BA9D.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/>.
#
# BA9D Find the Longest Repeat in a String

import argparse
from helpers import read_strings
from snp import  FindLongestRepeat
import sys
import time



if __name__=='__main__':
    sys.setrecursionlimit(1500)
    start = time.time()
    parser = argparse.ArgumentParser('BA9D Find the Longest Repeat in a String')
    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.sample:
        print (FindLongestRepeat('ATATCGTTTTATCGTT'))

    if args.extra:
        Input,Expected  = read_strings('data/LongestRepeat.txt',init=0)
        print (Input[0])
        Actual = FindLongestRepeat(Input[0])
        print (len(Expected[0]),len(Actual))
        print (Expected[0])
        print (Actual)

    if args.rosalind:
        Input  = read_strings('data/rosalind_ba9d.txt')
        Result = FindLongestRepeat(Input[0])
        print (Result)
        with open('ba9d.txt','w') as f:
            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')