[Biopython-dev] [Bug 1706] New: Problem with the Swiss Prot parser

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Mon Oct 25 14:19:03 EDT 2004


           Summary: Problem with the Swiss Prot parser
           Product: Biopython
           Version: 1.24
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: Biosql at hotmail.com

After installing the latest update of the Swiss Prot parser from cvs, I'm 
getting this error : 
Traceback (most recent call last):
  File "C:\Joe_script\Parser_Trembl.py", line 30, in ?
    cur_record = s_iterator.next()
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 166, in 
next  return self._parser.parse(File.StringHandle(data))
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 290, in 
parse  self._scanner.feed(handle, self._consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 332, in 
    self._scan_record(uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 337, in 
    fn(self, uhandle, consumer)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 468, in 
    self._scan_line('SQ', uhandle, consumer.sequence_header, exactly_one=1)
  File "C:\Python23\Lib\site-packages\Bio\SwissProt\SProt.py", line 359, in 
    read_and_call(uhandle, event_fn, start=line_type)
  File "C:\Python23\Lib\site-packages\Bio\ParserSupport.py", line 300, in 
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'SQ':
RA   Dujon B., Sherman D., Fischer G., Durrens P., Casaregola S.,

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