[Biopython-dev] Notification: incoming/55

[Rich Grenyer]

Found the same problem on Friday with BioPython1.00a4 on both a 
MacPython2.2 and a Linux Python2.1 installation.

Rich





>JitterBug notification
>
>new message incoming/55
>
>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
>
>====> ORIGINAL MESSAGE FOLLOWS <====
>
>>From newgene at bigfoot.com Sat Jan 26 13:22:55 2002
>Received: from localhost (localhost [127.0.0.1])
>	by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id g0QIMtA00434
>	for <biopython-bugs at pw600a.bioperl.org>; Sat, 26 Jan 2002 
>13:22:55 -0500
>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
>
>
>
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>Biopython-dev at biopython.org
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-- 
___________________________

Rich Grenyer
Mammalian Evolution and Conservation
Department of Biology and Biochemistry
Imperial College at Silwood Park
Sunningdale
Berkshire
SL5 7PY
UNITED KINGDOM

Tel: +00 44 (0)20 7594 2328
Fax: +00 44 (0)20 7594 2339
Mob: +00 44 (0)7967 632093
email: r.grenyer at ic.ac.uk
WWW: http://www.bio.ic.ac.uk/evolve/people/rich

___________________________