[Biopython-dev] [Bug 1758] genbank parser chokes on /transl_except

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

http://bugzilla.open-bio.org/show_bug.cgi?id=1758





------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2005-03-08 17:25 -------
Created an attachment (id=199)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=199&action=view)
Test case - a reduced version of NT_033779.gbk

Confirms bug exists in BioPython 1.30 / CVS version of Bio/GenBank/__init__.py
as follows.

The attchement is an reduced version of NT_033779.gbk with only a few features
and only a fraction of the full sequence.

Traceback (most recent call last):
  File "C:\TEMP\genbank\test004.py", line 52, in ?
    cur_record = gb_iterator.next()
  File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 129, in
next
    return self._parser.parse(File.StringHandle(data))
  File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 240, in
parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python23\lib\site-packages\Bio\GenBank\__init__.py", line 1264, in
feed
    self._parser.parseFile(handle)
  File "C:\Python23\lib\site-packages\Martel\Parser.py", line 332, in parseFile

    self.parseString(fileobj.read())
  File "C:\Python23\lib\site-packages\Martel\Parser.py", line 360, in
parseString
    self._err_handler.fatalError(result)
  File "C:\Python23\lib\xml\sax\handler.py", line 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 6841



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