[BioPython] Problem with BLAST parser in NCBIStandalone

[Jeffrey Chang]

Most likely the BLAST format has changed.  You'll have to send some
sample output for us to update it.

Jeff



On Thu, May 09, 2002 at 11:51:43AM +1000, Chris Francis wrote:
> I'm having problems parsing output blast files using the 
> NCBIStandalone.BlastParser.
> 
> >>>blast_results = open('TRblast.out','r')
> >>>br = cStringIO.StringIO(blast_results.read())
> >>>b_parser = NCBIStandalone.BlastParser()
> >>>b_record = b_parser.parse(br)
> 
> This gives:
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 515, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 84, in feed
>     self._scan_rounds(uhandle, consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 140, in _scan_rounds
>     self._scan_alignments(uhandle, consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 261, in _scan_alignments
>     self._scan_masterslave_alignment(uhandle, consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 364, in _scan_masterslave_alignment
>     consumer.multalign(line)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 769, in multalign
>     name = string.rstrip(line[:self._name_length])
> TypeError: sequence index must be integer
> 
> Alternatively, with using cStringIO I get:
> 
> >>>b_record = b_parser.parse(blast_results)
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 515, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/usr/lib/python2.2/site-packages/Bio/Blast/NCBIStandalone.py", line 
> 81, in feed
>     read_and_call_until(uhandle, consumer.noevent, contains='BLAST')
>   File "/usr/lib/python2.2/site-packages/Bio/ParserSupport.py", line 366, in 
> read_and_call_until
>     line = safe_readline(uhandle)
>   File "/usr/lib/python2.2/site-packages/Bio/ParserSupport.py", line 442, in 
> safe_readline
>     raise SyntaxError, "Unexpected end of stream."
> SyntaxError: Unexpected end of stream.
> 
> My input blast file isn't formatted in HTML, is this an issue? I sincerely 
> appreciate any assistance with this problem.
> 
> C.Francis
> 
> 
> 
> 
> 
> 
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