[BioPython] Parsing error when parsing a blast report

[Brad Chapman]

Hello Pieter and Bertrand;

Pieter:
> >I've tried to parse some output I got through NCBIWWW.Blast.  But I
> >receive the following error:
[...]
> >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,

The problem isn't the parser, but rather BLASTing against NCBI. This
problem is fixed in CVS and will be in the next release -- Catherine
reported it back in March:

http://portal.open-bio.org/pipermail/biopython/2004-March/001903.html

So you can either use CVS, or the quick fix is to change:

b_results = NCBIWWW.blast(program='tblastn',  database='nr', 
query=sequence, expect=0.001, entrez_query='Canis familiaris[ORGN]')

to:

b_results = NCBIWWW.blast(program='tblastn',  database='nr', 
query=sequence, expect=0.001, entrez_query='Canis familiaris[ORGN]',
format_type = "HTML")

Bertrand:
> 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.

If you get this finished and working, we would definitely be willing
to accept it into Biopython -- a parser for XML blast output is
currently missing but desired.

Hope this helps -- let us know if that doesn't fix the problem or
there are any other questions.
Brad