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<h1 class="epydoc">Source Code for <a href="Bio.Align.Generic-module.html">Module Bio.Align.Generic</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000-2004 Brad Chapman.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2001 Iddo Friedberg.</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2007-2010 by Peter Cock.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># All rights reserved.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</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">Contains classes to deal with generic sequence alignment stuff not</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-docstring">specific to a particular program or format.</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring">Classes:</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> - Alignment</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"epytext en"</tt> <tt class="py-comment">#Don't just use plain text in epydoc API pages!</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"># biopython</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</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="Module Bio.Seq=Bio.Seq-module.html,Class Bio.Seq.Seq=Bio.Seq.Seq-class.html"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-1', 'Seq', 'link-1');">Seq</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-2', 'Seq', 'link-1');">Seq</a></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</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.SeqRecord=Bio.SeqRecord-module.html,Class Bio.SeqRecord.SeqRecord=Bio.SeqRecord.SeqRecord-class.html"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-4', 'SeqRecord', 'link-4');">SeqRecord</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-5', 'SeqRecord', 'link-4');">SeqRecord</a></tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</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-keyword">import</tt> <tt id="link-7" 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-7', 'Alphabet', 'link-7');">Alphabet</a></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="Alignment"></a><div id="Alignment-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="Alignment-toggle" onclick="return toggle('Alignment');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html">Alignment</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="Alignment-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Alignment-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent a set of alignments (DEPRECATED).</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> This is a base class to represent alignments, which can be subclassed</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> to deal with an alignment in a specific format.</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> With the introduction of the MultipleSeqAlignment class in Bio.Align,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> this base class is deprecated and is likely to be removed in future</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"> releases of Biopython.</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Alignment.__init__"></a><div id="Alignment.__init__-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="Alignment.__init__-toggle" onclick="return toggle('Alignment.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-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">alphabet</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__init__-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a new Alignment object.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"><tt class="py-docstring"> - alphabet - The alphabet to use for the sequence objects that are</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"> created. This alphabet must be a gapped type.</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"> e.g.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> >>> print align</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG Alpha</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> ACT-CTAGCTAG Beta</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG Gamma</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-8" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-8', 'Bio', 'link-0');">Bio</a></tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</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">"With the introduction of the MultipleSeqAlignment class in Bio.Align, this base class is deprecated and is likely to be removed in a future release of Biopython."</tt><tt class="py-op">,</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="Class Bio.BiopythonDeprecationWarning=Bio.BiopythonDeprecationWarning-class.html"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-10', 'BiopythonDeprecationWarning', 'link-10');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-11', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-12" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-12', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">)</tt> \ </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> <tt class="py-keyword">or</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">alphabet</tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name"><a title="Bio.Alphabet
Bio.Alphabet.Alphabet" class="py-name" href="#" onclick="return doclink('link-13', 'Alphabet', 'link-7');">Alphabet</a></tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Class Bio.Alphabet.AlphabetEncoder=Bio.Alphabet.AlphabetEncoder-class.html"><a title="Bio.Alphabet.AlphabetEncoder" class="py-name" href="#" onclick="return doclink('link-14', 'AlphabetEncoder', 'link-14');">AlphabetEncoder</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</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">"Invalid alphabet argument"</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</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>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment"># hold everything at a list of SeqRecord objects</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
