mm9_blat.py

import subprocess
import sys
#fa file to blat
fa = sys.argv[1]

print fa

for genome in open("/nas3/gpratt/ens/mm9.genome"):
    line = genome.strip().split()
    #wraps blat and blats against hg19 without getting memory errors
    
    call = ["blat","-out=pslx", "-t=dnax", "-q=prot", "/nas3/yeolab/Genome/ucsc/mm9/chromosomes/mm9.2bit:%s:1-%s" %(line[0], line[1]), fa, "mm9.%s" % (line[0])]
    print call
    print subprocess.call(call)