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Module ClustalIO
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<h1 class="epydoc">Source Code for <a href="Bio.SeqIO.ClustalIO-module.html">Module Bio.SeqIO.ClustalIO</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 2006, 2007 by Peter Cock. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</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"># license. Please see the LICENSE file that should have been included</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"># as part of this package.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring">"""Bio.SeqIO support for the "clustal" (aka ClustalW) file format.</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">You were expected to use this module via the Bio.SeqIO functions.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">This module has now been replaced by Bio.AlignIO.ClustalIO, and is</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">deprecated."""</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-name">warnings</tt><tt class="py-op">.</tt><tt class="py-name">warn</tt><tt class="py-op">(</tt><tt class="py-string">"Bio.SeqIO.ClustalIO is deprecated. You can continue to read"</tt> \ </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">" and write 'clustal' files with Bio.SeqIO, but this is now"</tt> \ </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-op">+</tt> <tt class="py-string">" handled via Bio.AlignIO internally."</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-name">DeprecationWarning</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-comment">#For reading alignments:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Alphabet=Bio.Alphabet-module.html,Class Bio.Alphabet.Alphabet=Bio.Alphabet.Alphabet-class.html"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-1', 'Alphabet', 'link-1');">Alphabet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Variable Bio.Alphabet.single_letter_alphabet=Bio.Alphabet-module.html#single_letter_alphabet"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-2', 'single_letter_alphabet', 'link-2');">single_letter_alphabet</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-3', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-4" 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-4', 'Seq', 'link-4');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-5', 'Seq', 'link-4');">Seq</a></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-6', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Module Bio.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html,Package Bio.builders.SeqRecord=Bio.builders.SeqRecord-module.html,Package Bio.writers.SeqRecord=Bio.writers.SeqRecord-module.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-7', 'SeqRecord', 'link-7');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-8', 'SeqRecord', 'link-7');">SeqRecord</a></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-comment">#For writing alignments:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-9" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-9', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-10" class="py-name" targets="Package Bio.SeqIO=Bio.SeqIO-module.html"><a title="Bio.SeqIO" class="py-name" href="#" onclick="return doclink('link-10', 'SeqIO', 'link-10');">SeqIO</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Module Bio.AlignIO.Interfaces=Bio.AlignIO.Interfaces-module.html,Module Bio.SeqIO.Interfaces=Bio.SeqIO.Interfaces-module.html"><a title="Bio.AlignIO.Interfaces
Bio.SeqIO.Interfaces" class="py-name" href="#" onclick="return doclink('link-11', 'Interfaces', 'link-11');">Interfaces</a></tt> <tt class="py-keyword">import</tt> <tt id="link-12" class="py-name" targets="Class Bio.SeqIO.Interfaces.SequenceWriter=Bio.SeqIO.Interfaces.SequenceWriter-class.html"><a title="Bio.SeqIO.Interfaces.SequenceWriter" class="py-name" href="#" onclick="return doclink('link-12', 'SequenceWriter', 'link-12');">SequenceWriter</a></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-13" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-13', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Package Bio.Clustalw=Bio.Clustalw-module.html"><a title="Bio.Clustalw" class="py-name" href="#" onclick="return doclink('link-14', 'Clustalw', 'link-14');">Clustalw</a></tt> <tt class="py-keyword">import</tt> <tt id="link-15" class="py-name" targets="Class Bio.Clustalw.ClustalAlignment=Bio.Clustalw.ClustalAlignment-class.html"><a title="Bio.Clustalw.ClustalAlignment" class="py-name" href="#" onclick="return doclink('link-15', 'ClustalAlignment', 'link-15');">ClustalAlignment</a></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment">#This is a generator function!</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">#TODO - Should the default be Gapped(single_letter_alphabet) instead?</tt> </tt>
