Trees | Indices | Help |
---|
|
1 # Copyright 2006 by Peter Cock. All rights reserved. 2 # This code is part of the Biopython distribution and governed by its 3 # license. Please see the LICENSE file that should have been included 4 # as part of this package. 5 6 from Bio.Seq import Seq 7 from Bio.SeqRecord import SeqRecord 8 from Bio.Nexus import Nexus 9 10 #You can get a couple of example files here: 11 #http://www.molecularevolution.org/resources/fileformats/ 12 13 #This is a generator function!15 """Returns SeqRecord objects from a Nexus file 16 17 Thus uses the Bio.Nexus module to do the hard work.""" 18 n = Nexus.Nexus(handle) 19 for id in n.original_taxon_order : 20 if id in n.matrix : 21 seq = n.matrix[id] 22 else : 23 #Missing the sequence? 24 seq = Seq("", n.alphabet) 25 #ToDo - Can we extract any annotation too? 26 yield SeqRecord(seq, id=id, name=id, description="") 27 #All done 28 return29
Trees | Indices | Help |
---|
Generated by Epydoc 3.0.1 on Thu Feb 7 11:51:48 2008 | http://epydoc.sourceforge.net |