</div><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="Alignment._str_line"></a><div id="Alignment._str_line-def"><a name="L62"></a><tt class="py-lineno"> 62</tt> <a class="py-toggle" href="#" id="Alignment._str_line-toggle" onclick="return toggle('Alignment._str_line');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#_str_line">_str_line</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">record</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment._str_line-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment._str_line-expanded"><a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a truncated string representation of a SeqRecord (PRIVATE).</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> This is a PRIVATE function used by the __str__ method.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</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">record</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-15', 'seq', 'link-15');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op"><=</tt> <tt class="py-number">50</tt><tt class="py-op">:</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s %s"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-16', 'seq', 'link-15');">seq</a></tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-17', 'id', 'link-17');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s...%s %s"</tt> \ </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-18', 'seq', 'link-15');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">44</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-19', 'seq', 'link-15');">seq</a></tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-20', 'id', 'link-17');">id</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="Alignment.__str__"></a><div id="Alignment.__str__-def"><a name="L73"></a><tt class="py-lineno"> 73</tt> <a class="py-toggle" href="#" id="Alignment.__str__-toggle" onclick="return toggle('Alignment.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__str__-expanded"><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a multi-line string summary of the alignment.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> This output is intended to be readable, but large alignments are</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> shown truncated. A maximum of 20 rows (sequences) and 50 columns</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> are shown, with the record identifiers. This should fit nicely on a</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> single screen. e.g.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> >>> print align</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG Alpha</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> ACT-CTAGCTAG Beta</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG Gamma</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"> See also the alignment's format method.</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">rows</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-name">lines</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"%s alignment with %i rows and %i columns"</tt> \ </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">rows</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Align.Generic.Alignment.get_alignment_length()=Bio.Align.Generic.Alignment-class.html#get_alignment_length"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-21', 'get_alignment_length', 'link-21');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">rows</tt> <tt class="py-op"><=</tt> <tt class="py-number">20</tt><tt class="py-op">:</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.extend()=Bio.Align.MultipleSeqAlignment-class.html#extend,Method Bio.SCOP.Raf.SeqMap.extend()=Bio.SCOP.Raf.SeqMap-class.html#extend,Method Bio.Seq.MutableSeq.extend()=Bio.Seq.MutableSeq-class.html#extend"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-22', 'extend', 'link-22');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Align.Generic.Alignment._str_line()=Bio.Align.Generic.Alignment-class.html#_str_line"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-23', '_str_line', 'link-23');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.extend
Bio.SCOP.Raf.SeqMap.extend
Bio.Seq.MutableSeq.extend" class="py-name" href="#" onclick="return doclink('link-24', 'extend', 'link-22');">extend</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-25', '_str_line', 'link-23');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">rec</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">18</tt><tt class="py-op">]</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-26', 'append', 'link-26');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"..."</tt><tt class="py-op">)</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">lines</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-27', 'append', 'link-26');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Align.Generic.Alignment._str_line" class="py-name" href="#" onclick="return doclink('link-28', '_str_line', 'link-23');">_str_line</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</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 class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt> </tt>
</div><a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> </tt>
<a name="Alignment.__repr__"></a><div id="Alignment.__repr__-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="Alignment.__repr__-toggle" onclick="return toggle('Alignment.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__repr__-expanded"><a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a representation of the object for debugging.</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> The representation cannot be used with eval() to recreate the object,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> which is usually possible with simple python ojects. For example:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> <Bio.Align.Generic.Alignment instance (2 records of length 14,</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"> SingleLetterAlphabet()) at a3c184c></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"> The hex string is the memory address of the object, see help(id).</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> This provides a simple way to visually distinguish alignments of</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> the same size.