More efficient algorithm for shortest superstring search

Question

My problem below is NP-complete, however, I\'m trying to find at least a marginally faster string search function or module that might help in reducing some of the computation t

Answer 1

This should do it.

import itertools as it

SEQUENCES = ['AGG', 'AGT', 'CCG', 'CGT', 'GAG', 'GGA', 'GGT', 'GTA', 'GTG', 'TAG', 'TGG']
LONGEST_SUPERSTRING = ''.join(SEQUENCES)

def find_shortest_superstring():
    current_shortest = LONGEST_SUPERSTRING
    trim = len(current_shortest)-1
    seen_prefixes = set()
    for perm in it.permutations(SEQUENCES):
        candidate_string = ''.join(perm)[:trim]
        if candidate_string in seen_prefixes:
            continue
        seen_prefixes.add(candidate_string)
        while is_superstring(candidate_string):
            current_shortest = candidate_string
            candidate_string = candidate_string[:-1]
            trim = len(current_shortest)-1
    return current_shortest

def is_superstring(s):
    return all(seq in s for seq in SEQUENCES)

def main():
    print 'Searching for shortest superstring containing all strings.'
    ss = find_shortest_superstring()
    print 'Found shortest superstring containing all strings:\n{}'.format(ss)

if __name__ == '__main__':
    main()

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The code takes about 15 seconds to run and produces the following output:

Searching for shortest superstring containing all strings.
Found shortest superstring containing all strings:
CCGTAGGTGGAGT