import random
random.seed(0)
myseq = [random.choice(['a', 'c', 'g', 't']) for i in range(1000)]
myseq[:10]

readlen = 25
starts = [random.randint(0, len(myseq)-readlen) for i in range(500)]
reads = [myseq[start:start+readlen] for start in  starts]
reads[0]

kg = KmerGraph()
kg.readstograph(reads,16)
kg.collisions
len(kg.kmers)

def findstart(self, path):
  """Traverse the current path, looking for a node with available edges"""
  start = None
  for i in range(len(path)):
    if len(self.neighbors[self.kmers[path[i]]]) > 0:
      start = path[i]
      break
  return start

def extendpath(self, path):
  start = self.findstart(path)
  splicepoint = start
  if start != None:
    newpath = []
    while len(self.neighbors[self.kmers[start]]) > 0:
      next_kmer = self.neighbors[self.kmers[start]].popleft()
      start = self.kmers.index(next_kmer)
      newpath.append(start)
    path[splicepoint:splicepoint+1] = newpath
  return start

for k in range(9,19):
  kg = KmerGraph()
  kg.readstograph(reads, k)
  nodes = len(kg.kmers)
  maxi = 0
  maxl = -1
  for i in range(nodes):
    path = [i]
    next = kg.extendpath(path)
    while (next != None):
      next = kg.extendpath(path)
    if len(path) > maxl:
      maxi = i
      maxl = len(path)
    kg = KmerGraph()
    kg.readstograph(reads, k)

  print k, maxi, maxl

from collections import deque
import random
random.seed(0)
myseq = [random.choice(['a', 'c', 'g', 't']) for i in range(1000)]
print myseq[:10]

readlen = 25
starts = [random.randint(0, len(myseq)-readlen) for i in range(500)]
reads = [myseq[start:start+readlen] for start in  starts]
print reads[0]

results = "coverage.png"
coverage = [0] * len(myseq)
for start in starts:
  for i in range(start, start+readlen):
    coverage[i] += 1

import matplotlib, numpy
matplotlib.use('Agg')
import matplotlib.pyplot as plt
fig=plt.figure(figsize=(4,2))
plt.plot(coverage)
fig.tight_layout()
plt.savefig(results)
results

k = 16
kmers = []
kmergraph = {}

for read in reads:
  read = "".join(read)
  for i in range(len(read) - k - 1):
    kmer_a = read[i:i+k]
    kmer_b = read[i+1:i+k+1]
    if kmer_a not in kmers:
       kmers.append(kmer_a)
    if kmer_b not in kmers:
       kmers.append(kmer_b)
    if kmer_a not in kmergraph.keys():
       kmergraph[kmer_a] = deque([kmer_b])
    elif kmer_b not in kmergraph[kmer_a]:
       kmergraph[kmer_a].append(kmer_b)
    if kmer_b not in kmergraph.keys():
       kmergraph[kmer_b] = deque([])

#print kmers[:10]

def findstart(kmers, kmergraph, path):
  start = None
  for i in range(len(path)):
    if len(kmergraph[kmers[path[i]]]) > 0:
      start = path[i]
      break
  return start

def extendpath(kmers, kmergraph, path):
  start = findstart(kmers, kmergraph, path)
  splicepoint = start
  if start != None:
    newpath = []
    while len(kmergraph[kmers[start]]) > 0:
      next_kmer = kmergraph[kmers[start]].popleft()
      start = kmers.index(next_kmer)
      newpath.append(start)
    path[splicepoint:splicepoint+1] = newpath
  return start

for i in range(330,331):
  start = i
  print start, 
  path = [start]
  next = extendpath(kmers, kmergraph, path)
  while (next != None):
    next = extendpath(kmers, kmergraph, path)
  print len(path)
  k = 16
  kmers = []
  kmergraph = {}

  for read in reads:
    read = "".join(read)
    for i in range(len(read) - k - 1):
      kmer_a = read[i:i+k]
      kmer_b = read[i+1:i+k+1]
      if kmer_a not in kmers:
	 kmers.append(kmer_a)
      if kmer_b not in kmers:
	 kmers.append(kmer_b)
      if kmer_a not in kmergraph.keys():
	 kmergraph[kmer_a] = deque([kmer_b])
      elif kmer_b not in kmergraph[kmer_a]:
	 kmergraph[kmer_a].append(kmer_b)
      if kmer_b not in kmergraph.keys():
	 kmergraph[kmer_b] = deque([])

  #print kmers[:10]

assembly = kmers[path[0]]
for i in range(1, len(path)):
  assembly += kmers[path[i]][-1]

len(assembly)

def wrap(seq):
  start = 0
  for i in range(60, len(seq), 60):
    print seq[start: i]
    start = i
  print seq[start:]

print ">myseq"
wrap("".join(myseq))
print
print ">assembly"
wrap(assembly)
print