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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link="#0563C1" vlink="#954F72"><div class=WordSection1><p class=MsoNormal>Hi<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>How do I get the alignment out of Align.PairwiseAligner?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I have the following code<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='background:white'><span style='font-size:9.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-GB'>aligner = Align.PairwiseAligner()<o:p></o:p></span></p><pre style='background:white'><span style='font-size:9.0pt;color:black'>alignments = aligner.align(</span><span style='font-size:9.0pt;color:#94558D'>self</span><span style='font-size:9.0pt;color:black'>.sequence1, </span><span style='font-size:9.0pt;color:#94558D'>self</span><span style='font-size:9.0pt;color:black'>.sequence2)<br></span><b><span style='font-size:9.0pt;color:navy'>for </span></b><span style='font-size:9.0pt;color:black'>alignment </span><b><span style='font-size:9.0pt;color:navy'>in </span></b><span style='font-size:9.0pt;color:navy'>sorted</span><span style='font-size:9.0pt;color:black'>(alignments):<o:p></o:p></span></pre><pre style='margin-left:36.0pt;background:white'><span style='font-size:9.0pt;color:black'>logging.debug(alignment)<br>logging.debug(alignment.score)<br>logging.debug(alignment.target)<br>logging.debug(alignment.query)<br>logging.debug(alignment.path)<br>logging.debug(</span><span style='font-size:9.0pt;color:navy'>dir</span><span style='font-size:9.0pt;color:black'>(alignment))<o:p></o:p></span></pre><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>my example<o:p></o:p></p><p class=MsoNormal>Query 193 residues long. <o:p></o:p></p><p class=MsoNormal>Target 6 residues long.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>out of this I can get the <o:p></o:p></p><p class=MsoNormal>alignment – which appears to be a line separated string of query, alignment, target. <o:p></o:p></p><p class=MsoNormal>In my example:<o:p></o:p></p><p class=MsoNormal>MEKLEVGIYTRAREGEIACGDACLVKRVEGVIFLAVGDGIGHGPEAARAAEIAIASMESSMNTGLVNIFQLCHRELRGTRGAVAALCRVDRRQGLWQAAIVGNIHVKILSAKGIITPLATPGILGYNYPHQLLIAKGSYQEGDLFLIHSDGIQEGAVPLALLANYRLTAEELVRLIGEKYGRRDDDVAVIVAR<o:p></o:p></p><p class=MsoNormal>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|XX|XX-----<o:p></o:p></p><p class=MsoNormal>--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RANDOM-----<o:p></o:p></p><p class=MsoNormal>score – the alignment score (I can also get this with aligner.score)<o:p></o:p></p><p class=MsoNormal>target – self.sequence2<o:p></o:p></p><p class=MsoNormal>query – self.sequence1<o:p></o:p></p><p class=MsoNormal>path – I think this is what I want, but I don’t know how to interpret this – it is something the following in the above example: ((0, 0), (182, 0), (188, 6), (193, 6))<o:p></o:p></p><p class=MsoNormal>is this documented somewhere?<o:p></o:p></p><p class=MsoNormal>It looks like 0-181 no alignment, 182 to 187 adds a score of 6. 188 to 193 keeps the score at 6.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>when I dir(alignment) I only see the above options<o:p></o:p></p><p class=MsoNormal>['__class__', '__cmp__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__gt_<o:p></o:p></p><p class=MsoNormal>_', '__hash__', '__init__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subc<o:p></o:p></p><p class=MsoNormal>lasshook__', '__weakref__', '_format_psl', 'path', 'query', 'score', 'target']<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>what I’m after is the middle row of the alignment (above). Is the only option to split alignment on carriage return? <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thanks<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>John<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>--<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>John Berrisford<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>PDBe<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>European Bioinformatics Institute (EMBL-EBI)<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>European Molecular Biology Laboratory<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>Wellcome Trust Genome Campus<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>Hinxton<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>Cambridge CB10 1SD UK<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'>Tel: +44 1223 492529<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><a href="http://www.pdbe.org/"><span style='color:#0563C1'>http://www.pdbe.org</span></a><o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><a href="http://www.facebook.com/proteindatabank"><span style='color:#0563C1'>http://www.facebook.com/proteindatabank</span></a><o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-GB'><a href="http://twitter.com/PDBeurope"><span style='color:#0563C1'>http://twitter.com/PDBeurope</span></a><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>