[Biopython-dev] Notification: incoming/55

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chapmanb changed notes

Message summary for PR#55
	From: newgene at bigfoot.com
	Subject: GenBank parser problem?
	Date: Sat, 26 Jan 2002 13:22:55 -0500
	0 replies 	0 followups
	Notes: NCBI added a new "linear" word to the LOCUS line which broke the parser here.
Fixed in revision 1.17 of genbank_format.py, and tests added for this case.



====> ORIGINAL MESSAGE FOLLOWS <====

>From newgene at bigfoot.com Sat Jan 26 13:22:55 2002
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Date: Sat, 26 Jan 2002 13:22:55 -0500
Message-Id: <200201261822.g0QIMtA00434 at pw600a.bioperl.org>
From: newgene at bigfoot.com
To: biopython-bugs at bioperl.org
Subject: GenBank parser problem?

Full_Name: Chunlei Wu
Module: Bio/GenBank
Version: 1.00a4 
OS: win2000
Submission from: pathg01-178.mdacc.tmc.edu (143.111.173.178)


Python version: ActivePython 2.1.1

Symptom:

>>> from Bio import GenBank
>>> gi=GenBank.search_for("NM_007355")[0]
>>> ncbi_dict=GenBank.NCBIDictionary(parser=GenBank.FeatureParser())
>>> record=ncbi_dict[gi]
Traceback (most recent call last):
  File "<interactive input>", line 1, in ?
  File "C:\Python21\Bio\GenBank\__init__.py", line 1555, in __getitem__
    return self.parser.parse(handle)
  File "C:\Python21\Bio\GenBank\__init__.py", line 268, in parse
    self._scanner.feed(handle, self._consumer)
  File "C:\Python21\Bio\GenBank\__init__.py", line 1250, in feed
    self._parser.parseFile(handle)
  File "C:\Python21\Martel\Parser.py", line 230, in parseFile
    self.parseString(fileobj.read())
  File "C:\Python21\Martel\Parser.py", line 258, in parseString
    self._err_handler.fatalError(result)
  File "C:\Python21\lib\xml\sax\handler.py", line 38, in fatalError
    raise exception
ParserPositionException: error parsing at or beyond character 55
>>> 


Did GenBank change the format?
Thanks.

Chunlei