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Scripts for automating blasts

Francois Jeanmougin pingouin at .u-strasbg.fr
Thu Jun 20 08:51:28 EST 1996


In article <4q9lc6$po0 at master.ftn.net>,
	gordonm at Adenine.Neither_Here.Nor.There (Gordon MacPherson) writes:
> Does anyone have any scripts which automate blast searches with large numbers
>of sequence files?
>
>Thanks.
>
	cadeau :
----------------------------------------------------------------------------
#!/usr/bin/csh

source /us1/user/pingouin/.cshrc

foreach file (`cat liste`)
        echo $file
        blast $file genembl -batch -def 
end
---------------------------------------------------------------------------
	replace the path for your .cshrc file after the word source.
	create a list with all the sequence names  (one per line) and call
	it "liste" according to the script. Add your options or let the
	-def options. You can change blast by another gcg programm.

WARNING : This will work only if you start GCG in your .cshrc. Else, add
a line to start gcg.


						Hope this help,
							Francois.
-- 
Francois Jeanmougin
Service de bioinformatique / bioinformatic service
IGBMC 
BP 163 
67404 Illkirch France
tel : (33) 88 65 32 71
e-mail : jeanmougin at igbmc.u-strasbg.fr

Les petits pois sont rouges (STTELLLA)




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