#!/usr/bin/env python
#-*- coding:utf-8 -*-

import re
import sys

AMINOS = {
    "A": "GC.",
    "R": "(?:CG.|AGA|AGG)",
    "N": "(?:AAT|AAC)",
    "D": "(?:GAT|GAC)",
    "C": "(?:TGT|TGC)",
    "Q": "(?:CAA|CAG)",
    "E": "(?:GAG|GAA)",
    "G": "GG.",
    "H": "(?:CAT|CAC)",
    "I": "(?:ATT|ATC|ATA)",
    "L": "(?:CT.|TTA|TTG)",
    "K": "(?:AAA|AAG)",
    "M": "ATG",
    "F": "(?:TTT|TTC)",
    "P": "CC.",
    "S": "(?:TC.|AGT|AGC)",
    "T": "AC.",
    "W": "TGG",
    "Y": "(?:TAT|TAC)",
    "V": "GT."
}

def inverse(st):
    M = {"C": "G", "G": "C", "A": "T", "T": "A"}
    return "".join(M[c] for c in st)

with open(sys.argv[1]) as fp:
    pattern = "".join(AMINOS.get(c, "") for c in fp.read())
    regex = re.compile(pattern)

with open(sys.argv[2]) as fp:
    sequence = "".join(line.strip() for line in fp)

for match in regex.finditer(sequence):
    print "Match at %d to %d" % (match.start(), match.end())

sequence = inverse(sequence)
for match in regex.finditer(sequence):
    print "Match at inverse %d to %d" % (match.start(), match.end())