##################################
#                                #
# Last modified 8/6/2009         # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string

try:
	import psyco
	psyco.full()
except:
	pass

def run():

    if len(sys.argv) < 7:
        print 'usage: python %s [species1regionfilename chrField] species1-getallgenes-filename liftover-to-species2-filename liftover-to-species2-filename-failures liftover-to-species2-intersect-with-species2-filename-getallgenes outpufilename ' % sys.argv[0]
        sys.exit(1)

    species1regionfilename = sys.argv[1]
    species1StartField = int9sys.argv[2])
    species1gag = sys.argv[3]
    liftOvertoSpecies2 = sys.argv[4]
    liftOvertoSpecies2failures = sys.argv[5]
    liftOvertoSpecies2gag = sys.argv[6]
    outputfilename = sys.argv[7]


    outfile = open(outputfilename, 'w')

    listoflines = open(regionfilename)
    lineslist = listoflines.readlines()

    outfile.close() 

run()