FreqArray.py

import math

def computeFreqs(text, k_mer):

	sizeArr = int(math.pow(4,k_mer)) 
	array = [None] * sizeArr
	for i in range(sizeArr):
		array[i] = 0

	end = len(text) - k_mer
	for i in range(end + 1):
		pattern = text[i:i+k_mer]
		numberOfPattern = patternToNumber(pattern)
		array[numberOfPattern] = array[numberOfPattern] + 1

	print(" ".join(str(x) for x in array))

def patternToNumber(pat):

	if len(pat) == 0:
		return 0
	symbol = pat[len(pat) - 1] 
	prefix = pat[0:len(pat) - 1]

	return 4*patternToNumber(prefix) + symbolToNumber(symbol)

def symbolToNumber(letter):

	if letter == 'A':
		return 0
	elif letter == 'C':
		return 1
	elif letter == 'G':
		return 2
	elif letter == 'T':
		return 3

computeFreqs('TACTATCTCGTGATTAGTACAGCCGAACCAACACATGATCCACATTTTCAGGAGGAACGTTACCATGCGCTTCCCCTTAAGTTAATCAGAGTACAAAAGCTCCTGGACAGCTGCGGATGGCTGCACATGTTGTCGAACTTCATATTCTCGATACTAGTCACGCTCCCGTAAGAAGTGCTGATCCGAAATTTGGCTATATTACAGCAGCTGGCTGAAGTGAGTCTGTCTGGAATGGGTCAAGAGGGCTATCGTCCAGTCGCAAAGTTGATCGCTCCGTTAGCTAATTAACTACTGCCCGTCATTGGTGCTCACGGATTACTGAGTCTTGACTGTTCGGCTGATTTGGCCATCTTGGGTGACCCGAGACAATTGATCCCCGTACTAAGTAGATACTCACACAAACGGGTGGTTGTAATGTGGCCGTCTCCCTCGTGGCACGACGGCACTCAGCCCGCAGCGTCCAAAGGAGGACGTAGATCATGTACTTGTTACGTTATGACTGACGTATGGTATCCAGAGCATCTCCGTCCTCGAGGCACTCTTGAAGTAAGTCAGAAAGCCCTCGGTTGTAAACGGGTTTCACGAACGGACCAGATTGAGCCCCTTCGGAGTATCTAGCCGGATCATTGAGTCGCCGGGCCGCCCGCAAGCACGTAGAAGCCGTC', 6)