called like: python removesorted.py haystack needles, only works on sorted files, remove needles from haystack.

removesorted.py

import sys
haystack = open(sys.argv[1])
needles = open(sys.argv[2])
needle = needles.readline()[:-1]
counter = 0
while 1:
    hay = haystack.readline()[:-1]
    if not hay: break
    if hay == needle:
        needle = needles.readline()[:-1]
        counter = 0
    else:
        print hay
        counter += 1
        if counter > 100:
            print counter, needle
            break

haystack.close()
needles.close()