[BioPython] problems when parsing blast output

Alessandro S. Nascimento as_nascimento at yahoo.com.br
Mon Jan 16 20:29:02 EST 2006


Hi all,

I am trying to write something very simpleto parse very extense blast 
output file. But when I try something as described in web's cookbook i 
get the following error message:


asn at frodo:~/fool/programming/python$ ./teste_asn.py
Traceback (most recent call last):
  File "./teste_asn.py", line 10, in ?
    b_record = b_iterator.next()
  File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", 
line 1342, in next
    return self._parser.parse(File.StringHandle(data))
  File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", 
line 567, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", 
line 95, in feed
    self._scan_header(uhandle, consumer)
  File "/usr/lib/python2.4/site-packages/Bio/Blast/NCBIStandalone.py", 
line 127, in _scan_header
    read_and_call(uhandle, consumer.query_info, start='Query=')
  File "/usr/lib/python2.4/site-packages/Bio/ParserSupport.py", line 
300, in read_and_call
    raise SyntaxError, errmsg
SyntaxError: Line does not start with 'Query=':
Reference for composition-based statistics:

Does anyone have any idea?

Thanks so much

Alessandro


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