[BioPython] New User problem with GenBank

Cheung Auyeung cheung_auyeung at yahoo.com
Fri Jul 4 14:26:29 EDT 2003


Hi

I try to follow the GenBank tortorila from the Biopython Tutorial and 
Cookbook and I get the following error messages:

auyeung at sunday auyeung]$ python
Python 2.2.2 (#1, Feb 24 2003, 19:13:11)
[GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
 >>> from Bio import GenBank
 >>> gi_list = GenBank.search_for("Opuntia AND rpl16")
 >>> record_parser = GenBank.FeatureParser()
 >>> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser)
 >>> gb_seqrecord = ncbi_dict[gi_list[0]]
Traceback (most recent call last):
   File "<stdin>", line 1, in ?
   File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 
1563, in __getitem__
     return self.parser.parse(handle)
   File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 
268, in parse
     self._scanner.feed(handle, self._consumer)
   File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 
1255, in feed
     self._parser.parseFile(handle)
   File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 338, 
in parseFile
     self.parseString(fileobj.read())
   File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 366, 
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 1108

Any suggestion to fix the problem?

Thanks

Cheung



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