[Biopython-dev] [Bug 2131] New: SProt.py fails to parse the current Swiss-Prot version 51.0

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Nov 1 22:50:46 UTC 2006


           Summary: SProt.py fails to parse the current Swiss-Prot version
           Product: Biopython
           Version: 1.24
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: Biosql at hotmail.com


I'm running on a mac OS 10.4, python 2.5 and tried to parse the Swiss-Prot .dat
file whit the latest SProt.py version and get this : 

Traceback (most recent call last):
  File "Parser_SProt_to_DB.py", line 37, in <module>
    cur_record = s_iterator.next()
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 166, in
    return self._parser.parse(File.StringHandle(data))
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 290, in
    self._scanner.feed(handle, self._consumer)
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 332, in
    self._scan_record(uhandle, consumer)
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 337, in
    fn(self, uhandle, consumer)
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 369, in
    self._scan_line('ID', uhandle, consumer.identification, exactly_one=1)
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 359, in
    read_and_call(uhandle, event_fn, start=line_type)
  File "/sw/lib/python2.5/site-packages/Bio/ParserSupport.py", line 301, in
  File "/sw/lib/python2.5/site-packages/Bio/SwissProt/SProt.py", line 526, in
    self.data.sequence_length = int(cols[4])
ValueError: invalid literal for int() with base 10: 'AA.'

Any clue ?

Thanks !

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