[Biopython-dev] [Bug 2531] Nexus and fasta parsers have a problem with identical taxa names

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2531


fkauff at biologie.uni-kl.de changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




------- Comment #6 from fkauff at biologie.uni-kl.de  2008-06-30 11:38 EST -------
Handling a handle works like a charm for me with the attachment provided:

>>> handle=open('eg.nex')
>>> n=Nexus.Nexus(handle)
>>> n.matrix.keys()
['HI99.Line5.copy', 'am', 'HI99.Line1.copy', 'ezo', 'HI99.Line0.copy',
'DI05.Line5.copy', 'DI05.Line0.copy', 'DI05.Line8.copy1', 'DI05.Line1.copy1',
'HI99.Line3.copy', 'HI99.Line1.copy1', 'DI05.Line1.copy', 'DI05.Line9.copy',
'DI05.Line8.copy', 'HI99.Line4.copy', 'vir', 'DI05.Line8', 'DI05.Line9',
'HI99.Line2.copy', 'DI05.Line2', 'DI05.Line3', 'DI05.Line0', 'DI05.Line1',
'DI05.Line6', 'DI05.Line7', 'DI05.Line4', 'DI05.Line5', 'HI99.Line1',
'HI99.Line0', 'HI99.Line3', 'HI99.Line2', 'HI99.Line5', 'HI99.Line4']

However, Nexus.py needs unique taxon names. Non-unique taxon names won't make
much sense in a nexus file imho. If Nexus.py encounters non-unique names, they
are unified by adding a suffix (.copy, .copy1, ...) to it. Could this cause
problems to SeqIO.NexusIO?

Frank


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