[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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