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Module Interfaces
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<h1 class="epydoc">Source Code for <a href="Bio.AlignIO.Interfaces-module.html">Module Bio.AlignIO.Interfaces</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 2008-2010 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"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-docstring">AlignIO support module (not for general use).</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">Unless you are writing a new parser or writer for Bio.AlignIO, you should not</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">use this module. It provides base classes to try and simplify things.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-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 class="py-op">,</tt> <tt id="link-3" class="py-name" targets="Class Bio.Alphabet.Gapped=Bio.Alphabet.Gapped-class.html"><a title="Bio.Alphabet.Gapped" class="py-name" href="#" onclick="return doclink('link-3', 'Gapped', 'link-3');">Gapped</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="AlignmentIterator"></a><div id="AlignmentIterator-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <a class="py-toggle" href="#" id="AlignmentIterator-toggle" onclick="return toggle('AlignmentIterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html">AlignmentIterator</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignmentIterator-expanded"><a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for building MultipleSeqAlignment iterators.</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> You should write a next() method to return Aligment</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> objects. You may wish to redefine the __init__</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> method as well.</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Should the default be Gapped(single_letter_alphabet) instead?</tt> </tt>
<a name="AlignmentIterator.__init__"></a><div id="AlignmentIterator.__init__-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="AlignmentIterator.__init__-toggle" onclick="return toggle('AlignmentIterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentIterator-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-param">seq_count</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-param">alphabet</tt> <tt class="py-op">=</tt> <tt id="link-4" class="py-name"><a title="Bio.Alphabet.single_letter_alphabet" class="py-name" href="#" onclick="return doclink('link-4', 'single_letter_alphabet', 'link-2');">single_letter_alphabet</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentIterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentIterator.__init__-expanded"><a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-docstring">"""Create an AlignmentIterator object.</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> handle - input file</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> count - optional, expected number of records per alignment</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> Recommend for fasta file format.</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> alphabet - optional, e.g. Bio.Alphabet.generic_protein</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> Note when subclassing:</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> - there should be a single non-optional argument, the handle,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> and optional count and alphabet IN THAT ORDER.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> - you do not have to require an alphabet (?).</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> - you can add additional optional arguments."""</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-5', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-6" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-6', 'handle', 'link-5');">handle</a></tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">records_per_alignment</tt> <tt class="py-op">=</tt> <tt class="py-name">seq_count</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">alphabet</tt> <tt class="py-op">=</tt> <tt class="py-name">alphabet</tt> </tt>
</div><a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-comment"># You may want to subclass this, for example #</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-comment"># to read through the file to find the first record,#</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> <tt class="py-comment"># or if additional arguments are required. #</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="AlignmentIterator.next"></a><div id="AlignmentIterator.next-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="AlignmentIterator.next-toggle" onclick="return toggle('AlignmentIterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next">next</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="AlignmentIterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentIterator.next-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the next alignment in the file.</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> This method should be replaced by any derived class to do something</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> useful."""</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">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"This object should be subclassed"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-comment"># You SHOULD subclass this, to split the file up #</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-comment"># into your individual alignments and convert these #</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-comment"># into MultipleSeqAlignment objects. #</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="AlignmentIterator.__iter__"></a><div id="AlignmentIterator.__iter__-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="AlignmentIterator.__iter__-toggle" onclick="return toggle('AlignmentIterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__iter__">__iter__</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="AlignmentIterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentIterator.__iter__-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over the entries as MultipleSeqAlignment objects.</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> Example usage for (concatenated) PHYLIP files:</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> myFile = open("many.phy","r")</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> for alignment in PhylipIterator(myFile):</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> print "New alignment:"</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> for record in alignment:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> print record.id</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> print record.seq</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> myFile.close()"""</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">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.File.UndoHandle.next()=Bio.File.UndoHandle-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.PopGen.GenePop.Controller._FileIterator.next()=Bio.PopGen.GenePop.Controller._FileIterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.File.UndoHandle.next
