Re: RE : Problem with the Swiss Prot parser (BUG#1706)

On Nov 2, 2004, at 10:18 AM, Jonathan Boulais wrote:

> After installing the latest update of the Swiss Prot parser from cvs, 
> I'm
> getting this error :
> Traceback (most recent call last):
>   File "C:\Joe_script\Parser_Trembl.py", line 30, in ?
>     cur_record = s_iterator.next()
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 166, in
> next  return self._parser.parse(File.StringHandle(data))
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 290, in
> parse  self._scanner.feed(handle, self._consumer)
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 332, in
> feed
>     self._scan_record(uhandle, consumer)
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 337, in
> _scan_record
>     fn(self, uhandle, consumer)
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 468, in
> _scan_sq
>     self._scan_line('SQ', uhandle, consumer.sequence_header, 
> exactly_one=1)
>   File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 
> 359, in
> _scan_line
>     read_and_call(uhandle, event_fn, start=line_type)
>   File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 300, 
> in
> read_and_call
>     raise SyntaxError, errmsg
> SyntaxError: Line does not start with 'SQ':
> RA   Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S.,
>
> ------- Additional Comment #1 From Jeffrey Chang 2004-10-25 14:47 
> -------
> Try grabbing the latest Bio/SwissProt/SProt.py file from the CVS 
> (cvs.biopython.org).  There's been
> some fixes to the parser, which might fix your problem.  If it does 
> not, then please send some sample
> code and data file.
>
> Jeff
> ---------------------------------------------------------------
> Hi Jeff,
> I've updated the  whole Biopython package from the cvs on a Windows 
> machine and a Mac OS/X machine.
> Both cpu gave me the same error (see above).
> I'm sending you the script that I wrote. Before you check it out, I 
> have to say that I'm a biologist
> who's handling a little bit of Python. So don't pull your hair off 
> when you'll have a peak on it !
> I wrote this script to be able to parse the Uniprot flat file, which 
> has been established by the Swiss Prot group.
> The structure of the file is the same as Swiss Prot and it's been 
> working well before the new adjustments that Uniprot/Swiss Prot made 
> on their flat files.
> I won't send you the flat file, cuz you can download it from this link 
> :
> ftp://ftp!
> .uniprot.org/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz
> Thank you very much for the help !
> Jonathan Boulais
> University of Montreal


Hi Jonathan,

I am able to parse the entire uniprot_sprot.dat.gz file successfully 
with the current swiss-prot parser.  I have attached the current 
SProt.py file from the cvs.  Please install this over the current one, 
and check to make sure that this version is indeed the one accessed 
from your script.  For example, do:

>>> from Bio.SwissProt import SProt
>>> print SProt.__file__
/Users/jchang/lib/jchang/python/Bio/SwissProt/SProt.pyc

And make sure that you have copied this file in that location.  Please 
let me know if there are further problems.

Jeff

SProt.py
Description: Binary data

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