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-comment">#A doctest for __repr__ would be nice, but __class__ comes out differently</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-comment">#if run via the __main__ trick.</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"<%s instance (%i records of length %i, %s) at %x>"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">__class__</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</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-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-29', 'get_alignment_length', 'link-21');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><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-op">,</tt> <tt id="link-30" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-30', 'id', 'link-17');">id</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-comment">#This version is useful for doing eval(repr(alignment)),</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-comment">#but it can be VERY long:</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-comment">#return "%s(%s, %s)" \</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-comment"># % (self.__class__, repr(self._records), repr(self._alphabet))</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> </tt>
<a name="Alignment.format"></a><div id="Alignment.format-def"><a name="L128"></a><tt class="py-lineno">128</tt> <a class="py-toggle" href="#" id="Alignment.format-toggle" onclick="return toggle('Alignment.format');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#format">format</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.format-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.format-expanded"><a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the alignment as a string in the specified file format.</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> The format should be a lower case string supported as an output</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> format by Bio.AlignIO (such as "fasta", "clustal", "phylip",</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> "stockholm", etc), which is used to turn the alignment into a</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> string.</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> >>> print align.format("fasta")</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"> >Alpha</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> >Beta</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"> ACT-CTAGCTAG</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> >Gamma</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-docstring"> >>> print align.format("phylip")</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"> 3 12</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> Alpha ACTGCTAGCT AG</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> Beta ACT-CTAGCT AG</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"> Gamma ACTGCTAGAT AG</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> <BLANKLINE></tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> For Python 2.6, 3.0 or later see also the built in format() function.</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-comment">#See also the __format__ added for Python 2.6 / 3.0, PEP 3101</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-comment">#See also the SeqRecord class and its format() method using Bio.SeqIO</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name" targets="Method Bio.Align.Generic.Alignment.__format__()=Bio.Align.Generic.Alignment-class.html#__format__,Method Bio.Phylo.BaseTree.Tree.__format__()=Bio.Phylo.BaseTree.Tree-class.html#__format__,Method Bio.SeqRecord.SeqRecord.__format__()=Bio.SeqRecord.SeqRecord-class.html#__format__"><a title="Bio.Align.Generic.Alignment.__format__
Bio.Phylo.BaseTree.Tree.__format__
Bio.SeqRecord.SeqRecord.__format__" class="py-name" href="#" onclick="return doclink('link-31', '__format__', 'link-31');">__format__</a></tt><tt class="py-op">(</tt><tt id="link-32" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-32', 'format', 'link-32');">format</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="Alignment.__format__"></a><div id="Alignment.__format__-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="Alignment.__format__-toggle" onclick="return toggle('Alignment.__format__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__format__">__format__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format_spec</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__format__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__format__-expanded"><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the alignment as a string in the specified file format.</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"> This method supports the python format() function added in</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> Python 2.6/3.0. The format_spec should be a lower case</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> string supported by Bio.AlignIO as an output file format.</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"> See also the alignment's format() method."""</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">format_spec</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</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="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-33" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-33', 'Bio', 'link-0');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-34" class="py-name" targets="Package Bio.AlignIO=Bio.AlignIO-module.html"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-34', 'AlignIO', 'link-34');">AlignIO</a></tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt id="link-35" 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-35', 'handle', 'link-35');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-36" class="py-name"><a title="Bio.AlignIO" class="py-name" href="#" onclick="return doclink('link-36', 'AlignIO', 'link-34');">AlignIO</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-37', 'write', 'link-37');">write</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-38', 