutableSeq-class.html#reverse_complement,Method Bio.Seq.Seq.reverse_complement()=Bio.Seq.Seq-class.html#reverse_complement,Function Bio.Seq.reverse_complement()=Bio.Seq-module.html#reverse_complement"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-482', 'reverse_complement', 'link-482');">reverse_complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-483" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-483', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">,</tt> <tt id="link-484" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-484', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-comment">#Return a Seq</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">#Don't use the MutableSeq reverse_complement method as it is 'in place'.</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-485" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-485', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">.</tt><tt id="link-486" class="py-name"><a title="Bio.Seq.MutableSeq.toseq" class="py-name" href="#" onclick="return doclink('link-486', 'toseq', 'link-245');">toseq</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-487" class="py-name"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-487', 'reverse_complement', 'link-482');">reverse_complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-comment">#Assume its a string, turn it into a Seq,</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#do the reverse complement, and turn this back to a string</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#TODO - Find a more efficient way to do this without code duplication?</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-488" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-488', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-489" class="py-name"><a title="Bio.AlignAce.Parser.AlignAceConsumer.sequence
Bio.Emboss.primer3_format.sequence
Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.IntelliGenetics._RecordConsumer.sequence
Bio.Rebase._RecordConsumer.sequence
Bio.Std.sequence
Bio.builders.SeqRecord.sequence
Bio.expressions.fasta.sequence
Bio.expressions.genbank.sequence
Bio.expressions.swissprot.sprot38.sequence
Bio.formatdefs.sequence
Bio.formatdefs.sequence.sequence
Martel.test.test_swissprot38.sequence
Martel.test.testformats.swissprot38.sequence" class="py-name" href="#" onclick="return doclink('link-489', 'sequence', 'link-355');">sequence</a></tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-490" class="py-name"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-490', 'reverse_complement', 'link-482');">reverse_complement</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-491" class="py-name"><a title="Bio.Crystal.Crystal.tostring
Bio.EUtils.POM.ElementNode.tostring
Bio.Prosite.Pattern.Prosite.tostring
Bio.Seq.MutableSeq.tostring
Bio.Seq.Seq.tostring
BioSQL.BioSeq.DBSeq.tostring" class="py-name" href="#" onclick="return doclink('link-491', 'tostring', 'link-73');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt> <tt class="py-op">:</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Quick self test"</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-492" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-492', 'Bio', 'link-7');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-493" class="py-name"><a title="Bio.Data" class="py-name" href="#" onclick="return doclink('link-493', 'Data', 'link-3');">Data</a></tt><tt class="py-op">.</tt><tt id="link-494" class="py-name"><a title="Bio.Data.IUPACData" class="py-name" href="#" onclick="return doclink('link-494', 'IUPACData', 'link-4');">IUPACData</a></tt> <tt class="py-keyword">import</tt> <tt id="link-495" 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-495', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">,</tt> <tt id="link-496" 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-496', 'ambiguous_rna_values', 'link-496');">ambiguous_rna_values</a></tt><tt class="py-comment">#</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-497" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-497', 'Bio', 'link-7');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-498" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-498', 'Alphabet', 'link-0');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-499" class="py-name"><a title="Bio.Alphabet.generic_dna" class="py-name" href="#" onclick="return doclink('link-499', 'generic_dna', 'link-349');">generic_dna</a></tt><tt class="py-op">,</tt> <tt id="link-500" class="py-name"><a title="Bio.Alphabet.generic_rna" class="py-name" href="#" onclick="return doclink('link-500', 'generic_rna', 'link-326');">generic_rna</a></tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">sets</tt> <tt class="py-keyword">import</tt> <tt class="py-name">Set</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-501" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-501', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">ambig_char</tt><tt class="py-op">,</tt> <tt id="link-502" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-502', 'values', 'link-93');">values</a></tt> <tt class="py-keyword">in</tt> <tt id="link-503" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-503', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_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="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-name">compl_values</tt> <tt class="py-op">=</tt> <tt id="link-504" class="py-name"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-504', 'reverse_complement', 'link-482');">reverse_complement</a></tt><tt class="py-op">(</tt><tt id="link-505" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-505', 'values', 'link-93');">values</a></tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s={%s} --> {%s}=%s"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">ambig_char</tt><tt class="py-op">,</tt> <tt id="link-506" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-506', 'values', 'link-93');">values</a></tt><tt class="py-op">,</tt> <tt class="py-name">compl_values</tt><tt class="py-op">,</tt> <tt id="link-507" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-507', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt><tt class="py-op">[</tt><tt class="py-name">ambig_char</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">compl_values</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt id="link-508" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-508', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">[</tt><tt id="link-509" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_complement" class="py-name" href="#" onclick="return doclink('link-509', 'ambiguous_dna_complement', 'link-5');">ambiguous_dna_complement</a></tt><tt class="py-op">[</tt><tt class="py-name">ambig_char</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-510" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-510', 's', 'link-114');">s</a></tt> <tt class="py-keyword">in</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-511" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-511', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></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 