import sys
import os

infile1 = sys.argv[1] # scaffold report #1 -- filename
infile2 = sys.argv[2] # scaffold report #2 -- filename
infile3 = sys.argv[3] # scaffold report #3 -- filename or "False"
baitfile = sys.argv[4] # Bait file -- filename
outfile = sys.argv[5] # output filename
ins_path = sys.argv[6]

cmd = r"python " + str(ins_path) + " " + str(infile1) + " " + str(infile2) + " " + str(infile3) + " " + str(baitfile) + " " str(outfile)