'handle', 'link-35');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">format_spec</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-39" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-39', 'handle', 'link-35');">handle</a></tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment">#Follow python convention and default to using __str__</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_all_seqs"></a><div id="Alignment.get_all_seqs-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="Alignment.get_all_seqs-toggle" onclick="return toggle('Alignment.get_all_seqs');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_all_seqs">get_all_seqs</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="Alignment.get_all_seqs-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_all_seqs-expanded"><a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"> <tt class="py-docstring">"""Return all of the sequences involved in the alignment (DEPRECATED).</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> The return value is a list of SeqRecord objects.</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> This method is deprecated, as the Alignment object itself now offers</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> much of the functionality of a list of SeqRecord objects (e.g.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"> iteration or slicing to create a sub-alignment). Instead use the</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> Python builtin function list, i.e. my_list = list(my_align)</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-40" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-40', 'Bio', 'link-0');">Bio</a></tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</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">"This method is deprecated, since the alignment object"</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-string">"now acts more like a list. Instead of calling "</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-string">"align.get_all_seqs() you can use list(align)"</tt><tt class="py-op">,</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-41" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-41', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-42', 'BiopythonDeprecationWarning', 'link-10');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> </tt>
</div><a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> </tt>
<a name="Alignment.__iter__"></a><div id="Alignment.__iter__-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="Alignment.__iter__-toggle" onclick="return toggle('Alignment.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-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="Alignment.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__iter__-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-docstring">"""Iterate over alignment rows as SeqRecord objects.</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> >>> for record in align:</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.id</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> ... print record.seq</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"> Alpha</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> Beta</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> ACT-CTAGCTAG</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"> Gamma</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> </tt>
</div><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_seq_by_num"></a><div id="Alignment.get_seq_by_num-def"><a name="L222"></a><tt class="py-lineno">222</tt> <a class="py-toggle" href="#" id="Alignment.get_seq_by_num-toggle" onclick="return toggle('Alignment.get_seq_by_num');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_seq_by_num">get_seq_by_num</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">number</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_seq_by_num-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_seq_by_num-expanded"><a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve a sequence by row number (DEPRECATED).</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-docstring"> Returns:</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-docstring"> - A Seq object for the requested sequence.</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"><tt class="py-docstring"> Raises:</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-docstring"> - IndexError - If the specified number is out of range.</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"><tt class="py-docstring"> NOTE: This is a legacy method. In new code where you need to access</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"><tt class="py-docstring"> the rows of the alignment (i.e. the sequences) consider iterating</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-docstring"> over them or accessing them as SeqRecord objects.</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt id="link-43" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-43', 'Bio', 'link-0');">Bio</a></tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</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">"This is a legacy method and is likely to be removed in a future release of Biopython. In new code where you need to access the rows of the alignment (i.e. the sequences) consider iterating over them or accessing them as SeqRecord objects."</tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-44', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.BiopythonDeprecationWarning" class="py-name" href="#" onclick="return doclink('link-45', 'BiopythonDeprecationWarning', 'link-10');">BiopythonDeprecationWarning</a></tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt class="py-name">number</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-46', 'seq', 'link-15');">seq</a></tt> </tt>
</div><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> </tt>
