[BioPython] Blast and multiple processors

[Daniel Tomso]

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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