<a name="ClustalIterator"></a><div id="ClustalIterator-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <a class="py-toggle" href="#" id="ClustalIterator-toggle" onclick="return toggle('ClustalIterator');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.ClustalIO-module.html#ClustalIterator">ClustalIterator</a><tt class="py-op">(</tt><tt class="py-param">handle</tt><tt class="py-op">,</tt> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-16', 'single_letter_alphabet', 'link-2');">single_letter_alphabet</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="ClustalIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ClustalIterator-expanded"><a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> <tt class="py-docstring">"""Reads a Clustalw file returning a SeqRecord object iterator.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> The entire file is loaded at once, but the SeqRecord objects</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> are only created "on request".</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> For more information on the file format, please see:</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> http://www.bioperl.org/wiki/ClustalW_multiple_alignment_format</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"> You might like to look at Bio.Clustalw which has an interface</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> to the command line tool clustalw, and can also clustal alignment</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> files into Bio.Clustalw.ClustalAlignment objects.</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> We call this the "clustal" format which is consistent with EMBOSS.</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> Sadly BioPerl calls it the "clustalw" format, so we can't match</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> them both.</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Variable Bio.LocusLink.web_parse.handle=Bio.LocusLink.web_parse-module.html#handle,Variable Bio.Ndb.handle=Bio.Ndb-module.html#handle"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-17', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.readline()=Bio.EUtils.ReseekFile.ReseekFile-class.html#readline,Method Bio.File.SGMLHandle.readline()=Bio.File.SGMLHandle-class.html#readline,Method Bio.File.UndoHandle.readline()=Bio.File.UndoHandle-class.html#readline,Method Bio.SGMLExtractor.SGMLExtractorHandle.readline()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#readline"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-18', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> <tt class="py-keyword">return</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">7</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">'CLUSTAL'</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</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">"Did not find CLUSTAL header"</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-comment">#There should be two blank lines after the header line</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-19', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-20', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Class Bio.EUtils.DTDs.LinkOut.strip=Bio.EUtils.DTDs.LinkOut.strip-class.html,Method Bio.File.SGMLStripper.strip()=Bio.File.SGMLStripper-class.html#strip,Method Bio.SGMLExtractor.SGMLExtractor.strip()=Bio.SGMLExtractor.SGMLExtractor-class.html#strip"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-21', 'strip', 'link-21');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-op">:</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-22', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-23', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-comment">#If the alignment contains entries with the same sequence</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">#identifier (not a good idea - but seems possible), then this</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">#dictionary based parser will merge their sequences. Fix this?</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-24" class="py-name" targets="Variable Bio.expressions.fasta.ids=Bio.expressions.fasta-module.html#ids"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-24', 'ids', 'link-24');">ids</a></tt> <tt class="py-op">=</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-name">seqs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-comment">#Use the first block to get the sequence identifiers</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-25', 'strip', 'link-21');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op"><></tt> <tt class="py-string">""</tt> <tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><></tt> <tt class="py-string">" "</tt> <tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-comment">#Sequences identifier...</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Nexus.Trees.Tree.split()=Bio.Nexus.Trees.Tree-class.html#split,Method Bio.Restriction.Restriction.RestrictionBatch.split()=Bio.Restriction.Restriction.RestrictionBatch-class.html#split"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-26', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-comment">#We expect there to be two fields, there can be an optional</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#"sequence number" field containing the letter count.</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">2</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">3</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">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Could not parse line:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt id="link-27" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-27', 'ids', 'link-24');">ids</a></tt><tt class="py-op">.</tt><tt id="link-28" 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-28', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">seqs</tt><tt class="py-op">.</tt><tt id="link-29" 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-29', 'append', 'link-28');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</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">fields</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt> <tt class="py-op">:</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment">#This MAY be an old style file with a letter count...