kc-py1.py

#!/usr/bin/env python

import sys

base_for = "ACGT"
base_rev = "TGCA"
comp_tab = str.maketrans(base_for, base_rev)

def count_kmer(h, k, seq):
	l = len(seq)
	if l < k: return
	for i in range(l - k + 1):
		kmer_for = seq[i:(i+k)]
		if 'N' in kmer_for: continue
		kmer_rev = kmer_for.translate(comp_tab)[::-1]
		if kmer_for < kmer_rev: kmer = kmer_for
		else: kmer = kmer_rev
		if kmer in h:
			h[kmer] += 1
		else: h[kmer] = 1

def count_stdin(k):
	counter = {}
	seq = []
	for line in sys.stdin:
		if line[0] == '>':
			if len(seq) > 0:
				count_kmer(counter, k, ''.join(seq))
				seq = []
		else:
			seq.append(line[:-1])
	if len(seq) > 0:
		count_kmer(counter, k, ''.join(seq).upper())
	return counter

def print_hist(counter):
	hist = [0] * 256
	for kmer in counter:
		cnt = counter[kmer]
		if cnt > 255: cnt = 255
		hist[cnt] += 1
	for i in range(1, 256):
		print("{}\t{}".format(i, hist[i]))

counter = count_stdin(31)
print_hist(counter)