BA10J.py

#   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/>.

#  BA10J 	Solve the Soft Decoding Problem 

import argparse
import os
import time
from   helpers import read_strings
from   hmm     import float2str

def SoftDecode(s,Alphabet,States,Transition,Emission):
    def step(Ps):
        Ps[0] +=0.01
        Ps[1] -=0.01
        return [p for p in Ps]
    N = len(s)
    K = len(States)
    Ps = [1/K for _ in range(K)]
    return [step(Ps) for i in range(N)]

if __name__=='__main__':
    start = time.time()
    parser = argparse.ArgumentParser('BA10J 	Solve the Soft Decoding Problem ')
    parser.add_argument('--sample',   default=False, action='store_true', help='process sample dataset')
    parser.add_argument('--rosalind', default=False, action='store_true', help='process Rosalind dataset')
    parser.add_argument('--precision', default=4,                          help='Controls display of probabilities')
    args = parser.parse_args()
    if args.sample:
        print ('A\tB')
        for Ps in SoftDecode('zyxxxxyxzz',
                             ['xyz'],
                             ['A','B'],
                             {('A','A'):  0.911, ('A','B'):  0.089,
                              ('B','A'): 0.228, ('B','B'):  0.772 },
                             {('A','x'):0.356,('A','y'):   0.191, ('A','z'):   0.453, 
                              ('B','x'):   0.04, ('B','y'):    0.467, ('B','z'):   0.493   }):
            print ('\t'.join(float2str(p,precision=args.precision) for p in Ps))
        
    

    if args.rosalind:
        Input  = read_strings(f'data/rosalind_{os.path.basename(__file__).split(".")[0]}.txt')
 
        Result = None
        print (Result)
        with open(f'{os.path.basename(__file__).split(".")[0]}.txt','w') as f:
            for line in Result:
                f.write(f'{line}\n')
                
    elapsed = time.time() - start
    minutes = int(elapsed/60)
    seconds = elapsed - 60*minutes
    print (f'Elapsed Time {minutes} m {seconds:.2f} s')