</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt id="link-30" 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-30', 'letters', 'link-30');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</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">"Could not parse line, bad sequence number:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</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">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op"><></tt> <tt id="link-31" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-31', 'letters', 'link-30');">letters</a></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">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Could not parse line, invalid sequence number:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">else</tt> <tt class="py-op">:</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-comment">#Sequence consensus line...</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">pass</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-32', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-33', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> <tt class="py-keyword">break</tt> <tt class="py-comment">#end of file</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-34', 'strip', 'link-21');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment">#Loop over any remaining blocks...</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-35" class="py-name" targets="Variable Bio.EUtils.POM.True=Bio.EUtils.POM-module.html#True"><a title="Bio.EUtils.POM.True" class="py-name" href="#" onclick="return doclink('link-35', 'True', 'link-35');">True</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-comment">#There should be a blank line between each block.</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Also want to ignore any consensus line from the</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#previous block.</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-op">(</tt><tt class="py-keyword">not</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.EUtils.DTDs.LinkOut.strip
Bio.File.SGMLStripper.strip
Bio.SGMLExtractor.SGMLExtractor.strip" class="py-name" href="#" onclick="return doclink('link-36', 'strip', 'link-21');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-string">""</tt> <tt class="py-keyword">or</tt> <tt class="py-name">line</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">==</tt><tt class="py-string">" "</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-37" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-37', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-38', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> <tt class="py-keyword">break</tt> <tt class="py-comment"># end of file</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">line</tt> <tt class="py-op">:</tt> <tt class="py-keyword">break</tt> <tt class="py-comment"># end of file</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-39" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-39', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-40', 'ids', 'link-24');">ids</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">fields</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt class="py-name">rstrip</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt id="link-41" class="py-name"><a title="Bio.Nexus.Trees.Tree.split
Bio.Restriction.Restriction.RestrictionBatch.split" class="py-name" href="#" onclick="return doclink('link-41', 'split', 'link-26');">split</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-comment">#We expect there to be two fields, there can be an optional</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#"sequence number" field containing the letter count.</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">2</tt> <tt class="py-keyword">or</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">3</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Could not parse line:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op"><></tt> <tt id="link-42" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-42', 'ids', 'link-24');">ids</a></tt><tt class="py-op">[</tt><tt id="link-43" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-43', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</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">"Identifiers out of order? Got '%s' but expected '%s'"</tt> \ </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-44', 'ids', 'link-24');">ids</a></tt><tt class="py-op">[</tt><tt id="link-45" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-45', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-comment">#Append the sequence</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-46" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-46', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</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">fields</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</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">#This MAY be an old style file with a letter count...</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt> <tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt id="link-47" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-47', 'letters', 'link-30');">letters</a></tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">fields</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt> <tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</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">"Could not parse line, bad sequence number:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</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">seqs</tt><tt class="py-op">[</tt><tt id="link-48" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-48', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">,</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-op"><></tt> <tt id="link-49" class="py-name"><a title="Bio.Alphabet.Alphabet.letters