id="link-512" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-512', 'Seq', 'link-32');">Seq</a></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-513" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-513', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt id="link-514" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-514', 'Seq', 'link-32');">Seq</a></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-515" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-515', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-516" class="py-name"><a title="Bio.Alphabet.generic_dna" class="py-name" href="#" onclick="return doclink('link-516', 'generic_dna', 'link-349');">generic_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-string">""</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt id="link-517" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_values" class="py-name" href="#" onclick="return doclink('link-517', 'ambiguous_rna_values', 'link-496');">ambiguous_rna_values</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"> <tt id="link-518" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-518', 'Seq', 'link-32');">Seq</a></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-519" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_rna_values" class="py-name" href="#" onclick="return doclink('link-519', 'ambiguous_rna_values', 'link-496');">ambiguous_rna_values</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt id="link-520" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-520', 'Seq', 'link-32');">Seq</a></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-521" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-521', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-522" class="py-name"><a title="Bio.Alphabet.generic_rna" class="py-name" href="#" onclick="return doclink('link-522', 'generic_rna', 'link-326');">generic_rna</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s -> %s [RC]"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-523" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-523', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-524" class="py-name"><a title="Bio.Seq.MutableSeq.reverse_complement
Bio.Seq.Seq.reverse_complement
Bio.Seq.reverse_complement" class="py-name" href="#" onclick="return doclink('link-524', 'reverse_complement', 'link-482');">reverse_complement</a></tt><tt class="py-op">(</tt><tt id="link-525" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-525', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s -> %s [RNA]"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-526" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-526', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-527" class="py-name" targets="Function Bio.Seq.transcribe()=Bio.Seq-module.html#transcribe,Method Bio.Transcribe.Transcribe.transcribe()=Bio.Transcribe.Transcribe-class.html#transcribe,Function Bio.utils.transcribe()=Bio.utils-module.html#transcribe"><a title="Bio.Seq.transcribe
Bio.Transcribe.Transcribe.transcribe
Bio.utils.transcribe" class="py-name" href="#" onclick="return doclink('link-527', 'transcribe', 'link-527');">transcribe</a></tt><tt class="py-op">(</tt><tt id="link-528" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-528', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"%s -> %s [DNA]"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-529" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-529', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-530" class="py-name" targets="Function Bio.Seq.back_transcribe()=Bio.Seq-module.html#back_transcribe,Method Bio.Transcribe.Transcribe.back_transcribe()=Bio.Transcribe.Transcribe-class.html#back_transcribe,Function Bio.utils.back_transcribe()=Bio.utils-module.html#back_transcribe"><a title="Bio.Seq.back_transcribe
Bio.Transcribe.Transcribe.back_transcribe
Bio.utils.back_transcribe" class="py-name" href="#" onclick="return doclink('link-530', 'back_transcribe', 'link-530');">back_transcribe</a></tt><tt class="py-op">(</tt><tt id="link-531" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-531', 's', 'link-114');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<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">#Quick check of the count method</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt class="py-name">letter</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"ABCDEFGHIjklmnopqrstuvwyz"</tt> <tt class="py-op">:</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt id="link-532" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-532', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">letter</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-533" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-533', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">letter</tt><tt class="py-op">)</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt id="link-534" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-534', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">letter</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-535" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-535', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-name">letter</tt><tt class="py-op">)</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-name">my_str</tt> <tt class="py-op">=</tt> <tt class="py-string">"AAAATGACGGCGGCGGCT"</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">my_obj</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt class="py-name">my_str</tt><tt class="py-op">,</tt> <tt id="link-536" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-536', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-537" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-537', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">5</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-538" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-538', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-539" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-539', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"ATG"</tt><tt class="py-op">)</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">3</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-540" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-540', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-541" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-541', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">my_obj</tt> <tt class="py-keyword">in</tt> <tt class="py-op">[</tt><tt