<a name="Alignment.__len__"></a><div id="Alignment.__len__-def"><a name="L240"></a><tt class="py-lineno">240</tt> <a class="py-toggle" href="#" id="Alignment.__len__-toggle" onclick="return toggle('Alignment.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__len__-expanded"><a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns the number of sequences in the alignment.</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"><tt class="py-docstring"> Use len(alignment) to get the number of sequences (i.e. the number of</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"><tt class="py-docstring"> rows), and alignment.get_alignment_length() to get the length of the</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"><tt class="py-docstring"> longest sequence (i.e. the number of columns).</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"><tt class="py-docstring"> This is easy to remember if you think of the alignment as being like a</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"><tt class="py-docstring"> list of SeqRecord objects.</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">)</tt> </tt>
</div><a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_alignment_length"></a><div id="Alignment.get_alignment_length-def"><a name="L252"></a><tt class="py-lineno">252</tt> <a class="py-toggle" href="#" id="Alignment.get_alignment_length-toggle" onclick="return toggle('Alignment.get_alignment_length');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_alignment_length">get_alignment_length</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="Alignment.get_alignment_length-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_alignment_length-expanded"><a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-docstring">"""Return the maximum length of the alignment.</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> All objects in the alignment should (hopefully) have the same</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"> length. This function will go through and find this length</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> by finding the maximum length of sequences in the alignment.</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.get_alignment_length()</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"> 12</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"> If you want to know the number of sequences in the alignment,</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> use len(align) instead:</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"><tt class="py-docstring"> >>> len(align)</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"><tt class="py-docstring"> 3</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">max_length</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">record</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</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">record</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-47', 'seq', 'link-15');">seq</a></tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">max_length</tt><tt class="py-op">:</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt class="py-name">max_length</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">record</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-48', 'seq', 'link-15');">seq</a></tt><tt class="py-op">)</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">max_length</tt> </tt>
</div><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> </tt>
<a name="Alignment.add_sequence"></a><div id="Alignment.add_sequence-def"><a name="L282"></a><tt class="py-lineno">282</tt> <a class="py-toggle" href="#" id="Alignment.add_sequence-toggle" onclick="return toggle('Alignment.add_sequence');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#add_sequence">add_sequence</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">descriptor</tt><tt class="py-op">,</tt> <tt class="py-param">sequence</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-param">weight</tt> <tt class="py-op">=</tt> <tt class="py-number">1.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.add_sequence-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.add_sequence-expanded"><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a sequence to the alignment.</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-docstring"> This doesn't do any kind of alignment, it just adds in the sequence</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"><tt class="py-docstring"> object, which is assumed to be prealigned with the existing</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"><tt class="py-docstring"> sequences.</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> - descriptor - The descriptive id of the sequence being added.</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> This will be used as the resulting SeqRecord's</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"> .id property (and, for historical compatibility,</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> also the .description property)</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> - sequence - A string with sequence info.</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> - start - You can explicitly set the start point of the sequence.</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> This is useful (at least) for BLAST alignments, which can</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> just be partial alignments of sequences.</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"> - end - Specify the end of the sequence, which is important</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> for the same reason as the start.</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> - weight - The weight to place on the sequence in the alignment.</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"><tt class="py-docstring"> By default, all sequences have the same weight. (0.0 =></tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"> no weight, 1.0 => highest weight)</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">new_seq</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Seq
Bio.Seq.Seq" class="py-name" href="#" onclick="return doclink('link-49', 'Seq', 'link-1');">Seq</a></tt><tt class="py-op">(</tt><tt id="link-50" class="py-name" targets="Method Bio.FSSP.FSSPAlignDict.sequence()=Bio.FSSP.FSSPAlignDict-class.html#sequence,Method Bio.GenBank._FeatureConsumer.sequence()=Bio.GenBank._FeatureConsumer-class.html#sequence,Method Bio.GenBank._RecordConsumer.sequence()=Bio.GenBank._RecordConsumer-class.html#sequence,Method Bio.Phylo.PhyloXMLIO.Writer.sequence()=Bio.Phylo.PhyloXMLIO.Writer-class.html#sequence"><a title="Bio.FSSP.FSSPAlignDict.sequence
