[Biopython-dev] [Bug 3119] Bio.Nexus can't parse file from Prank 100701 (1st July 2010)

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http://bugzilla.open-bio.org/show_bug.cgi?id=3119





------- Comment #4 from fkauff at biologie.uni-kl.de  2010-07-28 04:20 EST -------
Slashes in Taxon names may cause troubles (even when properly quoted), not only
for Bio.Nexus, but also for many other programs. If you want to use / or other
special characters in taxon names, better use a " or ' around them. It might be
best to avoid them entirely, my experience is that at one point during file
processing there will be a software that complains.

The translate statement in the nexus file ends both with a , AND a ; after the
second taxon, which is also not nexus compliant.

Frank




(In reply to comment #0)
> I've been updating test_Prank_tool.py to cope with the latest version of Prank,
> 1 July 2010 from http://www.ebi.ac.uk/goldman-srv/prank/src/prank/
> 
> Some changes are simple, such as removing tests using feature of Prank which
> have been removed. One test is failing due to some big changes in the NEXUS
> output from Prank, and this may be due to a problem with our parser:
> 
> >>> from Bio.Nexus import Nexus
> >>> n = Nexus.Nexus("output_prank_v100701.nex")
> Traceback (most recent call last):
> ...
> Bio.Nexus.Nexus.NexusError: Taxon AK1H_ECOLI: Illegal character / in line: 
> (check dimensions / interleaving)
> 
> I will attach the file, it is created by the unit test as output.2.nex but
> is usually deleted.
> 
> Peter
> 


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