[BioPython] Running local blast (Problem solved!)
Sebastian Bassi
sbassi@asalup.org
Fri, 25 Oct 2002 23:08:40 -0300
Hi,
Now it works! I really donīt know why, because I changed so many things
at once, I donīt know wich change made it works.
I will post now the working version if someone is interested in picking
up the difference(s). I wonīt do it because Iīm tired of debugging my
programs and now that it works its time to look at the results!
Thank to everybody. I will stay here since I have a lot to learn on
Python an BioPython.
Here is the program:
# BATCH BLAST. By Sebastian Bassi for Advanta Seeds.
from Bio.Blast import NCBIStandalone
import os
import string
import re
pathdb="d:\\projects\\bioinfo-adv\\blast\\data\\atal.faa"
blastexe="d:\\projects\\bioinfo-adv\\blast\\blastall.exe"
pathin="D:\\projects\\bioinfo-adv\\set-cd-small\\"
filesentr="D:\\projects\\bioinfo-adv\\set-cd-small"
pathout="blastbatch\\out"
print "OK 1"
cont = 0
# mando todos los files de set-cd-complete a una lista
listaentrada=os.listdir(filesentr)
for x in listaentrada:
cont = cont + 1
blast_out, error_info = NCBIStandalone.blastall(blastexe, 'blastx',
pathdb, pathin+x)
salida=open(pathout+x+".blasted.txt","w")
salida.writelines(blast_out)
salida.close()
print "Blast numero "+`cont`+" "+x
print "FIN"
print "OK 2 re ok"
--
Best regards,
//=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\
\=// IT Manager Advanta Seeds - Balcarce Research Center - \=//
//=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\
\=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=//
ASALUP investiga: http://argentinaworks.asalup.org