Bio.GenBank.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.PopGen.GenePop.Controller._FileIterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.UniGene.Iterator.next" class="py-name" href="#" onclick="return doclink('link-7', 'next', 'link-7');">next</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> </tt>
<a name="AlignmentWriter"></a><div id="AlignmentWriter-def"><a name="L71"></a><tt class="py-lineno"> 71</tt> <a class="py-toggle" href="#" id="AlignmentWriter-toggle" onclick="return toggle('AlignmentWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html">AlignmentWriter</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AlignmentWriter-expanded"><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for building MultipleSeqAlignment writers.</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> You should write a write_alignment() method.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> You may wish to redefine the __init__ method as well"""</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="AlignmentWriter.__init__"></a><div id="AlignmentWriter.__init__-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="AlignmentWriter.__init__-toggle" onclick="return toggle('AlignmentWriter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentWriter-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="AlignmentWriter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentWriter.__init__-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-8', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-9', 'handle', 'link-5');">handle</a></tt> </tt>
</div><a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> </tt>
<a name="AlignmentWriter.write_file"></a><div id="AlignmentWriter.write_file-def"><a name="L80"></a><tt class="py-lineno"> 80</tt> <a class="py-toggle" href="#" id="AlignmentWriter.write_file-toggle" onclick="return toggle('AlignmentWriter.write_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentWriter-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">alignments</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentWriter.write_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentWriter.write_file-expanded"><a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write an entire file containing the given alignments.</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> alignments - A list or iterator returning MultipleSeqAlignment objects</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> In general, this method can only be called once per file.</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> This method should be replaced by any derived class to do something</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> useful. It should return the number of alignments"""</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"This object should be subclassed"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-comment"># You SHOULD subclass this, to write the alignment #</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-comment"># objecta to the file handle #</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> </tt>
<a name="AlignmentWriter.clean"></a><div id="AlignmentWriter.clean-def"><a name="L95"></a><tt class="py-lineno"> 95</tt> <a class="py-toggle" href="#" id="AlignmentWriter.clean-toggle" onclick="return toggle('AlignmentWriter.clean');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.AlignmentWriter-class.html#clean">clean</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AlignmentWriter.clean-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AlignmentWriter.clean-expanded"><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to avoid getting newlines in the output."""</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">text</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">,</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">"\r"</tt><tt class="py-op">,</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">replace</tt><tt class="py-op">(</tt><tt class="py-string">" "</tt><tt class="py-op">,</tt> <tt class="py-string">" "</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter"></a><div id="SequentialAlignmentWriter-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter-toggle" onclick="return toggle('SequentialAlignmentWriter');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html">SequentialAlignmentWriter</a><tt class="py-op">(</tt><tt class="py-base-class">AlignmentWriter</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequentialAlignmentWriter-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SequentialAlignmentWriter-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-docstring">"""Base class for building MultipleSeqAlignment writers.</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"> This assumes each alignment can be simply appended to the file.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> You should write a write_alignment() method.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> You may wish to redefine the __init__ method as well"""</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter.__init__"></a><div id="SequentialAlignmentWriter.__init__-def"><a name="L106"></a><tt class="py-lineno">106</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter.__init__-toggle" onclick="return toggle('SequentialAlignmentWriter.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-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="SequentialAlignmentWriter.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequentialAlignmentWriter.__init__-expanded"><a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-10" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-10', 'handle', 'link-5');">handle</a></tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-11', 'handle', 'link-5');">handle</a></tt> </tt>
</div><a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter.write_file"></a><div id="SequentialAlignmentWriter.write_file-def"><a name="L109"></a><tt class="py-lineno">109</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter.write_file-toggle" onclick="return toggle('SequentialAlignmentWriter.write_file');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-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">alignments</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequentialAlignmentWriter.write_file-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequentialAlignmentWriter.write_file-expanded"><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write an entire file containing the given alignments.</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> alignments - A list or iterator returning MultipleSeqAlignment objects</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> In general, this method can only be called once per file."""</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method Bio.AlignIO.EmbossIO.EmbossWriter.write_header()=Bio.AlignIO.EmbossIO.EmbossWriter-class.html#write_header,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_header()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_header,Method Bio.NMR.xpktools.Peaklist.write_header()=Bio.NMR.xpktools.Peaklist-class.html#write_header,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_header()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_header,Method Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_header()=Bio.SeqIO.SeqXmlIO.SeqXmlWriter-class.html#write_header,Method Bio.SeqIO.SffIO.SffWriter.write_header()=Bio.SeqIO.SffIO.SffWriter-class.html#write_header"><a title="Bio.AlignIO.EmbossIO.EmbossWriter.write_header
