gistfile1.py

# -*- coding: utf-8 -*-
def kmer(sequence,k):
  length=len(sequence)
 #if the kmer size if greater than the lenght of the sequene
  if k>=length:
    print "You specified a kmer size, which if greater or equal to the length of the sequence"
    return 
  stepsize=k-1
  i=0
  kmers=[]
  while i+stepsize<length:
    kmers.append(sequence[i:i+k])
    i+=1
  print kmers

kmer("ABCDGFGFGFGFGFGG",90)

#OUTPUT ALL OF THE POSSIBLE KMERS FROM A PREDEFINED ALPHABET

def all_kmers(alphabet,k):
  nodenumber=len(alphabet)
  kmerTree=[]


  return kmerTree


def kmer_subtree(rootnode, length):
  return [rootnode,[]*length]

maintree=kmer_subtree('/',4)
print maintree