Bio.GenBank._FeatureConsumer.sequence
Bio.GenBank._RecordConsumer.sequence
Bio.Phylo.PhyloXMLIO.Writer.sequence" class="py-name" href="#" onclick="return doclink('link-50', 'sequence', 'link-50');">sequence</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-comment">#We are now effectively using the SeqRecord's .id as</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-comment">#the primary identifier (e.g. in Bio.SeqIO) so we should</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-comment">#populate it with the descriptor.</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-comment">#For backwards compatibility, also store this in the</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment">#SeqRecord's description property.</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">new_record</tt> <tt class="py-op">=</tt> <tt id="link-51" class="py-name"><a title="Bio.SeqRecord
Bio.SeqRecord.SeqRecord" class="py-name" href="#" onclick="return doclink('link-51', 'SeqRecord', 'link-4');">SeqRecord</a></tt><tt class="py-op">(</tt><tt class="py-name">new_seq</tt><tt class="py-op">,</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-52', 'id', 'link-17');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descriptor</tt><tt class="py-op">,</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt id="link-53" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer.description()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#description,Method Bio.Phylo.PhyloXMLIO.Writer.description()=Bio.Phylo.PhyloXMLIO.Writer-class.html#description"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer.description
Bio.Phylo.PhyloXMLIO.Writer.description" class="py-name" href="#" onclick="return doclink('link-53', 'description', 'link-53');">description</a></tt> <tt class="py-op">=</tt> <tt class="py-name">descriptor</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment"># hack! We really need to work out how to deal with annotations</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-comment"># and features in biopython. Right now, I'll just use the</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-comment"># generic annotations dictionary we've got to store the start</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-comment"># and end, but we should think up something better. I don't know</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment"># if I'm really a big fan of the LocatableSeq thing they've got</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-comment"># in BioPerl, but I'm not positive what the best thing to do on</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment"># this is...</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-54" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-54', 'start', 'link-54');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.annotations=BioSQL.BioSeq.DBSeqRecord-class.html#annotations"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-55', 'annotations', 'link-55');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'start'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-56', 'start', 'link-54');">start</a></tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-57" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-57', 'end', 'link-57');">end</a></tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-58', 'annotations', 'link-55');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'end'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-59" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-59', 'end', 'link-57');">end</a></tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-comment"># another hack to add weight information to the sequence</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">new_record</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="BioSQL.BioSeq.DBSeqRecord.annotations" class="py-name" href="#" onclick="return doclink('link-60', 'annotations', 'link-55');">annotations</a></tt><tt class="py-op">[</tt><tt class="py-string">'weight'</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">weight</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-61', 'append', 'link-26');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">new_record</tt><tt class="py-op">)</tt> </tt>
</div><a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> </tt>
<a name="Alignment.get_column"></a><div id="Alignment.get_column-def"><a name="L333"></a><tt class="py-lineno">333</tt> <a class="py-toggle" href="#" id="Alignment.get_column-toggle" onclick="return toggle('Alignment.get_column');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#get_column">get_column</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">col</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.get_column-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.get_column-expanded"><a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-docstring">"""Returns a string containing a given column.</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-docstring"> e.g.</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.get_column(0)</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"><tt class="py-docstring"> 'AAA'</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.get_column(3)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"><tt class="py-docstring"> 'G-G'</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-comment">#TODO - Support negative indices?</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">col_str</tt> <tt class="py-op">=</tt> <tt class="py-string">''</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">col</tt> <tt class="py-op">>=</tt> <tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">col</tt> <tt class="py-op"><=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Align.Generic.Alignment.get_alignment_length" class="py-name" href="#" onclick="return doclink('link-62', 'get_alignment_length', 'link-21');">get_alignment_length</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">rec</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">:</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-name">col_str</tt> <tt class="py-op">+=</tt> <tt class="py-name">rec</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-63', 'seq', 'link-15');">seq</a></tt><tt class="py-op">[</tt><tt class="py-name">col</tt><tt class="py-op">]</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">col_str</tt> </tt>
