[BioPython] Blast and multiple processors
Daniel Tomso
dtomso at athenixcorp.com
Thu Aug 4 16:40:17 EDT 2005
Hello, all.
I'm working on improving my BLAST throughput, and I have some questions
about how the program handles multiple processors and multiple
processes.
Specifically, I've been experimenting with using BioPython's
NCBIStandalone to handle 3 or 4 simultaneous blast requests, since my
system has 4 processors. I spin out the requests via
NCBIStandalone.blastall(blah, blah), then grab the blast_out and
blast_err file handles in a list. Afterwards, I use blast_out.read() to
collect the reports from each of the 4 processes.
Is this wise and/or efficient? My execution times do drop off when I
do, say, 4 jobs at a time instead of 1 at a time, so it is helping. Do
the processor flags for blastall accomplish this more efficiently?
Sorry if this is not specific enough, but any insight would be
welcome!!!!
Dan T.
Daniel J. Tomso
Senior Scientist, Bioinformatics
Athenix Corporation
2202 Ellis Road
Suite B
Durham, NC 27703
919.281.0920
dtomso at athenixcorp.com
www.athenixcorp.com
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