[Biopython-dev] uniprot release 49/biopython script no longer work

[gould at embl.de]

the simple script/error message which occurs when attempting to parse 
the result
from uniprot is as follows:


gould at milou:~> python
Python 2.4 (#1, Dec 10 2004, 11:49:12)
[GCC 3.3.1 (SuSE Linux)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.WWW import ExPASy
>>> from Bio.SwissProt import SProt
>>> from Bio import File
>>> acc='Q14155'
>>> 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()
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
166, in next
    return self._parser.parse(File.StringHandle(data))
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
290, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
332, in feed
    self._scan_record(uhandle, consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
337, in _scan_record
    fn(self, uhandle, consumer)
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
378, in _scan_dt
    self._scan_line('DT', uhandle, consumer.date, exactly_one=1)
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
359, in _scan_line
    read_and_call(uhandle, event_fn, start=line_type)
  File "/usr/local/lib/python2.4/site-packages/Bio/ParserSupport.py", line 301,
in read_and_call
    method(line)
  File "/usr/local/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line
551, in date
    assert rel_index >= 0, \
AssertionError: Could not find Rel. in DT line: DT   01-NOV-1997, integrated
into UniProtKB/Swiss-Prot.








Quoting Michiel De Hoon <mdehoon at c2b2.columbia.edu>:

> Could you post the error message that you're getting? Preferably, with a
> simple script that causes the error to appear?
>
> --Michiel.
>
> Michiel de Hoon
> Center for Computational Biology and Bioinformatics
> Columbia University
> 1150 St Nicholas Avenue
> New York, NY 10032
>
>
>
> -----Original Message-----
> From: biopython-dev-bounces at portal.open-bio.org on behalf of =
> gould at embl.de
> Sent: Thu 2/9/2006 4:37 AM
> To: biopython-dev at biopython.org
> Subject: [Biopython-dev] uniprot release 49/biopython script no longer =
> work
> =20
> hi
>
> I've been having problems with some of our applications here that use
> biopython
> scripts to retrieve a record from uniprot/swissprot given an accession
> nr/ID....As far as I'm aware the problem only occurred after the release =
> 49.0
> of uniprot/swissprot db yesterday...I see from the release notes that =
> some
> changes were made to the annotation format and suspect this is why the
> biopython scripts are no longer happy??....I've checked to make sure I =
> have
> the
> latest version of biopython but this has not remedied the =
> problem.....This
> problem would seem to lie with biopython but I was wondering if you
> are aware of this problem and if any fix is to be made available??
>
> thanks
>
> Kate Gould
>
>
> _________________________________________________________________________=