Bio.Alphabet.IUPAC.ExtendedIUPACDNA.letters
Bio.Alphabet.IUPAC.ExtendedIUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACAmbiguousRNA.letters
Bio.Alphabet.IUPAC.IUPACProtein.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousDNA.letters
Bio.Alphabet.IUPAC.IUPACUnambiguousRNA.letters
Bio.Alphabet.Reduced.HPModel.letters
Bio.Alphabet.Reduced.Murphy10.letters
Bio.Alphabet.Reduced.Murphy15.letters
Bio.Alphabet.Reduced.Murphy4.letters
Bio.Alphabet.Reduced.Murphy8.letters
Bio.Alphabet.Reduced.PC5.letters
Bio.Alphabet.SecondaryStructure.letters
Bio.Alphabet.SingleLetterAlphabet.letters
Bio.Alphabet.ThreeLetterProtein.letters
Bio.NeuralNetwork.Gene.Schema.SchemaDNAAlphabet.letters
Bio.SeqUtils.ProteinX.letters" class="py-name" href="#" onclick="return doclink('link-49', 'letters', 'link-30');">letters</a></tt> <tt class="py-op">:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</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">"Could not parse line, invalid sequence number:\n%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">line</tt><tt class="py-op">)</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">#Read in the next line</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-50', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.readline
Bio.File.SGMLHandle.readline
Bio.File.UndoHandle.readline
Bio.SGMLExtractor.SGMLExtractorHandle.readline" class="py-name" href="#" onclick="return doclink('link-51', 'readline', 'link-18');">readline</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="L130"></a><tt class="py-lineno">130</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-52" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-52', 'ids', 'link-24');">ids</a></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">seqs</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-name">alignment_length</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-53" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-53', 'i', 'link-39');">i</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-54" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-54', 'ids', 'link-24');">ids</a></tt><tt class="py-op">)</tt><tt class="py-op">)</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">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-55" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-55', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op"><></tt> <tt class="py-name">alignment_length</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</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">"Error parsing alignment - sequences of different length?"</tt><tt class="py-op">)</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt id="link-56" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.builders.SeqRecord
Bio.writers.SeqRecord" class="py-name" href="#" onclick="return doclink('link-56', 'SeqRecord', 'link-7');">SeqRecord</a></tt><tt class="py-op">(</tt><tt id="link-57" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq
Martel.Expression.Seq
Martel.Seq" class="py-name" href="#" onclick="return doclink('link-57', 'Seq', 'link-4');">Seq</a></tt><tt class="py-op">(</tt><tt class="py-name">seqs</tt><tt class="py-op">[</tt><tt id="link-58" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-58', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-59" 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-59', 'alphabet', 'link-59');">alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-60" 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-60', 'id', 'link-60');">id</a></tt><tt class="py-op">=</tt><tt id="link-61" class="py-name"><a title="Bio.expressions.fasta.ids" class="py-name" href="#" onclick="return doclink('link-61', 'ids', 'link-24');">ids</a></tt><tt class="py-op">[</tt><tt id="link-62" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-62', 'i', 'link-39');">i</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="ClustalWriter"></a><div id="ClustalWriter-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="ClustalWriter-toggle" onclick="return toggle('ClustalWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.SeqIO.ClustalIO.ClustalWriter-class.html">ClustalWriter</a><tt class="py-op">(</tt><tt class="py-base-class">SequenceWriter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClustalWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ClustalWriter-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""Write Clustal sequence alignments."""</tt> </tt>
<a name="ClustalWriter.__init__"></a><div id="ClustalWriter.__init__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="ClustalWriter.__init__-toggle" onclick="return toggle('ClustalWriter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.ClustalIO.ClustalWriter-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">handle</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ClustalWriter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ClustalWriter.__init__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-docstring">"""Creates the writer object.</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> Use the method write_file() to actually record your sequence records."""</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-63', 'handle', 'link-17');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-64" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-64', 'handle', 'link-17');">handle</a></tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> </tt>
