#!/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
#
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# template http://www.opensource.org/licenses/bsd-license.php
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#   "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/
#
# submitted by Ian Osgood
# modified by Sokolov Yura
# modified by bearophile
# modified by Justin Peel

from collections import defaultdict
import os


def gen_freq(seq, frame, frequencies):
    if frame != 1:
        ns = len(seq) + 1 - frame
        frequencies.clear()
        for ii in range(ns):
            frequencies[seq[ii:ii + frame]] += 1
        return ns, frequencies
    for nucleo in seq:
        frequencies[nucleo] += 1
    return len(seq), frequencies


def sort_seq(seq, length, frequencies):
    n, frequencies = gen_freq(seq, length, frequencies)

    l = sorted(list(frequencies.items()), reverse=True, key=lambda item: item)

    print('\n'.join("%s %.3f" % (st, 100.0*fr/n) for st,fr in l))


def find_seq(seq, s, frequencies):
    n,t = gen_freq(seq, len(s), frequencies)
    print("%d\t%s" % (t.get(s, 0), s))


def main():
    frequencies = defaultdict(int)
    with open(os.path.join(os.path.dirname(__file__), "knucleotide-input.txt")) as f:
        for line in f:
            if line[0] == ">":
                if line[1:3] == "TH":
                    break

        seq = []
        seq_append = seq.append
        for line in f:
            if line[0] in ">;":
                break
            seq_append(line)
    sequence = "".join(seq).replace('\n','').upper()

    for nl in 1,2:
        sort_seq(sequence, nl, frequencies)

    for se in "GGT GGTA GGTATT GGTATTTTAATT GGTATTTTAATTTATAGT".split():
        find_seq(sequence, se, frequencies)


def __benchmark__(*args):
    main()