</div><a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> </tt>
<a name="Alignment.__getitem__"></a><div id="Alignment.__getitem__-def"><a name="L355"></a><tt class="py-lineno">355</tt> <a class="py-toggle" href="#" id="Alignment.__getitem__-toggle" onclick="return toggle('Alignment.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic.Alignment-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Alignment.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Alignment.__getitem__-expanded"><a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-docstring">"""Access part of the alignment.</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> We'll use the following example alignment here for illustration:</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> >>> from Bio.Alphabet import IUPAC, Gapped</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> >>> align = Alignment(Gapped(IUPAC.unambiguous_dna, "-"))</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Alpha", "ACTGCTAGCTAG")</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Beta", "ACT-CTAGCTAG")</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Gamma", "ACTGCTAGATAG")</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Delta", "ACTGCTTGCTAG")</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-docstring"> >>> align.add_sequence("Epsilon","ACTGCTTGATAG")</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"><tt class="py-docstring"> You can access a row of the alignment as a SeqRecord using an integer</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"><tt class="py-docstring"> index (think of the alignment as a list of SeqRecord objects here):</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"><tt class="py-docstring"> >>> first_record = align[0]</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"><tt class="py-docstring"> >>> print first_record.id, first_record.seq</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-docstring"> Alpha ACTGCTAGCTAG</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-docstring"> >>> last_record = align[-1]</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-docstring"> >>> print last_record.id, last_record.seq</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-docstring"> Epsilon ACTGCTTGATAG</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"><tt class="py-docstring"> You can also access use python's slice notation to create a sub-alignment</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"><tt class="py-docstring"> containing only some of the SeqRecord objects:</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"><tt class="py-docstring"> >>> sub_alignment = align[2:5]</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-docstring"> >>> print sub_alignment</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-docstring"> Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG Gamma</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTTGCTAG Delta</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTTGATAG Epsilon</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"><tt class="py-docstring"> This includes support for a step, i.e. align[start:end:step], which</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"><tt class="py-docstring"> can be used to select every second sequence:</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"><tt class="py-docstring"> >>> sub_alignment = align[::2]</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"> >>> print sub_alignment</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> Gapped(IUPACUnambiguousDNA(), '-') alignment with 3 rows and 12 columns</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG Alpha</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG Gamma</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTTGATAG Epsilon</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"><tt class="py-docstring"> Or to get a copy of the alignment with the rows in reverse order:</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-docstring"> >>> rev_alignment = align[::-1]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-docstring"> >>> print rev_alignment</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-docstring"> Gapped(IUPACUnambiguousDNA(), '-') alignment with 5 rows and 12 columns</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTTGATAG Epsilon</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTTGCTAG Delta</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGATAG Gamma</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> ACT-CTAGCTAG Beta</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> ACTGCTAGCTAG Alpha</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-docstring"> Right now, these are the ONLY indexing operations supported. The use of</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"><tt class="py-docstring"> a second column based index is under discussion for a future update.</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-64" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index,Function Bio.SeqIO.index()=Bio.SeqIO-module.html#index"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-64', 'index', 'link-64');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-comment">#e.g. result = align[x]</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-comment">#Return a SeqRecord</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt id="link-65" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-65', 'index', 'link-64');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-66" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-66', 'index', 'link-64');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">slice</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> <tt class="py-comment">#e.g. sub_aling = align[i:j:k]</tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-comment">#Return a new Alignment using only the specified records.</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-comment">#TODO - See Bug 2554 for changing the __init__ method</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-comment">#to allow us to do this more cleanly.</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">sub_align</tt> <tt class="py-op">=</tt> <tt id="link-67" class="py-name" targets="Class Bio.Align.Generic.Alignment=Bio.Align.Generic.Alignment-class.html,Class Bio.Blast.Record.Alignment=Bio.Blast.Record.Alignment-class.html,Class Bio.Wise.psw.Alignment=Bio.Wise.psw.Alignment-class.html"><a title="Bio.Align.Generic.Alignment
