[Biopython-dev] Error parsing a genBank file

[Iddo Friedberg]

Hi,

I am getting an error on parsing a GenBank file. It's the E. coli K12 
Genome, downloaded from:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000913

Egads! How do I turn Martel's debug feature on? Setting it to level 2 in 
FeatureParser didn't seem to do much...


Thanks,

Iddo


 >>> gb_iter = GenBank.Iterator(open('ecoli_k12.gb'),fp)
 >>> fp = GenBank.FeatureParser()
 >>> cur_rec = gb_iter.next()
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/home/iddo/biopy_cvs/biopython/Bio/GenBank/__init__.py", line 
142, in next
     return self._parser.parse(File.StringHandle(data))
   File "/usr/home/iddo/biopy_cvs/biopython/Bio/GenBank/__init__.py", 
line 229, in parse
     self._scanner.feed(handle, self._consumer)
   File "/usr/home/iddo/biopy_cvs/biopython/Bio/GenBank/__init__.py", 
line 1251, in feed

   File "/usr/home/iddo/biopy_cvs/biopython/Martel/Parser.py", line 328, 
in parseFile
     self.parseString(fileobj.read())
   File "/usr/home/iddo/biopy_cvs/biopython/Martel/Parser.py", line 356, 
in parseString
     self._err_handler.fatalError(result)
   File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line 
38, in fatalError
     raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond 
character 1414769







-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://ffas.ljcrf.edu/~iddo