<a name="ClustalWriter.write_file"></a><div id="ClustalWriter.write_file-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="ClustalWriter.write_file-toggle" onclick="return toggle('ClustalWriter.write_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.SeqIO.ClustalIO.ClustalWriter-class.html#write_file">write_file</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">records</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
</div><div id="ClustalWriter.write_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ClustalWriter.write_file-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write an entire file containing the given records.</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> records - a SeqRecord iterator, or list of SeqRecords</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> Right now this code uses Bio.Clustalw.ClustalAlignment to do</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> the hard work - this may change in the future.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-comment"># ToDo - decide if using Bio.Clustalw.ClustalAlignment is</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># actually the best way to handle this.</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Copying that thirty lines of code (with slight tweaks)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># would be much simpler, and would probably run quicker and</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># use less memory as it doesn't build a ClustalAlignment</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># object.</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># The downside is code duplication.</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">length_of_sequences</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-65" class="py-name" targets="Variable Bio.expressions.blast.ncbiblast.alignment=Bio.expressions.blast.ncbiblast-module.html#alignment"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-65', 'alignment', 'link-65');">alignment</a></tt> <tt class="py-op">=</tt> <tt id="link-66" class="py-name"><a title="Bio.Clustalw.ClustalAlignment" class="py-name" href="#" onclick="return doclink('link-66', 'ClustalAlignment', 'link-15');">ClustalAlignment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-67" class="py-name" targets="Variable Bio.Emboss.primer3_format.record=Bio.Emboss.primer3_format-module.html#record,Variable Bio.Emboss.primersearch_format.record=Bio.Emboss.primersearch_format-module.html#record,Method Bio.GFF.Feature.record()=Bio.GFF.Feature-class.html#record,Variable Bio.LocusLink.web_parse.record=Bio.LocusLink.web_parse-module.html#record,Variable Bio.Ndb.record=Bio.Ndb-module.html#record,Function Bio.Std.record()=Bio.Std-module.html#record,Variable Bio.expressions.blocks.record=Bio.expressions.blocks-module.html#record,Variable Bio.expressions.embl.embl65.record=Bio.expressions.embl.embl65-module.html#record,Variable Bio.expressions.fasta.record=Bio.expressions.fasta-module.html#record,Variable Bio.expressions.genbank.record=Bio.expressions.genbank-module.html#record,Variable Bio.expressions.hmmpfam.record=Bio.expressions.hmmpfam-module.html#record,Variable Bio.expressions.swissprot.ipi.record=Bio.expressions.swissprot.ipi-module.html#record,Variable Bio.expressions.swissprot.speclist.record=Bio.expressions.swissprot.speclist-module.html#record,Variable Bio.expressions.swissprot.sprot38.record=Bio.expressions.swissprot.sprot38-module.html#record,Variable Bio.expressions.swissprot.sprot40.record=Bio.expressions.swissprot.sprot40-module.html#record,Variable Martel.test.test_swissprot38.record=Martel.test.test_swissprot38-module.html#record,Variable Martel.test.testformats.swissprot38.record=Martel.test.testformats.swissprot38-module.html#record"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-67', 'record', 'link-67');">record</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">records</tt> <tt class="py-op">:</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">length_of_sequences</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">length_of_sequences</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-68" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-68', 'record', 'link-67');">record</a></tt><tt class="py-op">.</tt><tt id="link-69" class="py-name" targets="Method Bio.GFF.Feature.seq()=Bio.GFF.Feature-class.html#seq,Method Bio.GFF.FeatureAggregate.seq()=Bio.GFF.FeatureAggregate-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-69', 'seq', 'link-69');">seq</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-keyword">elif</tt> <tt class="py-name">length_of_sequences</tt> <tt class="py-op"><></tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-70" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-70', 'record', 'link-67');">record</a></tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-71', 'seq', 'link-69');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</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">"Sequences must all be the same length"</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">length_of_sequences</tt> <tt class="py-op"><=</tt> <tt class="py-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Non-empty sequences are required"</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-comment">#ToDo, check alphabet for this sequence matches that</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#specified for the alignment. Not sure how the</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#alphabet.contains() method is intended to be used,</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#but it doesn't make sense to me right now.