#!/usr/bin/env python
# Copyright 2008-2010 Isaac Gouy
# Copyright (c) 2013, 2014, Regents of the University of California
# Copyright (c) 2017, 2021, Oracle and/or its affiliates.
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#
# Revised BSD license
#
# This is a specific instance of the Open Source Initiative (OSI) BSD license
# template http://www.opensource.org/licenses/bsd-license.php
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#   Neither the name of "The Computer Language Benchmarks Game" nor the name of
#   "The Computer Language Shootout Benchmarks" nor the name "nanobench" nor the
#   name "bencher" nor the names of its contributors may be used to endorse or
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# The Computer Language Benchmarks Game
# http://shootout.alioth.debian.org/
# contributed by Dominique Wahli
# modified by Justin Peel

from re import sub, finditer


def main(seq, iters):
    ilen = len(seq)

    seq = sub('>.*\n|\n', '', seq) * iters
    clen = len(seq)

    variants = (
          'agggtaaa|tttaccct',
          '[cgt]gggtaaa|tttaccc[acg]',
          'a[act]ggtaaa|tttacc[agt]t',
          'ag[act]gtaaa|tttac[agt]ct',
          'agg[act]taaa|ttta[agt]cct',
          'aggg[acg]aaa|ttt[cgt]ccct',
          'agggt[cgt]aa|tt[acg]accct',
          'agggta[cgt]a|t[acg]taccct',
          'agggtaa[cgt]|[acg]ttaccct')
    for f in variants:
        print(f, sum(1 for i in finditer(f, seq)))

    subst = {
          'B' : '(c|g|t)', 'D' : '(a|g|t)',   'H' : '(a|c|t)', 'K' : '(g|t)',
          'M' : '(a|c)',   'N' : '(a|c|g|t)', 'R' : '(a|g)',   'S' : '(c|g)',
          'V' : '(a|c|g)', 'W' : '(a|t)',     'Y' : '(c|t)'}
    for f, r in list(subst.items()):
        seq = sub(f, r, seq)

    print(ilen)
    print(clen)
    print(len(seq))


def __benchmark__(iters=4):
    import os
    with open(os.path.join(os.path.dirname(__file__), "knucleotide-input.txt")) as f:
        seq = f.read()
    main(seq, iters)
