[Biopython-dev] [Bug 2558] New: AlignIO nexus parsing chokes on superfluous comma

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

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

           Summary: AlignIO nexus parsing chokes on superfluous comma
           Product: Biopython
           Version: 1.47
          Platform: All
               URL: http://www.cs.utexas.edu/~rsuri/M3579.NX
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: rsuri at cs.utexas.edu


The URL above points to a nexus file (also available from TreeBase with Matrix
accession #M3579) that causes BioPython to raise an error when reading it with
the AlignIO module.  In the "Trees" section of the input file, the final taxon
("Lecanorales") has a trailing comma that causes BioPython to fail (search for
the line beginning with "59").  I've verified that manually deleting the
offending comma is a valid workaround.

I don't know what the nexus format specification says, but this is poor form
for BioPython, in my opinion.  It seems reasonable enough to allow for some
slack like this when reading formatted files.


-- 
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.