id="link-542" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-542', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-543" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-543', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-544" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-544', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-545" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-545', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">5</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-546" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-546', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-547" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-547', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">3</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-548" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-548', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-549" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-549', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-550" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-550', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-551" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-551', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">1</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-552" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-552', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-553" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-553', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-string">"AT"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">5</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-554" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-554', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-555" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-555', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">3</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-556" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-556', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-557" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-557', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-string">"CG"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-558" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-558', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt id="link-559" class="py-name"><a title="Bio.Seq.MutableSeq" class="py-name" href="#" onclick="return doclink('link-559', 'MutableSeq', 'link-69');">MutableSeq</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">)</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-560" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-560', 'start', 'link-75');">start</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-561" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-561', 'end', 'link-76');">end</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">my_str</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">my_str</tt><tt class="py-op">.</tt><tt id="link-562" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-562', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt><tt id="link-563" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-563', 'start', 'link-75');">start</a></tt><tt class="py-op">,</tt><tt id="link-564" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-564', 'end', 'link-76');">end</a></tt><tt class="py-op">)</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">my_str</tt><tt class="py-op">[</tt><tt id="link-565" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-565', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt id="link-566" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-566', 'end', 'link-76');">end</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-567" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-567', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</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">assert</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">.</tt><tt id="link-568" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-568', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">,</tt><tt id="link-569" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-569', 'start', 'link-75');">start</a></tt><tt class="py-op">,</tt><tt id="link-570" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-570', 'end', 'link-76');">end</a></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">assert</tt> <tt class="py-name">c</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">[</tt><tt id="link-571" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-571', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt id="link-572" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-572', 'end', 'link-76');">end</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-573" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-573', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-comment">#This one is a bit silly:</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">my_str</tt><tt class="py-op">[</tt><tt id="link-574" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-574', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt id="link-575" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-575', 'end', 'link-76');">end</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-576" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-576', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">my_obj</tt><tt class="py-op">[</tt><tt id="link-577" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-577', 'start', 'link-75');">start</a></tt><tt class="py-op">:</tt><tt id="link-578" class="py-name"><a title="Bio.GFF.easy.Location.end
Bio.Prosite.Pattern.PrositeMatch.end
Bio.expressions.blocks.end
Bio.expressions.embl.embl65.end
Bio.expressions.swissprot.sprot38.end
Martel.LAX.LAX.end
Martel.test.test_swissprot38.end
Martel.test.testformats.swissprot38.end" class="py-name" href="#" onclick="return doclink('link-578', 'end', 'link-76');">end</a></tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-579" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-579', 'count', 'link-78');">count</a></tt><tt class="py-op">(</tt><tt class="py-string">"A"</tt><tt class="py-op">)</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-580" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-580', 'translate', 'link-116');">translate</a></tt><tt class="py-op">(</tt><tt id="link-581" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-581', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGT"</tt><tt class="py-op">,</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt id="link-582" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-582', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-583" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-583', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">)</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-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-584" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-584', 'translate', 'link-116');">translate</a></tt><tt class="py-op">(</tt><tt id="link-585" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-585', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG"</tt><tt class="py-op">,</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt id="link-586" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-586', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-587" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-587', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-588" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-588', 'translate', 'link-116');">translate</a></tt><tt class="py-op">(</tt><tt id="link-589" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-589', 'Seq', 'link-32');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-string">"GCTGTTATGGGTCGTTGGAAGGGTGGTCGTGCTGCTGGTTAG"</tt><tt class="py-op">,</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"> <tt id="link-590" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-590', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-591" class="py-name"><a title="Bio.Alphabet.IUPAC.unambiguous_dna" class="py-name" href="#" onclick="return doclink('link-591', 'unambiguous_dna', 'link-264');">unambiguous_dna</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">stop_symbol</tt><tt class="py-op">=</tt><tt class="py-string">"@"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-name">ambig</tt> <tt class="py-op">=</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt id="link-592" class="py-name"><a title="Bio.Alphabet.IUPAC" class="py-name" href="#" onclick="return doclink('link-592', 'IUPAC', 'link-2');">IUPAC</a></tt><tt class="py-op">.