[BioPython] BLAST from inside python code?

[Brad Chapman]

Hi Deanne;
Nice to hear from you again!

> There's got to be a faster way of running blast from a python 
> program than simply
> writing a script to externally call blast and parse the 
> results, over and over (for big data sets).

Sure, install local BLAST and the NCBI databases... don't you work for 
a big pharma now? :-). Seriously, Jeff has code in
Bio.Blast.NCBIStandalone for interfacing with standalone BLAST.

The web based BLAST is really set up for case by case BLASTs -- in
general they don't want you using up all their computing power.
 You can also use the stable BLAST url -- there
is also a wrapper for this in Bio.Blast.NCBIWWW, courtesy of Jeff, but 
this server is about the same speed, in my experience.

> Anybody know of any  BLAST wrapper for python? 

I wrote a small Tkinter-based GUI that just does the job of BLASTing a
FASTA file against the stable blasturl and returning the results into
a big BLAST file you can parse later:

http://www.bioinformatics.org/bradstuff/brad-moinmoin/moin.cgi/MojoBlast

It is just the kind of thing you set up to BLAST all night while
you're sleeping, and then come back and deal with the results in the
morning. Don't know if this is kind of what you are looking for.

Hope this helps.
Brad