[Biopython-dev] buglet in BLASTX parsing

[Coleman, Michael]

Parsing by NCBIStandalone.py fails for BLASTX 2.2.5 output, due to a missing 'S2' line.  The current code seems to assume that either an S2 line or an immediate EOF will be hit.  The 2.2.5 output cleverly defeats this assumption by including an extra newline before the EOF.  :-)

One solution is to change the read_and_call to an attempt, like so

	attempt_read_and_call(uhandle, consumer.blast_cutoff, start='S2')

I'm not sure whether that's the best solution, though.

Mike

Mike Coleman, Scientific Programmer, +1 816 926 4419
Stowers Institute for Biomedical Research
1000 E. 50th St., Kansas City, MO  64110