[BioPython] Parsing error when parsing a blast report

[Bertrand FROTTIER]

I had the same problem last week.
I suppose it's because the NCBI is using BLAST 2.2.8 now, and the parser 
is not up-to-date yet. So I started working on a parser for the XML 
output. It's not completely over yet (missing multiple_alignment, 
support of PSI-BLAST, and a lot of testing) but I can send you the file 
if you want.

Pieter Laeremans a écrit :
> Hello,
> 
> I've tried to parse some output I got through NCBIWWW.Blast.  But I
> receive the following error:
> 
> 
> 
>>>>## working on region in file /tmp/python-8118EHE...
> 
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/tmp/python-8118EHE", line 14, in ?
>     record = parser.parse(b_results)
>   File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 48, in parse
>     self._scanner.feed(handle, self._consumer)
>   File "/usr/lib/python2.3/site-packages/Bio/Blast/NCBIWWW.py", line 97, in feed
>     has_re=re.compile(r'<b>.?BLAST'))
>   File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 335, in read_and_call_until
>     line = safe_readline(uhandle)
>   File "/usr/lib/python2.3/site-packages/Bio/ParserSupport.py", line 411, in safe_readline
>     raise SyntaxError, "Unexpected end of stream."
> SyntaxError: Unexpected end of stream.
> 
> 
> ---------------------------------------
> 
> This is the script I used to get this result.  I have no idea what 's
> wrong. Has anyone a clue ? thanks in advance,
> 
> Pieter
> 
> 
> ---------------------------------------
> 
> from Bio.Blast import *
> from Bio.Blast.NCBIWWW import *
> 
> # here used to be a longer sequence
> sequence="MKIPNIGNVMNKFEILGVVGEGAYGVVLKCRHKETHEIV"
> 
> b_results = NCBIWWW.blast(program='tblastn',  database='nr', query=sequence, expect=0.001, entrez_query='Canis familiaris[ORGN]')
> parser = NCBIWWW.BlastParser()
> record = parser.parse(b_results)
> 
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> 
> 

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