[BioPython] Trouble parsing BLAST reports

Jessica Leigh jleigh at dal.ca
Thu Jul 14 11:09:49 EDT 2005


Has anyone been having trouble parsing BLAST files?  I have a script I 
was using a couple of months ago to BLAST and parse the results, and it 
doesn't seem to work now.  It uses qblast.  Anyway, I don't use 
biopython very often, so I figured it was just me, and went back to the 
cookbook to go through the process step by step, and I'm having the same 
problem.  The actual BLASTing seems to work fine, but when I get to the:

b_record = b_parser.parse(blast_out)

part, I get an exception that ends with:

SyntaxError: Line does not contain 'Database':
[this line is then followed with a blank line]

I've taken a look at the blast_out stream, and it looks good: it's got 
lots of results in it, it's not the "This page will not refresh 
automatically..." page.  I'm guessing that NCBI has changed the output 
format just enough to break the parser.  Does anyone else get this?  Am 
I going to have to resort to writing my own parser?

Jessica



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