[Biopython-dev] [Bug 2340] SProt.py fails to parse the current Swiss-Prot version 54.0

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2340





------- Comment #2 from gould at embl.de  2007-07-26 12:06 EST -------
(In reply to comment #0)
> Hi, 
> 
> I'm running on a red hat linux box on python 2.3.4 and am trying to parse any
> swiss-prot record but the parser just seems to bomb out not throwing an error
> of where it actually fails. I'm guessing it has to do with the Release 54.0 of
> 24-Jul-07 of UniPROT with the addition of the new line type PE??
> 

(In reply to comment #1)
> Hi Kate,
> 
> Could you give us the URL of one or two specific SwissProt files you're having
> trouble with.
> 
> Also how are you trying to read the SwissProt files? e.g. with
> Bio.SeqIO.parse()?
> 
> If you could include the python error too, that could be helpful. Thanks.
> 
> Peter
> 

hi 
the following snippet of code is where the error occurs(this used to work no
problem before something changed in the last day or two I guess)

def getSequence(self,acc):
""" This method retrieves the most recent annotated sequence from the ExPASy
server for a given accession number. """

        from Bio.WWW import ExPASy
        from Bio.SwissProt import SProt
        from Bio import File

        if acc != '':
            try:
                results = ExPASy.get_sprot_raw(acc.strip()).read()
                sp_parser = SProt.RecordParser()
                sp_iterator = SProt.Iterator(File.StringHandle(results),
sp_parser)
                Record = sp_iterator.next()
                return Record.sequence.strip()
            except:
                return -1
        else:
            return acc


breaks at line : Record = sp_iterator.next() but doesn't print any error to
terminal....
some examples of accessions nrs used are: P01100, P12522 etc

thanks
Kate


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