[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 #6 from fkauff at biologie.uni-kl.de  2010-07-28 04:49 EST -------
I think this is a bug - taxa in a translate statement are separated by commas,
and after the last one, there is a semicolon, not both. Which makes sense.

You're welcome to report it - probably you have more info at hand how the file
was generated...

Frank

PS. I Updated tree parsing in Nexus to handle the 

tree * PRANK = ...

statement.


(In reply to comment #5)
> (In reply to comment #4)
> > 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.
> 
> Sure - but on the other hand, this why we test things too ;)
> 
> > The translate statement in the nexus file ends both with a , AND a ; after the
> > second taxon, which is also not nexus compliant.
> > 
> > Frank
> 
> So you think there is a problem with PRANK's output here? Would you like to
> report this or should I?
> 
> Peter
> 


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