#!/usr/bin/env python2.7 import sys if __name__ == "__main__": if len(sys.argv) is 1: exit("Filter mers, input is stdin, output is stdout, mers are argv") mers_to_delete = set() for mer in open(sys.argv[1], 'rU'): sp = mer.strip().split() if len(sp) == 2: mer = sp[0] mers_to_delete.add(mer) for line in sys.stdin: if line.split()[0] not in mers_to_delete: sys.stdout.write(line)