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_header
Bio.NMR.xpktools.Peaklist.write_header
Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_header
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_header
Bio.SeqIO.SffIO.SffWriter.write_header" class="py-name" href="#" onclick="return doclink('link-12', 'write_header', 'link-12');">write_header</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt id="link-13" 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,Method Bio.Seq.UnknownSeq.count()=Bio.Seq.UnknownSeq-class.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-13', 'count', 'link-13');">count</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">alignment</tt> <tt class="py-keyword">in</tt> <tt class="py-name">alignments</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalWriter.write_alignment()=Bio.AlignIO.ClustalIO.ClustalWriter-class.html#write_alignment,Method Bio.AlignIO.EmbossIO.EmbossWriter.write_alignment()=Bio.AlignIO.EmbossIO.EmbossWriter-class.html#write_alignment,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_alignment()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_alignment,Method Bio.AlignIO.NexusIO.NexusWriter.write_alignment()=Bio.AlignIO.NexusIO.NexusWriter-class.html#write_alignment,Method Bio.AlignIO.PhylipIO.PhylipWriter.write_alignment()=Bio.AlignIO.PhylipIO.PhylipWriter-class.html#write_alignment,Method Bio.AlignIO.PhylipIO.RelaxedPhylipWriter.write_alignment()=Bio.AlignIO.PhylipIO.RelaxedPhylipWriter-class.html#write_alignment,Method Bio.AlignIO.StockholmIO.StockholmWriter.write_alignment()=Bio.AlignIO.StockholmIO.StockholmWriter-class.html#write_alignment"><a title="Bio.AlignIO.ClustalIO.ClustalWriter.write_alignment
Bio.AlignIO.EmbossIO.EmbossWriter.write_alignment
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_alignment
Bio.AlignIO.NexusIO.NexusWriter.write_alignment
Bio.AlignIO.PhylipIO.PhylipWriter.write_alignment
Bio.AlignIO.PhylipIO.RelaxedPhylipWriter.write_alignment
Bio.AlignIO.StockholmIO.StockholmWriter.write_alignment" class="py-name" href="#" onclick="return doclink('link-14', 'write_alignment', 'link-14');">write_alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">alignment</tt><tt class="py-op">)</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt id="link-15" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-15', 'count', 'link-13');">count</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name" targets="Method Bio.AlignIO.EmbossIO.EmbossWriter.write_footer()=Bio.AlignIO.EmbossIO.EmbossWriter-class.html#write_footer,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_footer()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_footer,Method Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_footer()=Bio.SeqIO.Interfaces.SequentialSequenceWriter-class.html#write_footer,Method Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_footer()=Bio.SeqIO.SeqXmlIO.SeqXmlWriter-class.html#write_footer"><a title="Bio.AlignIO.EmbossIO.EmbossWriter.write_footer
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.write_footer
Bio.SeqIO.Interfaces.SequentialSequenceWriter.write_footer
Bio.SeqIO.SeqXmlIO.SeqXmlWriter.write_footer" class="py-name" href="#" onclick="return doclink('link-16', 'write_footer', 'link-16');">write_footer</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-17" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.Seq.UnknownSeq.count" class="py-name" href="#" onclick="return doclink('link-17', 'count', 'link-13');">count</a></tt> </tt>
</div><a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter.write_header"></a><div id="SequentialAlignmentWriter.write_header-def"><a name="L123"></a><tt class="py-lineno">123</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter.write_header-toggle" onclick="return toggle('SequentialAlignmentWriter.write_header');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_header">write_header</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="SequentialAlignmentWriter.write_header-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequentialAlignmentWriter.write_header-expanded"><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write any header.</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> This method should be replaced by any derived class to do something</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> useful."""</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter.write_footer"></a><div id="SequentialAlignmentWriter.write_footer-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter.write_footer-toggle" onclick="return toggle('SequentialAlignmentWriter.write_footer');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_footer">write_footer</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="SequentialAlignmentWriter.write_footer-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequentialAlignmentWriter.write_footer-expanded"><a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write any footer.</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> This method should be replaced by any derived class to do something</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> useful."""</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> </tt>
<a name="SequentialAlignmentWriter.write_alignment"></a><div id="SequentialAlignmentWriter.write_alignment-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="SequentialAlignmentWriter.write_alignment-toggle" onclick="return toggle('SequentialAlignmentWriter.write_alignment');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#write_alignment">write_alignment</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">alignment</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SequentialAlignmentWriter.write_alignment-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SequentialAlignmentWriter.write_alignment-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-docstring">"""Use this to write a single alignment.</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> This method should be replaced by any derived class to do something</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> useful."""</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">(</tt><tt class="py-string">"This object should be subclassed"</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-comment"># You SHOULD subclass this, to write the alignment #</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-comment"># objecta to the file handle #</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-comment">#####################################################</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> </tt><script type="text/javascript">
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