</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-comment">#Doing this works, but ClustalAlignment currently uses</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#the record.descrption when outputing the records.</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#alignment._records.append(record)</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> <tt class="py-comment">#Make sure we don't get any spaces in the record</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#identifier when output in the file by replacing</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#them with underscores:</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-72" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-72', 'alignment', 'link-65');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name" targets="Method Bio.Align.Generic.Alignment.add_sequence()=Bio.Align.Generic.Alignment-class.html#add_sequence,Method Bio.Nexus.Nexus.Nexus.add_sequence()=Bio.Nexus.Nexus.Nexus-class.html#add_sequence,Method Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence()=Bio.builders.SeqRecord.sequence.BuildSeqRecord-class.html#add_sequence"><a title="Bio.Align.Generic.Alignment.add_sequence
Bio.Nexus.Nexus.Nexus.add_sequence
Bio.builders.SeqRecord.sequence.BuildSeqRecord.add_sequence" class="py-name" href="#" onclick="return doclink('link-73', 'add_sequence', 'link-73');">add_sequence</a></tt><tt class="py-op">(</tt><tt id="link-74" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-74', 'record', 'link-67');">record</a></tt><tt class="py-op">.</tt><tt id="link-75" 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-75', 'id', 'link-60');">id</a></tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt><tt class="py-string">"_"</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt id="link-76" class="py-name"><a title="Bio.Emboss.primer3_format.record
Bio.Emboss.primersearch_format.record
Bio.GFF.Feature.record
Bio.LocusLink.web_parse.record
Bio.Ndb.record
Bio.Std.record
Bio.expressions.blocks.record
Bio.expressions.embl.embl65.record
Bio.expressions.fasta.record
Bio.expressions.genbank.record
Bio.expressions.hmmpfam.record
Bio.expressions.swissprot.ipi.record
Bio.expressions.swissprot.speclist.record
Bio.expressions.swissprot.sprot38.record
Bio.expressions.swissprot.sprot40.record
Martel.test.test_swissprot38.record
Martel.test.testformats.swissprot38.record" class="py-name" href="#" onclick="return doclink('link-76', 'record', 'link-67');">record</a></tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-77', 'seq', 'link-69');">seq</a></tt><tt class="py-op">.</tt><tt id="link-78" 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-78', 'tostring', 'link-78');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-79" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-79', 'alignment', 'link-65');">alignment</a></tt><tt class="py-op">.</tt><tt id="link-80" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_all_seqs()=Bio.Align.Generic.Alignment-class.html#get_all_seqs"><a title="Bio.Align.Generic.Alignment.get_all_seqs" class="py-name" href="#" onclick="return doclink('link-80', 'get_all_seqs', 'link-80');">get_all_seqs</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-number">0</tt> <tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</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">"Must have at least one sequence"</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="Bio.LocusLink.web_parse.handle
Bio.Ndb.handle" class="py-name" href="#" onclick="return doclink('link-81', 'handle', 'link-17');">handle</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.write()=Bio.AlignAce.Motif.Motif-class.html#write,Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.EUtils.sourcegen.SourceFile.write()=Bio.EUtils.sourcegen.SourceFile-class.html#write,Method Bio.EUtils.sourcegen.SourceGen.write()=Bio.EUtils.sourcegen.SourceGen-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write,Method Bio.Writer.Writer.write()=Bio.Writer.Writer-class.html#write,Method Bio.writers.SeqRecord.embl.WriteEmbl.write()=Bio.writers.SeqRecord.embl.WriteEmbl-class.html#write,Method Bio.writers.SeqRecord.fasta.WriteFasta.write()=Bio.writers.SeqRecord.fasta.WriteFasta-class.html#write"><a title="Bio.AlignAce.Motif.Motif.write
Bio.AlignIO.write
Bio.EUtils.sourcegen.SourceFile.write
Bio.EUtils.sourcegen.SourceGen.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.SeqIO.write
Bio.Writer.Writer.write
Bio.writers.SeqRecord.embl.WriteEmbl.write
