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

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 

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Parser_SProt.py
Description: Text document

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