KMP.py

#!/usr/bin/env python
# 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/>

# KMP Speeding Up Motif Finding http://rosalind.info/problems/kmp/

def kmp(s):
    '''
    A prefix of a length n string s is a substring s[1:j]; a suffix of s is a substring s[k:n]

    The failure array of s
    is an array P of length n for which P[k] is the length of the longest substring s[j:k]
    that is equal to some prefix s[1:k-j+1], where j cannot equal 1 (otherwise, P[k] would always equal k). By convention, P[1]=0

    Given: A DNA string s (of length at most 100 kbp) in FASTA format.

    Return: The failure array of s
'''
    def longest_substring(k,bound):
        '''
        Find longest substring. This is more complex than it needs to be
        if the string is short. For longer strings we need to exploit
        the fact that the longest substring for k cannot exceed the longest
        substrin for k-1 PLUS 1.
        '''
        for j in range(k-bound,k):
            if k-j<=bound:
                if s[j:k]==s[0:k-j]:
                    return k-j
        return 0

    result=[]
    longest=-1
    for k in range(1,len(s)+1):
        longest=longest_substring(k,longest+1)
        result.append(longest)
    return result

if __name__=='__main__':
    name=''
    strings=[]
    with open('c:/Users/Weka/Downloads/rosalind_kmp(1).txt') as f:
        for line in f:
            if (len(name))==0:
                name=line.strip()
            else:
                strings.append(line.strip())
    string=''.join(s for s in strings)

    print(' '.join(str(i) for i in kmp(string)))