Bio.Blast.Record.Alignment
Bio.Wise.psw.Alignment" class="py-name" href="#" onclick="return doclink('link-67', 'Alignment', 'link-67');">Alignment</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_alphabet</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">sub_align</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_records</tt><tt class="py-op">[</tt><tt id="link-68" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-68', 'index', 'link-64');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">sub_align</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-69" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index
Bio.SeqIO.index" class="py-name" href="#" onclick="return doclink('link-69', 'index', 'link-64');">index</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Row and Column indexing is not currently supported,"</tt>\ </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-op">+</tt><tt class="py-string">"but may be in future."</tt><tt class="py-op">)</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">(</tt><tt class="py-string">"Invalid index type."</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> </tt>
<a name="_test"></a><div id="_test-def"><a name="L430"></a><tt class="py-lineno">430</tt> <a class="py-toggle" href="#" id="_test-toggle" onclick="return toggle('_test');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Align.Generic-module.html#_test">_test</a><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_test-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_test-expanded"><a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-docstring">"""Run the Bio.Align.Generic module's doctests."""</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Running doctests..."</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-keyword">import</tt> <tt class="py-name">doctest</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-name">doctest</tt><tt class="py-op">.</tt><tt class="py-name">testmod</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-string">"Done"</tt> </tt>
</div><a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt id="link-70" class="py-name" targets="Function Bio.Align.Applications._Clustalw._test()=Bio.Align.Applications._Clustalw-module.html#_test,Function Bio.Align.Applications._Dialign._test()=Bio.Align.Applications._Dialign-module.html#_test,Function Bio.Align.Applications._Mafft._test()=Bio.Align.Applications._Mafft-module.html#_test,Function Bio.Align.Applications._Muscle._test()=Bio.Align.Applications._Muscle-module.html#_test,Function Bio.Align.Applications._Prank._test()=Bio.Align.Applications._Prank-module.html#_test,Function Bio.Align.Applications._Probcons._test()=Bio.Align.Applications._Probcons-module.html#_test,Function Bio.Align.Applications._TCoffee._test()=Bio.Align.Applications._TCoffee-module.html#_test,Function Bio.Align.Generic._test()=Bio.Align.Generic-module.html#_test,Function Bio.Align._test()=Bio.Align-module.html#_test,Function Bio.AlignIO.StockholmIO._test()=Bio.AlignIO.StockholmIO-module.html#_test,Function Bio.AlignIO._test()=Bio.AlignIO-module.html#_test,Function Bio.Application._test()=Bio.Application-module.html#_test,Function Bio.Blast.Applications._test()=Bio.Blast.Applications-module.html#_test,Function Bio.DocSQL._test()=Bio.DocSQL-module.html#_test,Function Bio.Emboss.Applications._test()=Bio.Emboss.Applications-module.html#_test,Function Bio.KEGG.Compound._test()=Bio.KEGG.Compound-module.html#_test,Function Bio.KEGG.Enzyme._test()=Bio.KEGG.Enzyme-module.html#_test,Function Bio.Motif._test()=Bio.Motif-module.html#_test,Function Bio.PDB.Selection._test()=Bio.PDB.Selection-module.html#_test,Function Bio.Seq._test()=Bio.Seq-module.html#_test,Function Bio.SeqFeature._test()=Bio.SeqFeature-module.html#_test,Function Bio.SeqIO.AceIO._test()=Bio.SeqIO.AceIO-module.html#_test,Function Bio.SeqIO.PhdIO._test()=Bio.SeqIO.PhdIO-module.html#_test,Function Bio.SeqIO.QualityIO._test()=Bio.SeqIO.QualityIO-module.html#_test,Function Bio.SeqIO._test()=Bio.SeqIO-module.html#_test,Function Bio.SeqRecord._test()=Bio.SeqRecord-module.html#_test,Function Bio.SeqUtils._test()=Bio.SeqUtils-module.html#_test,Function Bio.Sequencing.Applications._Novoalign._test()=Bio.Sequencing.Applications._Novoalign-module.html#_test,Function Bio.Statistics.lowess._test()=Bio.Statistics.lowess-module.html#_test,Function Bio.Wise._test()=Bio.Wise-module.html#_test,Function Bio.Wise.dnal._test()=Bio.Wise.dnal-module.html#_test,Function Bio.Wise.psw._test()=Bio.Wise.psw-module.html#_test"><a title="Bio.Align.Applications._Clustalw._test
Bio.Align.Applications._Dialign._test
Bio.Align.Applications._Mafft._test
Bio.Align.Applications._Muscle._test
Bio.Align.Applications._Prank._test
Bio.Align.Applications._Probcons._test
Bio.Align.Applications._TCoffee._test
Bio.Align.Generic._test
Bio.Align._test
Bio.AlignIO.StockholmIO._test
Bio.AlignIO._test
Bio.Application._test
Bio.Blast.Applications._test
Bio.DocSQL._test
Bio.Emboss.Applications._test
Bio.KEGG.Compound._test
Bio.KEGG.Enzyme._test
Bio.Motif._test
Bio.PDB.Selection._test
Bio.Seq._test
Bio.SeqFeature._test
Bio.SeqIO.AceIO._test
Bio.SeqIO.PhdIO._test
Bio.SeqIO.QualityIO._test
Bio.SeqIO._test
Bio.SeqRecord._test
Bio.SeqUtils._test
Bio.Sequencing.Applications._Novoalign._test
Bio.Statistics.lowess._test
Bio.Wise._test
Bio.Wise.dnal._test
Bio.Wise.psw._test" class="py-name" href="#" onclick="return doclink('link-70', '_test', 'link-70');">_test</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> </tt><script type="text/javascript">
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