PCOV.py

'''
    PCOV Genome Assembly with Perfect Coverage

    Copyright (C) 2017 Greenweaves Software Pty Ltd

    This 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 software 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 GNU Emacs.  If not, see <http://www.gnu.org/licenses/>
'''

from rosalind import dbru,read_strings

def pcov(S):
    k=len(S[0])
    _,deBruijn=dbru(S,include_revc=False)
    fragments=[]
    (prefix,suffix)=deBruijn[0]
    while len(fragments)<len(deBruijn):
        fragments.append(prefix)
        for (a,b) in deBruijn:
            if a==suffix:
                prefix,suffix=a,b
                break

    superstring=[]
    for i in range(len(S)-k+2):
        if i==0:
            superstring.append(fragments[i])
        else:
            superstring.append(fragments[i][-1])

    return ''.join(superstring)

if __name__=='__main__':
    print (pcov(read_strings('c:/Users/Weka/Downloads/rosalind_pcov.txt')))