[BioPython] swissprot parser problem

[Iddo Friedberg]

Works for me. Can you try the latest version off CVS and see if this 
repeats?

Thanks,

Iddo

Asa Ben-Hur wrote:
> While iterating over the newest (40.44) swissprot flat file
> using a swissprot parser
>     sprotFile = open(sprotFileName)
>     s_parser = SProt.RecordParser()
>     s_iterator = SProt.Iterator(sprotFile, s_parser)
> I get the following error:
> 
>   File "extract.py", line 20, in ecExtract
>     s_record = s_iterator.next()
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 168, in next
>     return self._parser.parse(File.StringHandle(data))
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 289, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 332, in feed
>     self._scan_record(uhandle, consumer)
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 337, in _scan_record
>     fn(self, uhandle, consumer)
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 411, in _scan_reference
>     self._scan_ra(uhandle, consumer)
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 433, in _scan_ra
>     one_or_more=1)
>   File "/usr/local/lib/python2.2/site-packages/Bio/SwissProt/SProt.py",
> line 359, in _scan_line
>     read_and_call(uhandle, event_fn, start=line_type)
>   File "/usr/local/lib/python2.2/site-packages/Bio/ParserSupport.py", line
> 331, in read_and_call
>     raise SyntaxError, errmsg
> SyntaxError: Line does not start with 'RA':
> RP   550-559; 573-580 AND 584-601 (DELTA-1).
> 
> No error occurs on an earlier release 40 file.
> This could be related to the fact that swissprot now has
> multiple RP lines (was not the case in earlier versions)
> Indeed, the entry that caused the error has multiple RP lines.
> Its accession no. is Q14738.
> 
> -Asa
> 
> 
> ^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^!^
> Asa Ben-Hur
> Postdoc, Brutlag Bioinformatics Group
> Stanford
> 
> 
> 
> 
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
> 
> 

-- 
Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://bioinformatics.ljcrf.edu/~iddo