generating a kmer tree with python

kmer_tree

# -*- 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

#returns a list of lists 
def makesubtree(rootnode, number_of_child_nodes):
  subtree=[[] for i in range(4)]
  subtree.insert(0,rootnode)
  return subtree

def make_alphabetsubtree(alphabet):
  #initialise the alphabet subtree as an empty list
  alphabet_subtree=[]
  for letter in alphabet:
    alphabet_subtree.append([letter])
  return alphabet_subtree
    
#test the makesubtree function
print makesubtree('/',4)

#make the main tree
maintree=makesubtree('/',4)
print maintree
#insert a subtree into the maintree
sub1=['A']
maintree.append(sub1)
print maintree

sub2=make_alphabetsubtree('ACGT')
print sub2
sub2.insert(0,'/')

#append alphabet subtree

def appendtotree(roottree,parent,node):
  if parent<1 or parent>4:
    print "Please select a tree level between 1 and 4"

  roottree[parent].append(node)

  return roottree

print appendtotree(sub2,1,sub1)

#make the final roottree
final_tree=make_alphabetsubtree('ACGT')
final_tree.insert(0,'/')

#try to append an 'A' node to all parents in level1
for i in range(4):
  for letter in 'ATCG':
    appendtotree(final_tree,i+1,[letter])

print final_tree

for k in range(4):
  for i in range(4):
    for letter in 'ATCG':
      appendtotree(final_tree[k+1],i+1,[letter])

print "new tree"
print ""

print final_tree

print "=======NEW SECTION========="

#make a test tree
test_tree=make_alphabetsubtree('ACD')
test_tree.insert(0,'/')
for i in range(3):
  for letter in 'ACD':
    appendtotree(test_tree,i+1,[letter])

print test_tree
print test_tree[1:4]

print "========PARENTNODE==========="
for parentnode in test_tree[1:4]:
  print parentnode[0]
  for childnode in parentnode:
    print childnode

print "=================TESTING CONCANTENATION================"
#make an empty dictionary to hold the kmers
kmer_dict={}
for parentnode in test_tree[1:4]:
    kmer_dict[parentnode[0]]=[]
    #initialise the root string
    
    for childnode in parentnode:
      root=parentnode[0]
      root+=childnode[0]
      print root
      kmer_dict[parentnode[0]].append(root)


print "==================FINAL KMER DICT==========="
print kmer_dict