[BioPython] Biopython GenBank
JINLING HUANG
jinling@cs.uga.edu
Tue, 19 Nov 2002 09:25:25 -0500 (EST)
Hello,
I am writing a script to parse GenBank records using biopython.
Essentially I just copied the script from the biopython tutorial as
follows:
from Bio import GenBank
gb_file = 'ncbiSamples'
gb_handle = open(gb_file, 'r')
fp1 = open('ncbiSeq', 'w+')
feature_parser = GenBank.FeatureParser()
gb_iterator = GenBank.Iterator(gb_handle, feature_parser)
while 1:
cur_record = gb_iterator.next()
if cur_record is None:
break
print cur_record.id
sequence=cur_record.seq.data
print sequence
fp1.write('>'+cur_record.id[:-2]+'\n'+sequence+'\n')
The script worked well for some records. The I got error messages:
Traceback (most recent call last):
File "getSeq.py", line 13, in ?
cur_record = gb_iterator.next()
File "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
183, in next return self._parser.parse(File.StringHandle(data))
File "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
268, in parse self._scanner.feed(handle, self._consumer)
File "/bio/python2.2/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
1252, in feed self._parser.parseFile(handle)
File "/bio/python2.2/lib/python2.2/site-packages/Martel/Parser.py", line
338, in parseFile self.parseString(fileobj.read())
File "/bio/python2.2/lib/python2.2/site-packages/Martel/Parser.py", line
366, in parseString self._err_handler.fatalError(result)
File "/bio/python2.2/lib/python2.2/xml/sax/handler.py", line 38, in
fatalError raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond
character 1525
Has everyone encountered the same problem? How do we get rid of this
problem?
Best wishes,
Jinling Huang