[Biopython-dev] Notification: incoming/68

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Fri May 3 20:09:48 EDT 2002

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new message incoming/68

Message summary for PR#68
	From: cdewey at eecs.berkeley.edu
	Subject: PRIVATE: SwissProt Parser error
	Date: Fri, 3 May 2002 20:09:47 -0400
	0 replies 	0 followups


>From cdewey at eecs.berkeley.edu Fri May  3 20:09:48 2002
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Date: Fri, 3 May 2002 20:09:47 -0400
Message-Id: <200205040009.g4409ldo015560 at pw600a.bioperl.org>
From: cdewey at eecs.berkeley.edu
To: biopython-bugs at bioperl.org
Subject: PRIVATE: SwissProt Parser error

Full_Name: Colin Dewey
Module: Bio/SwissProt/SProt.py
OS: Windows 2000
Submission from: dsl092-003-035.sfo1.dsl.speakeasy.net (

I get an error while trying to create an index for a SwissProt format file
containing SwissProt AC P30613.  It seems to fail on the two lines:

RP   VARIANTS S-332; S-336; K-354 DEL; D-361; T-392; H-498; Q-510 AND
RP   W-532.

Here is the error output:

>>> SProt.index_file('sprot_text.txt', 'sprot_index.txt')
Traceback (most recent call last):
  File "<interactive input>", line 1, in ?
  File "Bio\SwissProt\SProt.py", line 868, in index_file
  File "Bio\SwissProt\SProt.py", line 168, in next
  File "Bio\SwissProt\SProt.py", line 289, in parse
  File "Bio\SwissProt\SProt.py", line 332, in feed
  File "Bio\SwissProt\SProt.py", line 337, in _scan_record
  File "Bio\SwissProt\SProt.py", line 411, in _scan_reference
  File "Bio\SwissProt\SProt.py", line 433, in _scan_ra
  File "Bio\SwissProt\SProt.py", line 359, in _scan_line
  File "Bio\ParserSupport.py", line 331, in read_and_call
SyntaxError: Line does not start with 'RA':
RP   W-532.

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