compare.py

from __future__ import print_function
import sys
from collections import defaultdict

def parse(fn):
 loci = set()

 with open(fn) as F:
   for L in F:
     L = L.strip()
     if L.startswith('#'):
       continue
     fields = L.split()
     chrom, pos = fields[0:2]
     if not chrom.startswith('chr'):
       chrom = 'chr%s' % chrom
     loci.add((chrom, pos))
 return loci

def main():
 l1, l2 = parse(sys.argv[1]), parse(sys.argv[2])
 print('Counts', len(l1), len(l2))
 print('Common', len(l1 & l2))

main()