[Biopython-dev] Notification: incoming/87

[biopython-bugs at bioperl.org]

JitterBug notification

bienstam moved PR#87 from incoming to fixed-bugs
Message summary for PR#87
	From: rickard.sandberg at mtc.ki.se
	Subject: genbank_format 2 added tags
	Date: Tue, 8 Oct 2002 07:46:53 -0400
	0 replies 	0 followups
	Notes: Included in 1.10. Closing bug report. 


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>From rickard.sandberg at mtc.ki.se Tue Oct  8 07:46:57 2002
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Date: Tue, 8 Oct 2002 07:46:53 -0400
Message-Id: <200210081146.g98Bkr4P000656 at pw600a.bioperl.org>
From: rickard.sandberg at mtc.ki.se
To: biopython-bugs at bioperl.org
Subject: genbank_format 2 added tags

Full_Name: Rickard Sandberg
Module: genbank_format.py
Version: 1.00a4
OS: linux
Submission from: generic2.mtc.ki.se (130.237.137.207)


When parsing entries in GenBank (GID:9627127 and 14270686 for example). You get
parser Error:

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line 1555, 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 1250, in
feed
    self._parser.parseFile(handle)
  File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 230, in
parseFile
    self.parseString(fileobj.read())
  File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 258, in
parseString
    self._err_handler.fatalError(result)
  File "/usr/lib/python2.2/xml/sax/handler.py", line 38, in fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond character
60674

However, I found that the reason being that the 2 documents contained Feature
Tags not present in the genbank_format.py file.

So, when I added "snoRNA" in feature_key_names and
"isolation_source" in the feature_qualifier_names
it works.

Also, I added the possible use of "linear" in the 
residue_type in the LOCUS definition, which I think was the reason for
parserError in some files I had couple of months ago.

Bye