014_LCSM.py

#!/usr/bin/env python
'''
A solution to a ROSALIND bioinformatics problem.

Problem Title: Finding a Shared Motif
Rosalind ID: LCSM
Rosalind #: 014
URL: http://rosalind.info/problems/lcsm/
'''

from scripts import ReadFASTA

def LongestSubstring(string_list):
	'''Extracts all substrings from the first string in a list, and sends longest substring candidates to be checked.'''
	longest = ''
	for start_index in xrange(len(string_list[0])):
		for end_index in xrange(len(string_list[0]), start_index, -1):
			# Break if the length becomes too small, as it will only get smaller.
			if end_index - start_index <= len(longest):
				break
			elif CheckSubstring(string_list[0][start_index:end_index], string_list):
				longest =  string_list[0][start_index:end_index]

	return longest

def CheckSubstring(find_string, string_list):
	'Checks if a given substring appears in all members of a given collection of strings and returns True/False.'
	for string in string_list:
		if (len(string) < len(find_string)) or (find_string not in string):
			return False
	return True


if __name__ == '__main__':
    fasta_list = ReadFASTA('data/rosalind_lcsm.txt')
    dna = []
    for fasta in fasta_list:
    	dna.append(fasta[1])

    lcsm = LongestSubstring(dna)
    print lcsm
    with open('output/014_LCSM.txt', 'w') as output_data:
    	output_data.write(lcsm)