[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|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #13 from fkauff at biologie.uni-kl.de  2008-07-01 04:36 EST -------
Just uploaded a new Nexus.py to CVS.
First, the taxlabels command in a taxa block is now ignored. For a standard
nexus file, taxon labels are in the matrix, and a taxon block is irrelevant.
The only exception are transposed matrices, which are not supported by Nexus.py
anyway.
Without the added confusion of a separate taxlabels command, it is now fairly
easy to deal with duplicate names. Both self.taxlabels and self.matrix now
carry the same set of unique taxon names.
All example files seem to work fine for me. unless I hear otherwise, I close
this bug. 


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