Bio.writers.SeqRecord.fasta.WriteFasta.write" class="py-name" href="#" onclick="return doclink('link-82', 'write', 'link-82');">write</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-83" class="py-name"><a title="Bio.expressions.blast.ncbiblast.alignment" class="py-name" href="#" onclick="return doclink('link-83', 'alignment', 'link-65');">alignment</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-comment">#Don't close the handle. Doing so would prevent this code</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#from writing concatenated Clustal files which might be used</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#in phylogenetic bootstrapping (very common with phylip).</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#self.handle.close()</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-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="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-comment"># Run a quick self-test</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment">#This is a truncated version of the example in Tests/cw02.aln</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#Notice the inclusion of sequence numbers (right hand side)</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">aln_example1</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-string">"""CLUSTAL W (1.81) multiple sequence alignment</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-string">gi|4959044|gb|AAD34209.1|AF069 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN 50</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-string">gi|671626|emb|CAA85685.1| ---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFR 41</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-string"> * *: :: :. :* : :. : . :* :: .</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-string">gi|4959044|gb|AAD34209.1|AF069 LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW 100</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-string">gi|671626|emb|CAA85685.1| VTPQPG-----------------VPPEEAGAAVAAESSTGT--------- 65</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-string"> : ** **:... *.*** .. </tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-string">gi|4959044|gb|AAD34209.1|AF069 LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT 150</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-string">gi|671626|emb|CAA85685.1| WTTVWTDGLTSLDRYKG-----RCYHIEPVPG------------------ 92</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-string"> .:* * *: .* :* : :* .* </tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-string">gi|4959044|gb|AAD34209.1|AF069 SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE 200</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-string">gi|671626|emb|CAA85685.1| -EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIP 141</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-string"> *::. . .:: :*..* :* .* .. . : . : </tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-string">gi|4959044|gb|AAD34209.1|AF069 VPTTRAQRRA 210</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-string">gi|671626|emb|CAA85685.1| VAYVKTFQGP 151</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-string"> *. .:: : .</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-string"> </tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-comment">#This example is a truncated version of the dataset used here:</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">#http://virgil.ruc.dk/kurser/Sekvens/Treedraw.htm</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment">#with the last record repeated twice (deliberate toture test)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">aln_example2</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-string">"""CLUSTAL X (1.83) multiple sequence alignment</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-string">V_Harveyi_PATH --MKNWIKVAVAAIA--LSAA------------------TVQAATEVKVG</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-string">B_subtilis_YXEM MKMKKWTVLVVAALLAVLSACG------------NGNSSSKEDDNVLHVG</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-string">B_subtilis_GlnH_homo_YCKK MKKALLALFMVVSIAALAACGAGNDNQSKDNAKDGDLWASIKKKGVLTVG</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-string">YA80_HAEIN MKKLLFTTALLTGAIAFSTF-----------SHAGEIADRVEKTKTLLVG</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-string">FLIY_ECOLI MKLAHLGRQALMGVMAVALVAG---MSVKSFADEG-LLNKVKERGTLLVG</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-string">E_coli_GlnH --MKSVLKVSLAALTLAFAVS------------------SHAADKKLVVA</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-string">Deinococcus_radiodurans -MKKSLLSLKLSGLLVPSVLALS--------LSACSSPSSTLNQGTLKIA</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIG</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIG</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-string"> : . : :.</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-string">V_Harveyi_PATH MSGRYFPFTFVKQ--DKLQGFEVDMWDEIGKRNDYKIEYVTANFSGLFGL</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-string">B_subtilis_YXEM ATGQSYPFAYKEN--GKLTGFDVEVMEAVAKKIDMKLDWKLLEFSGLMGE</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-string">B_subtilis_GlnH_homo_YCKK TEGTYEPFTYHDKDTDKLTGYDVEVITEVAKRLGLKVDFKETQWGSMFAG</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-string">YA80_HAEIN TEGTYAPFTFHDK-SGKLTGFDVEVIRKVAEKLGLKVEFKETQWDAMYAG</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-string">FLIY_ECOLI LEGTYPPFSFQGD-DGKLTGFEVEFAQQLAKHLGVEASLKPTKWDGMLAS</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-string">E_coli_GlnH TDTAFVPFEFKQG--DKYVGFDVDLWAAIAKELKLDYELKPMDFSGIIPA</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-string">Deinococcus_radiodurans MEGTYPPFTSKNE-QGELVGFDVDIAKAVAQKLNLKPEFVLTEWSGILAG</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI TDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI TDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-string"> ** .: *::::. : :. . ..: </tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-string">V_Harveyi_PATH LETGRIDTISNQITMTDARKAKYLFADPYVVDG-AQI</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-string">B_subtilis_YXEM