[BioPython] GenBank parsing
Kyle Dent
clayton_kd at yahoo.com
Sat Apr 29 15:05:09 UTC 2006
Dear All,
My script was successfully implementing the Genbank
parser until just today I was trying to get it to
parse a genpept file. After much experimentation I
discovered that it was actually having trouble parsing
even newly downloaded GenBank files as well
(downloaded of NCBI).
I wanted to ask if anyone is aware of this problem, I
understand the flat file format was updated this month
and is probably the cause of this.
The output which I am getting:
Traceback (most recent call last):
File "C:\work\GB CDS Extractor.py", line 289, in
open1_clicked
loadGenBank(self, self.gbFilePath)
File "C:\work\GB CDS Extractor.py", line 75, in
loadGenBank
cur_record = genBank_Iterator.next()
File
"C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py",
line 129, in nex
t
return self._parser.parse(File.StringHandle(data))
File
"C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py",
line 219, in par
se
self._scanner.feed(handle, self._consumer)
File
"C:\Python24\Lib\site-packages\Bio\GenBank\__init__.py",
line 1259, in fe
ed
self._parser.parseFile(handle)
File
"C:\Python24\Lib\site-packages\Martel\Parser.py", line
328, in parseFile
self.parseString(fileobj.read())
File
"C:\Python24\Lib\site-packages\Martel\Parser.py", line
356, in parseStrin
g
self._err_handler.fatalError(result)
File "C:\Python24\lib\xml\sax\handler.py", line 38,
in fatalError
raise exception
Martel.Parser.ParserPositionException: error parsing
at or beyond character 136
With thanks,
Kyle
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
More information about the Biopython
mailing list