[Biopython-dev] [Bug 1669] New: SwissProt Parser error - cannot read recent SwissProt entries

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Jul 17 13:42:13 EDT 2004


           Summary: SwissProt Parser error - cannot read recent SwissProt
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: major
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: kris at math.princeton.edu

RX field of a SwissProt entry can, in newer records, be more than 1 line long,
while Sprot.py only accepts one line per record. See error message below. RX is
database reference of the article relevant to the entry, and Swissprot has
recently added DOI references as well. RA should be the next field after RX, but
if there are two RX lines in the record, parser chokes. 

Traceback (most recent call last):
  File "<stdin>", line 1, in ?
  File "find_pdb_orgs.py", line 33, in parse_yeast
  File "Bio/SwissProt/SProt.py", line 166, in next
    return self._parser.parse(File.StringHandle(data))
  File "Bio/SwissProt/SProt.py", line 290, in parse
    self._scanner.feed(handle, self._consumer)
  File "Bio/SwissProt/SProt.py", line 333, in feed
    self._scan_record(uhandle, consumer)
  File "Bio/SwissProt/SProt.py", line 338, in _scan_record
    fn(self, uhandle, consumer)
  File "Bio/SwissProt/SProt.py", line 414, in _scan_reference
    self._scan_ra(uhandle, consumer)
  File "Bio/SwissProt/SProt.py", line 436, in _scan_ra
  File "Bio/SwissProt/SProt.py", line 360, in _scan_line
    read_and_call(uhandle, event_fn, start=line_type)
  File "Bio/ParserSupport.py", line 300, in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'RA':
RX   DOI=10.1128/JB.183.20.5942-5955.2001;

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