</tt><tt id="link-593" 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-593', 'IUPACAmbiguousDNA', 'link-593');">IUPACAmbiguousDNA</a></tt><tt class="py-op">.</tt><tt id="link-594" 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-594', 'letters', 'link-594');">letters</a></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">for</tt> <tt class="py-name">c1</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ambig</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">for</tt> <tt class="py-name">c2</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ambig</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">for</tt> <tt class="py-name">c3</tt> <tt class="py-keyword">in</tt> <tt class="py-name">ambig</tt> <tt class="py-op">:</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt id="link-595" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-595', 'values', 'link-93');">values</a></tt> <tt class="py-op">=</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt id="link-596" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-596', 'translate', 'link-116');">translate</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">+</tt><tt class="py-name">b</tt><tt class="py-op">+</tt><tt class="py-name">c</tt><tt class="py-op">,</tt> <tt id="link-597" class="py-name"><a title="Bio.CDD.cdd_format.table
Bio.expressions.blast.ncbiblast.table" class="py-name" href="#" onclick="return doclink('link-597', 'table', 'link-353');">table</a></tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> \ </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt id="link-598" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-598', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">[</tt><tt class="py-name">c1</tt><tt class="py-op">]</tt> \ </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">b</tt> <tt class="py-keyword">in</tt> <tt id="link-599" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-599', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">[</tt><tt class="py-name">c2</tt><tt class="py-op">]</tt> \ </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-600" class="py-name"><a title="Bio.Data.IUPACData.ambiguous_dna_values" class="py-name" href="#" onclick="return doclink('link-600', 'ambiguous_dna_values', 'link-495');">ambiguous_dna_values</a></tt><tt class="py-op">[</tt><tt class="py-name">c3</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-name">t</tt> <tt class="py-op">=</tt> <tt id="link-601" class="py-name"><a title="Bio.GFF.Feature.translate
Bio.GFF.FeatureAggregate.translate
Bio.Seq.translate
Bio.SeqUtils.translate
Bio.Translate.Translator.translate
Bio.utils.translate" class="py-name" href="#" onclick="return doclink('link-601', 'translate', 'link-116');">translate</a></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 class="py-op">)</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt id="link-602" class="py-name"><a title="Bio.Data.CodonTable
Bio.Data.CodonTable.CodonTable" class="py-name" href="#" onclick="return doclink('link-602', 'CodonTable', 'link-9');">CodonTable</a></tt><tt class="py-op">.</tt><tt id="link-603" 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-603', 'TranslationError', 'link-603');">TranslationError</a></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">assert</tt> <tt class="py-string">"*"</tt> <tt class="py-keyword">in</tt> <tt id="link-604" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-604', 'values', 'link-93');">values</a></tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-string">"*"</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">assert</tt> <tt id="link-605" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-605', 'values', 'link-93');">values</a></tt> <tt class="py-op">==</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"*"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-string">"X"</tt> <tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-606" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-606', 'values', 'link-93');">values</a></tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> \ </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-string">"translate('%s') = '%s' not '%s'"</tt> \ </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-op">%</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 class="py-op">,</tt> <tt class="py-name">t</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-607" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-607', 'values', 'link-93');">values</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-string">"Z"</tt> <tt class="py-op">:</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-608" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-608', 'values', 'link-93');">values</a></tt> <tt class="py-op">==</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-string">"E"</tt><tt class="py-op">,</tt> <tt class="py-string">"Q"</tt><tt class="py-op">)</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">elif</tt> <tt class="py-name">t</tt><tt class="py-op">==</tt><tt class="py-string">"B"</tt> <tt class="py-op">:</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-609" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-609', 'values', 'link-93');">values</a></tt> <tt class="py-op">==</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">"D"</tt><tt class="py-op">,</tt> <tt class="py-string">"N"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-610" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.EUtils.MultiDict._BaseMultiDict.values
Bio.GenBank.NCBIDictionary.values
Bio.Mindy.BaseDB.DictLookup.values
Bio.Prosite.ExPASyDictionary.values
Bio.Prosite.Prodoc.ExPASyDictionary.values
Bio.PubMed.Dictionary.values
Bio.SwissProt.SProt.ExPASyDictionary.values
Bio.config.Registry.Registry.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values
Martel.Parser.MartelAttributeList.values" class="py-name" href="#" onclick="return doclink('link-610', 'values', 'link-93');">values</a></tt> <tt class="py-op">==</tt> <tt class="py-name">Set</tt><tt class="py-op">(</tt><tt class="py-name">t</tt><tt class="py-op">)</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> </tt><script type="text/javascript">
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