[Biopython-dev] [Bug 1492] New: Martel Parser fails on Bio.db["protein-genbank-cgi"] entry

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

http://bugzilla.bioperl.org/show_bug.cgi?id=1492

           Summary: Martel Parser fails on Bio.db["protein-genbank-cgi"]
                    entry
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Martel/Mindy
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: henschel at mpi-cbg.de


# Hi There!

#The following few lines broke on a rather simple parsing, however it looks
#reproducible (using biopython 1.21 on python 2.2.2)
#It works for most other entries I tested.

from Bio import GenBank
from Bio import db

genbank=db["protein-genbank-cgi"]
parser=GenBank.FeatureParser()
h=genbank["3891376"]
res=parser.parse(h)
# Causes Error: Martel.Parser.ParserPositionException: error parsing at or 
#beyond character 4462

>>> print genbank["3891376"].read() # still works though!
# Hope it makes sense to you
# Cheers, Andreas



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