LQTGKLDTISNQVAVTDERKETYNFTKPYAYAG-TQI</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-string">B_subtilis_GlnH_homo_YCKK LNSKRFDVVANQVG-KTDREDKYDFSDKYTTSR-AVV</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-string">YA80_HAEIN LNAKRFDVIANQTNPSPERLKKYSFTTPYNYSG-GVI</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-string">FLIY_ECOLI LDSKRIDVVINQVTISDERKKKYDFSTPYTISGIQAL</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-string">E_coli_GlnH LQTKNVDLALAGITITDERKKAIDFSDGYYKSG-LLV</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-string">Deinococcus_radiodurans LQANKYDVIVNQVGITPERQNSIGFSQPYAYSRPEII</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLV</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-string">HISJ_E_COLI LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLV</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-string"> *.: . * . * *: :</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-string"></tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-string">"""</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-84" class="py-name" targets="Method Bio.Pathway.Rep.HashSet.HashSet.list()=Bio.Pathway.Rep.HashSet.HashSet-class.html#list"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-84', 'list', 'link-84');">list</a></tt><tt class="py-op">(</tt><tt id="link-85" class="py-name" targets="Class Bio.AlignIO.ClustalIO.ClustalIterator=Bio.AlignIO.ClustalIO.ClustalIterator-class.html,Function Bio.SeqIO.ClustalIO.ClustalIterator()=Bio.SeqIO.ClustalIO-module.html#ClustalIterator"><a title="Bio.AlignIO.ClustalIO.ClustalIterator
Bio.SeqIO.ClustalIO.ClustalIterator" class="py-name" href="#" onclick="return doclink('link-85', 'ClustalIterator', 'link-85');">ClustalIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">aln_example1</tt><tt class="py-op">)</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">assert</tt> <tt class="py-number">2</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">records</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">assert</tt> <tt class="py-name">records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-86" 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-86', 'id', 'link-60');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"gi|4959044|gb|AAD34209.1|AF069"</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">records</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-87" 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-87', 'id', 'link-60');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"gi|671626|emb|CAA85685.1|"</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">records</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-88', 'seq', 'link-69');">seq</a></tt><tt class="py-op">.</tt><tt id="link-89" 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-89', 'tostring', 'link-78');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> \ </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-string">"MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNN"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-string">"LLGTPGESTEEELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDW"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-string">"LNSVRQTGNTTRSRQRGNQSWRAVSRTNPNSGDFRFSLEINVNRNNGSQT"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-string">"SENESEPSTRRLSVENMESSSQRQMENSASESASARPSRAERNSTEAVTE"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-string">"VPTTRAQRRA"</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">records</tt> <tt class="py-op">=</tt> <tt id="link-90" class="py-name"><a title="Bio.Pathway.Rep.HashSet.HashSet.list" class="py-name" href="#" onclick="return doclink('link-90', 'list', 'link-84');">list</a></tt><tt class="py-op">(</tt><tt id="link-91" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator
Bio.SeqIO.ClustalIO.ClustalIterator" class="py-name" href="#" onclick="return doclink('link-91', 'ClustalIterator', 'link-85');">ClustalIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-name">aln_example2</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-number">9</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">records</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">assert</tt> <tt class="py-name">records</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-92" class="py-name"><a title="Bio.Data.CodonTable.id
Bio.Encodings.IUPACEncoding.id
Bio.GFF.Feature.id" class="py-name" href="#" onclick="return doclink('link-92', 'id', 'link-60');">id</a></tt> <tt class="py-op">==</tt> <tt class="py-string">"HISJ_E_COLI"</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">records</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-93" class="py-name"><a title="Bio.GFF.Feature.seq
Bio.GFF.FeatureAggregate.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-93', 'seq', 'link-69');">seq</a></tt><tt class="py-op">.</tt><tt id="link-94" 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-94', 'tostring', 'link-78');">tostring</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> \ </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-string">"MKKLVLSLSLVLAFSSATAAF-------------------AAIPQNIRIG"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-string">"TDPTYAPFESKNS-QGELVGFDIDLAKELCKRINTQCTFVENPLDALIPS"</tt> <tt class="py-op">+</tt> \ </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-string">"LKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLV"</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> </tt><script type="text/javascript">
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