[Biopython-dev] Notification: incoming/69

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new message incoming/69

Message summary for PR#69
	From: Jeffrey Chang <jchang at smi.stanford.edu>
	Subject: Re: [Biopython-dev] Notification: incoming/68
	Date: Mon, 6 May 2002 16:39:18 -0700
	0 replies 	0 followups

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

>From jchang at springfield.stanford.edu Mon May  6 19:39:35 2002
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Date: Mon, 6 May 2002 16:39:18 -0700
From: Jeffrey Chang <jchang at smi.stanford.edu>
To: cdewey at eecs.berkeley.edu, biopython-bugs at bioperl.org
Cc: biopython-dev at biopython.org
Subject: Re: [Biopython-dev] Notification: incoming/68
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In-Reply-To: <200205040009.g4409mdo015564 at pw600a.bioperl.org>; from biopython-bugs at bioperl.org on Fri, May 03, 2002 at 08:09:48PM -0400

It looks like the SwissProt format has been changed.

In SProt.py,
    def _scan_rp(self, uhandle, consumer):
        self._scan_line('RP', uhandle, consumer.reference_position,
                        exactly_one=1)
change exactly_one to one_or_more:
    def _scan_rp(self, uhandle, consumer):
        self._scan_line('RP', uhandle, consumer.reference_position,
                        one_or_more=1)

jeff



On Fri, May 03, 2002 at 08:09:48PM -0400, biopython-bugs at bioperl.org wrote:
> JitterBug notification
> 
> 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
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From cdewey at eecs.berkeley.edu Fri May  3 20:09:48 2002
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id g4409ldo015560
> 	for <biopython-bugs at pw600a.bioperl.org>; Fri, 3 May 2002 20:09:47 -0400
> 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
> Version: 
> OS: Windows 2000
> Submission from: dsl092-003-035.sfo1.dsl.speakeasy.net (66.92.3.35)
> 
> 
> 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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