[Biopython-dev] [Bug 1745] New: Genbank parser and REGION fields

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1745

           Summary: Genbank parser and REGION fields
           Product: Biopython
           Version: Not Applicable
          Platform: Sun
        OS/Version: SunOS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Martel/Mindy
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mkersz at ccr.jussieu.fr


The Genbank parser chokes on the REGION field of a Genbank record:

Traceback (most recent call last):
  File "./GenBank2Features.py", line 44, in ?
    cr = gb_iterator.next()
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line
129, in next
    return self._parser.parse(File.StringHandle(data))
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line
219, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/GenBank/__init__.py", line
1259, in feed
    self._parser.parseFile(handle)
  File "/usr/local/lib/python2.4/site-packages/Martel/Parser.py", line 328, in
parseFile
    self.parseString(fileobj.read())
  File "/usr/local/lib/python2.4/site-packages/Martel/Parser.py", line 356, in
parseString
    self._err_handler.fatalError(result)
  File "/usr/local/lib/python2.4/xml/sax/handler.py", line 38, in fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond character 172


The line in question (third one):

LOCUS       NC_004353            1237870 bp    DNA     linear   INV 19-APR-2004
DEFINITION  Drosophila melanogaster chromosome 4, complete sequence.
ACCESSION   NC_004353 REGION: 1..1237870

With  "REGION: 1..1237870" deleted, everything goes fine.



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