BA9N.py

#!/usr/bin/env python

#   Copyright (C) 2020 Greenweaves Software Limited

#   This program is free software: you can redistribute it and/or modify
#   it under the terms of the GNU General Public License as published by
#   the Free Software Foundation, either version 3 of the License, or
#   (at your option) any later version.

#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.

#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <https://www.gnu.org/licenses/>.

# BA9N 	Find All Occurrences of a Collection of Patterns in a String

import argparse
import os
import time
from   helpers import read_strings
from   snp import EvenBetterBWMatching



def format(Result):
    return ' '.join(sorted([str(pos) for pos in Result]))

if __name__=='__main__':
    start = time.time()
    parser = argparse.ArgumentParser('BA9N Find All Occurrences of a Collection of Patterns in a String ')
    parser.add_argument('--panama',   default=False, action='store_true', help='process panama bananas')
    parser.add_argument('--sample',   default=False, action='store_true', help='process sample dataset')
    parser.add_argument('--extra',   default=False, action='store_true', help='process extra dataset')
    parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
    args = parser.parse_args()

    if args.panama:
        print (EvenBetterBWMatching('panamabananas', ['ana'], K=5))

    if args.sample:
        print (EvenBetterBWMatching('AATCGGGTTCAATCGGGGT', ['ATCG', 'GGGT'], K=5))

    if args.extra:
        Input,Expected  = read_strings('data/MultiplePatternMatching.txt',init=0)
        Actual = format(EvenBetterBWMatching(Input[0],Input[1:]))
        print (Expected[0])
        print()
        print (Actual)

    if args.rosalind:
        Input  = read_strings(f'data/rosalind_{os.path.basename(__file__).split(".")[0]}.txt')

        Result = format(EvenBetterBWMatching(Input[0],Input[1:]))

        with open(f'{os.path.basename(__file__).split(".")[0]}.txt','w') as f:
            print(Result)
            f.write(f'{Result}\n')

    elapsed = time.time() - start
    minutes = int(elapsed/60)
    seconds = elapsed - 60*minutes
    print (f'Elapsed Time {minutes} m {seconds:.2f} s')