[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





------- Comment #10 from biopython-bugzilla at maubp.freeserve.co.uk  2008-06-30 13:22 EST -------
Created an attachment (id=958)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=958&action=view)
Second example file

Using the first file where there is no TAXA block:

>>> from Bio.Nexus import Nexus
>>> n = Nexus.Nexus(open('dup_names.nex'))
>>> print n.matrix.keys()
['CATH_HUMAN', 'CYS1_DICDI', 'CYS1_DICDI.copy', 'ALEU_HORVU']
>>> print n.original_taxon_order
['CYS1_DICDI', 'ALEU_HORVU', 'CATH_HUMAN', 'CYS1_DICDI.copy']

Then with a TAXA block,

>>> n2 = Nexus.Nexus(open('dup_names2.nex'))
>>> print n2.matrix.keys()
['CATH_HUMAN', 'CYS1_DICDI', 'CYS1_DICDI.copy', 'ALEU_HORVU']
>>> print n2.original_taxon_order
['CYS1_DICDI', 'ALEU_HORVU', 'CATH_HUMAN', 'CYS1_DICDI']

Notice the different behaviour of the original_taxon_order list.  In the first
case it gets the modified names, in the second case it doesn't.

Is this deliberate Frank?  On the other hand, maybe Nexus files without a TAXA
block are rare in real life?  Are they?


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