[Biopython-dev] [Bug 2353] Swissprot (UniProt) files with ** lines fail to parse

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Aug 31 07:22:11 UTC 2007


------- Comment #8 from ibdeno at gmail.com  2007-08-31 03:22 EST -------
Hi, sorry for the late answer.

I downloaded SProt.py and installed it as before. The parser doesn't fail now
on the "**" lines. Strangely enough, though, it seems to fail again on "PE" 
(protein evidence) lines. See an example:

Traceback (most recent call last):
  File "./molsprot.py", line 196, in ?
  File "./molsprot.py", line 144, in main
    for record in iterator:
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 172, in
    return self._parser.parse(File.StringHandle(data))
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 296, in
    self._scanner.feed(handle, self._consumer)
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 338, in
    self._scan_record(uhandle, consumer)
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 343, in
    fn(self, uhandle, consumer)
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 495, in
    self._scan_line('SQ', uhandle, consumer.sequence_header, exactly_one=1)
  File "/sw/lib/python2.4/site-packages/Bio/SwissProt/SProt.py", line 365, in
    read_and_call(uhandle, event_fn, start=line_type)
  File "/sw/lib/python2.4/site-packages/Bio/ParserSupport.py", line 300, in
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'SQ':
PE   1: Evidence at protein level;

I didn't use CVS, just downloaded SProt.py from the link you sent. Perhaps I
should download other files?

Thank you!


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