[Biopython-dev] [Bug 2558] Bio.Nexus chokes on TRANSLATE block with superfluous comma

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2558


fkauff at biologie.uni-kl.de changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |INVALID




------- Comment #3 from fkauff at biologie.uni-kl.de  2008-08-04 05:12 EST -------
... as nobody objected and/or brought an additional example of 'trailing
commas', I close this bug.

Frank


(In reply to comment #2)
> I'm all for a little bit of slack in parsers, but this looks in my opinion like
> a straightforward syntax error in the nexus file. I work with nexus files
> daily, and have never encountered such a trailing comma. What really confuses
> me is that there are 58 taxa in the data set, and  no. 59 Lecanorales is in
> addition, with no data and no occurence in the tree. I don't think this is
> proper nexus format.
> 
> Frank
> 
> 
> 
> (In reply to comment #1)
> > This is an issue in the Bio.Nexus module, so its a job for Frank.  
> > 
> > Do you know if this affects all the NEXUS files from www.treebase.org? I've
> > tried downloading several trees, but their FTP site is just timing out for me. 
> > According to http://www.treebase.org/treebase/submit.html the request trees be
> > uploaded in the NEXUS file format so its possible that just a minority of their
> > trees have this trailing comma.
> > 
> > Note that this may be an invalid file (a TRANSLATE block with trailing comma),
> > but as you say it looks relatively straight forward to cope with.  However, I
> > have had a quick look at the Bio.Nexus code, and I don't entirely understand
> > what Frank's parser is doing here - so its not going to be a quick fix from me.
> > 
> > 


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.