kmer.py

f = open("output.txt", "w")

def count_ks(string, sub_string):
	count = 0
	sub_string_length = len(sub_string)
	for i in range(0, len(string) - sub_string_length + 1):
		if string[i:i+sub_string_length] == sub_string:
			count = count + 1

	return count


def k_mer(s, k):
	ls = []
	curr_count = 0

	for i in range(0,len(s) - k + 1):
		curr_count_ks = count_ks(s, s[i:i+k])
		if curr_count_ks > curr_count and curr_count_ks > 1:
			ls = [s[i:i+k]]
			curr_count = curr_count_ks
		elif curr_count_ks == curr_count and s[i:i+k] not in ls and curr_count_ks > 1:
			ls.append(s[i:i+k])
		else:
			pass
	return ls, curr_count


def patch(s, k, L, t):
	ls = []
	for i in range(len(s) - L + 1):
		current = k_mer(s[i:i+L], k)
		if current[1] == t and current[0][0] not in ls:
			ls.append(current[0][0])
	return ls

for i in patch("AGACAACGAAGTTAGTTAGATCCGCGGCGCACCCCAGCAGTATTGGTATCGTATAGCAATAGACGGCCCAACGCGCTGGTGCGCAAAATTGACAAAGTCGACACGAGGTCGCTATCTGCCAATCAGCAGGGTTGCCCGAGAGCCTCCAACCGAGCCAACACCGGCAACATTTGGGCGAGCGGGGGGGCATTCACTGTAAAGATGTCCGGCCGCGTGACGAAGGGGACATGGGATCCGAACAATTACGCATATGAAAGGAACCTGGCAAAGGCTGCGCGCCTATCCTAATCTCTTAGACAGCGTAGTCGAAACTGGACTGGCCCAACTACAAATGAGAAACCGACAGGTTACATAGGGTAATCAACCCCCTGATATTGAAAGCCACGAGTCATAAAGTGGCTTTTTGATAAGTGAGTTTAGTGTCTTTAGTCGTTATTGCTTAACGCCAACCGCAGACATAAGTTCGCGGAATGCCCTTTTCTATAGTTGAAAAAGGGTCACCCACATTTAGGGGGTTCGATCATGGGGTCAGTACCACCATTGGAGTAGGGTCAGTACCGTACGGGTCAGTACCGCGAGGGGTCAGTACCTGCCAGCAAGTTTCTTGCCTACTACCCCAGCAGGACAGCGGGTCAGTACCCCTTTGACAGGGGGGGTCAGTACCATATGGGTCAGTACCTAGGGTCAGTACCACGGGTCAGTACCGAAATTAGACTCACGAGCGGGTCAGTACCTTGGGTCAGTACCGATACTCCTGGGCCGGAGAAGGTGCCCAGTTCGGGTCAGTAGGGTCGGGTCAGTACCGGATGACGTAGCGTGGGGTCAGTACCGACCAGCCAGCGTCGTCCGTTATAGGAACTATTCAATGGGTCAGTACCATGCTTCTAAAACTAGATCTAAGTCGACCTCCTTAACTTATGGGTCAGTACCACCAGGACGGGCTTTCGGCTCGGGTCAGTACCTCGGGGGTCAGTACCTTCGGATGAGCGAGACGCTAGGACATGGGTCAGTACCATATAGAGTTAACAATCCTACAGGGGTCAGTACCTACCGATTTATCGCAAGCAGGGGGGTCAGTACCACTTACTTGTATCGTAGAGACATAGGGAGCCAGATTTTGTTTTACTCGCAGGGGTTTTAAAGCTCCGATGTGTCAAGAACTCCGTGGTAGGCCATACTCTGTTCTGAGACCCTATCTGTAAGGCGGGGCCTGAAGTTACTGGCCACTTTAGTGAGTAAAATTGACCGCTCGAGCCACTGGCCGACCTTCGATCCGCTTAGATCATCATATGGGAGAGAGATGTTTATAGATAGTGATCTCTGTGTTAATACAAGGAATCCAGCAGGCCCGCCTTCTGACACCAAAGCAGCAATCACGAAGCCGCTTCGATCCGGACACCTTCTTATGCCATGCCCGCTAATTTGACTCTCTCCTAACCAGTTCTATGCGCCAAGATGCCATTAAACATTGGAGTGTTCAACACGCACAGAGTATTAGACTCCGTGTTGGTCACATAGTGGCTATTATGGTCCAGTTGGCGGGCACTGCAGTCCGTCCAGTTGGCGTGTCCAGTTGGCGAATTGGTCCAGTTGGCGATGTTTGTTGCTCTAGATGTCCAGTTGGCGAATCCTAGAGAGTGTATTTATTGACGGTGTGAACACCTTCTTCCAGCGTGCCAGCGTCCAGTTGGCGTGGCGGAAACCGGCTGTCCAGTTGGCGGTAGAATAAGTTCGCGGCTAGTCCAGTTGGCGTCCAGTTGGCGGGGCGACGTCGTCCAGTTGGCGGGTCCAGTTGGCGTTGGGTCCAGTTGTCCAGTTGGCGAGATCAAGGACATAGGCAGATATATGTCCAGTTGGCGTTGATGTAGCTAAGTACTAGGGGACTCCGAAAGTCGGGTCCAGTTGGCGGGTCCAGTTGGCGGATCTGCAACCAAAGTAAACGTCCAGTTGGCGACTGGACAAACCAGATATGCTAACAGTCCGGCCCTGGGTGGTCCAGTTGGCGGAAGTCCAGTTGGCGGGTTGTCAGGTCACGGTGGTCCCCCCCGTATGGTCCAGTTGGCGTTCAACCGTCCAGTTGGCGACAAATCAGCTCTTACGGTCCAGTTGGCGTGGTTCCGAGGACAAACGTATCCTGTACACCCGAATTACAAGTCGCGCAACGTCACCTGGGTTGTTTGACGGACGCTGATATTGGCCGAGAACAATTAATGGCAGTGACCGCCCAGTACGGAGGGTGACGTGCTCGTACTAATTTGAGAGATGCGCTTTCCGGGGGTGAGGATCACGACCCTGTTTGAGGTATTATACTAAGGCTCAGAACTGCGCAAATGCCGCTCGGATGTTTTACAAGCCGCGCATTCCCCAGCTTTCTTCACTAGATTAAGCTGTTCTCGAATAGTCTTTACCCTTACTTGTTCGCGTACGCGACGGACTGCTTCTACAACTAATCTTAACACCAGCATTCCACAGCGTCTGCACAGACACCCAATGAACAATGCGCATTTTAAGACTGAAGCTGCGCCTATCGCGCTCCTTCCGTCGTAGACGACCACATCACTTCCCCGTTAACGATTTAGATTGAACATTTCTGCATCCCTAGGCACGATGCCAGTTATTGATGAGTGGCGAGTAGTAAGTTTTAAAAACGATATCCCACTAGGGGCAGGGCCCGCTAACTGTACCGTACATTATTTGCCGGTGCCGATTCTATGACTAAGGAAGAGGGTGATCGTTAAGCCTTGTCCAGTAAGTGAAAGGACGACTCCCCTCCCCAACCTACATCCTCCCCAAGAGGGTGGGTGCGCTCTACAGGACACCTCCCCAAGCTATAACTCTATGAATTCCTCCCCAACCAAAATTTTCCTCCCCCTCCCCAACCCCAAACTCTATGAATTGTCCTCCCCAAGGCGGAAACCTATCTGCCCTCCCCAACCAATTTTTTCGTCGAAGGTCAAAGCATCCCTTTATTTTACTCTATGAATTGCGCTAGCACCCTCCCCTCCCCAACTCCCCAGATCTTTAGAATCAGATCTTTAGCTCCCCAGATCTTTAGCTCCCCAATAAACTCAGATCTTTAGCCAATTCCAGCAGATCTTTAGTCTTTAGCCCAAATGGCAGCCCTCCCCAAAAGAGCCCAACGACTCTATGAATTATCAGCAGACAGATCTTTAGCTGACTTAAGTTGCTGGAACTCTCAGATCTTTAGGCAGATCTTTAGTACTGGCACGCACGGAACTCCCACGGAACTACGGAACTAAATTAGACCACGGAACTTTGTAAGTCACGGAACTGGACTTAAGTTCACGGAACTACTAGGACTTACACGGAACTTCAGATCTTTAGATTCTGTACACACGGCACGGAACTGTACCGCGCAACAACCTCCTCCGACAACCTCCTCGGCCCCACGGAACTGACTTACACGGAACTGACTTAAGTTGATCTTTACCACGGAACACGGAACTGTCTTTAGCACGGAACAACCTCCTCGTGACTTAAGTTGAAAGCCACAACCTCCTCCTCCGGACACAACCTCCTCCACAACCTCCTCACGCACGGAACTAACAACACAACCTCCTCTCCGGTAACGAGGGACTTAACACGGAACTCACAACCTCCTCCTGAACTCACGGAACAACCTCCTCGACAAAGCACGACAACCTCCTCTCCTCACAAACAACCTCCTCAACTGTGGGCAAGACTGGTTATCCTACTCCGGAACAACCTCCTACAACCTCCTCACCTCCTCCGATTCTTTCGGCATTTAAGACAACCTCCTCAACCTCCACAACCTCCTCCAACCTCCTCAATCCAAACTCGGATGAGAAAGTGACAACCTCCTCTTCTACAACCTCCTCTCGATTCTTTCTACAACCTCCTCCTCACAACCTCCTCCGATTCTTTCTCGATTCTTTCTTCTTTCGCTTTAGAGTGGCCCGGGTGGACGCTTTCGGGCCTCTCGATTCTTTCGCTCGATTCTTTCCTCAGGAGTCTAACCTCCTCGATTCTTTCTCGATTCTTTCTTCTATGAAAGCAAGAACGATATTTTCTCCAGAACGATATCGATATTGCTCGATTCTTTCGAAGTCTTTGATTAAGCACAAGTCGAATCTCGATTAGAACGATATGAACGATAGAACGATATATTCTACCCCCCGGATCAGAACGATATTTCTCTTTCCGTTCTCGATTCCTCGATTCTTTCTCGAGAACAGAACGATATATCTCGATTCTTTCAGAACGATATATATCAATTATCAAACGTCCGAGAACGATATGTATCTCCAGAACGATATACGCCACATCATTCAGAGAACGATATACTAGAACGATATTTATAAGAACGATATGATATTACGGATACAGAACGATATAGAACGATATTAGCGCGGGCTCCCGTCAGAACGATATCCAAGATTAAAGTTTTCAAGAACGATATACAGAACGATATTAGAACGATATGATATGCGTCGACATCTTAGAACGATATAAGCGTCCCTTCTTGCGATTGTGTCTAGTGGCGCGTCTACCTTAATCCTGTCAGTAACCTCGATCTAGCATCGAAGTGAACATCCACGGTCCTGTTGTTGGCATGGAGATTGGTATTGGCTATATTGTCGTTATTCGGCACCCTGCATTCATGCCCAGGATACCGAACTCCCCCCTGCCGAAGCTACGCCGCTCGGTCGCGCCTGACCGGTGTAAACAAGCTACGCGCGATCGTATTGGCTAGCATAAGCAGTCTGGGCTATGGCCCAATTTTCGCATAGTACGTAAGGGACTTAAGGTATTTGTCCAGGGCCCTCACCCCTGCAATCGCGGAGGACGTGCCATCGTGGCCCCTCTCGTCTTAGACACGGTATAAGCCCCGCACAGGCACATTAATGTCTTCGACTGAACGTGTTATGTGAGCTTAATACGAGACTGCACTTTAGTCTCGGAGTGGCTTGGGACCGATGTTGTTATTCGCTTTTAAACTGTTGGCCACCTGCGTCATACTGGGAGAATCTCGGGCACTGGTTGACCAGATCGGGTGGGTTTTCATTACTCGCTTGAACCCGATTCATTACTCCATGAGTGCTGCAGTCCATTATCCACCGTGCGTGAAAGTAAGTCTCACCGGTTCGAGTCATCCCAAGCGTCACGGCTCCTAACGTCTGTTTGTCAAAATACTACTTATGTTCTTGACAATCATTGTGCTTCCAGTAGTAACCCAACGAACGCTGGTGTAACCCAACGGCCCTCACTCGGTAGTAACCCAACGGGTAACCCAACGCAACGCTCGATGAACGAATGTGGGGTAACCCAACGGCTGGGCCGTGGCGCTCTCAAAGTGAACGGATGTAACCCAACGAAGTAACCCAGTAACCCAACGATCCGGGGTTAGTGTAACCCAACGATCCCCTGCCGATATTAAGTCGCTCGCTTACGTGCTGGCGTAACCCAACGAGTGGTGAAATAATTAATCAACGAGAGCAAGGGTAACCCAACGGGTAACCGTAACCCAACGTAACCCAACGACGTAACCCAGTAACCCAACGCCAAATACCTTATGTATGGGGTAACCCAACGAGTAACCCAACGTACCGGTAACCCAACGCAACGCAGAAAAGCTAGTATTCCGAAAATCGTACCGGAGTATGTAACCCAACGAGAAGGTCGGCCTTGGTTTGAGGATCCTGCGATGAACTCACACTTTTCGGGGCAATCCGACGAGTGCCGGGTAACCCGTAACCCAACGCAAGTTAAGGGCAACAGCATCAAGGTAACCCAACGTCGCATCTGACACGTCCCATTCCGCGGTGAGATTGGCACAGCTCTTAGCCGGCTCTAAGGGCAAGCCTAGTGTTGCATTAGTTTGTGGTACTAATCGCATAGCTTGCGCGTCCAGCCTCTCCTCTTCATGATCTCCTATACCCGTGACGGACGCCGCGCGAATCATTTGTGTTAGTTTGTTATCGATATGACAGAAGGCACTAAAAACAGGTCGAAGAGGTCCAGATTTAGCCATGTACTTAGGCGCTATACGTTTCCGAAGACGTAAAGAACTCGAGCTGTGTTTCCCACGTTCTTCACCATAAACTCGAAGCTGCGCATGAACCCAAGTGTAACTAGCTTCGTTCATCGCCCTATCGCCGTTGCTATAGGGGTCGAATAGCTCCACATTGAACCGCCCGAAATGGTCCCCTCTTGTAGAGCTTATGGGTCTCACTAAATTAAACACAATCCCTAAGAATAAAATGTCCGATGAGAGCTCCATAAGCTTTGGACGATCAAAAGGACTTGGACGGACGTCGGGATGATAATAACACTCGCCACCTACTCTTGACATTTCTCCACACAGGATTAGGGGACGAGGAGTATACAGTAATACAACAATTAGTCGCCGGAGCTAGCACGAATAGGAAAGTTTCTAAAGTGTGGAGTGCCGGGCACTCTTCGCGACGCCATATTACCCCCTTTTCCGACCCTTGCACTATGCAGAACCTCAAGTATAGAACGAAGGTATAGCTCATATAAGAATCCTGTATCTCGCAGACAGAGAGGAGACGGCACACTTCAAGACCGTCTCGCAGACAGGCACGAAACCAATGTCTTGCAAATCAATTACATATGCTTCCACAAAAGTGCTCTCGCAGACAGCCATAATTGATTAACTTCTCGCAGACTCTCGCAGACAGCAGACAGCGAGGAATCTCGCAGACAGCAGGCGATGGTAAGGGCATACTCTCTCTCGCTCTCGCAGACAGGGCAGATCGCAGGCTAGCATTTGGTCTCGCAGACAGCTTTTCTCGCAGACAGGTCCCTTCTCGCAGACAGGGATTTATCATCACGGTGGACGATGGTCTCGCAGACTCTCGCAGACAGCTAGTGGTGATCGCTATCTCGCAGACAGCTCTCTCGCAGACAGGTCTCTAGTACAGATATCTCGCAGACACTAGTACAGATATCTCGCAGACAGTCGCAGACAGCTAGTACAGATCTAAATGGGATCATACTCATGTCTAGTACAGATCATTATAGTTCTCGCAGACAGAGTTAGCACATTCTCGCAGACAGCTCTCGCAGACAGGAGTACGGGCACTAGTACAGATTCTCTAGTACAGATGAACTACGCCTAGTACAGACTACTAGTACAGATAGTACAGATCCTAGTACAGATGAACTAGTACAGATCTATGCAGCGCCACACAATTGCTAGTACAGATTCCGTTGTATATTAGGGTCATTGCTCGCTCAAAGGAAGTGTATTGTTCCCGTTTCTATCCGCGCCTAGTACAGATGATCTGTTAGCGCCCGTAGTACCAGAAACTGGCCCAGAGGGGATCTCGAAAAGCCTCTACTAGTACAGATCTAGCTACTAGTACAGATACAGATCATCTGGTCAACCTTCTCCTAGTACAGATTGTTCTCCTAGTCTAGTACAGATGCACTAGTACAGATAGCTAGTACAGATAGACAAGAGCAACTAGTACAGATAGCTAGTACAGATAGTTTACCACCTAATGGGAACGTTGGGAAATCTGCGTATCGTAGGAGTGGAAGGCATGGGGGTCCTTCCCTATGTGCCTCACCACCTAATGGGAGCTCAGAATCACGGGTAAGCGGGCAGGCGAGATCGGACGGATACCACTGAGTCTTGGGGCTTGCCATTCAAAAAACCTAATGGGAATGGGTTCGACCTAATGGGCTACCTAATGGGGGAATGGGAATACCTAATGGGATGGGGCGGACCTAATGGGTGACCTAATGGGACCTAATGGGAACCTAATGGGTAATGGGACCTAATGGGACCTAATGGGACCTAATGGGACCTAATGGGACCTAATGGGAACCTAATGGGTAATGGGACCTAATGGGGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACTGATCGAACT", 12, 525, 16):
	f.write(i + " ")