import sys f1 = open(sys.argv[1], 'r') f2 = open(sys.argv[2], 'r') f3 = open(sys.argv[2]+"_26756", 'w') uni_id_dic = {} for line in f1: uni_id_dic[line.strip()] = True for line in f2: if line.strip().split("\t")[3] in uni_id_dic: print >> f3, line,