reads_counter.py

import math

read_lin = 4
read_len = 16

def allindices(string, sub, listindex=[], offset=0):
	i = string.find(sub, offset)
	while i >= 0:
		listindex.append(i)
		i = string.find(sub, i + 1)
	return listindex

def search(kmer):
	with open('reads.fa') as f:
		results = []
		cont = f.read()
		print('kmer : ', kmer)
		results = allindices(cont, kmer)
	f.close()

	print('indices : ', results)
	reads = [ math.floor(x / (read_len + 1)) for x in results ]
	reads.sort(reverse = False)
	reads = list(dict.fromkeys(reads))
	print('reads   : ', reads)

	temp = []

	for x in reads:
		if x >= int(read_lin / 2):
			temp.append(int(x / (read_lin / 2)))
		else:
			temp.append(x)

	temp.sort(reverse = False)
	temp = list(dict.fromkeys(temp))
	print('results : ', len(temp))

	results.clear()
	reads.clear()


if __name__ == '__main__':

	kmers = [ 'jacques' ]
	for kmer in kmers:
		search(kmer)