def rand_kmer_coords(f,nodes):
N = {}
while len(N) < nodes:
rk = rand_kmer(f,nodes)
if rk['q'].count(2) < 3:
N[len(N)] = list(letters_to_coords(rk))
return N
def read_sequence(initial_read,H,Hp,W,k=None,known_path_length=2): forward_extension = [] backward_extension = [] forward_extension_bins = () backward_extension_bins = () initial_sequence = list(letters_to_coords(initial_read)) if not k: k = len(initial_sequence) while True: extended_sequence = initial_sequence + forward_extension extension = longest_path(extended_sequence[-k:],H,W,True) if extension: forward_extension += extension[0] forward_extension_bins += extension[1] if forward_extension_bins[-known_path_length:] in Hp: forward_extension_bins += Hp[forward_extension_bins[-known_path_length:]] break else: break while True: extended_sequence = backward_extension + initial_sequence extension = longest_path(extended_sequence[:k],H,W,False) if extension: backward_extension = extension[0] + backward_extension backward_extension_bins = extension[1] + backward_extension_bins if backward_extension_bins[:known_path_length] in Hp: backward_extension_bins = Hp[backward_extension_bins[:known_path_length]] + backward_extension_bins break else: break return forward_extension_bins,backward_extension_bins
def read_sequence(initial_read, H, Hp, W, k=None, known_path_length=2):
forward_extension = []
backward_extension = []
forward_extension_bins = ()
backward_extension_bins = ()
initial_sequence = list(letters_to_coords(initial_read))
if not k:
k = len(initial_sequence)
while True:
extended_sequence = initial_sequence + forward_extension
extension = longest_path(extended_sequence[-k:], H, W, True)
if extension:
forward_extension += extension[0]
forward_extension_bins += extension[1]
if forward_extension_bins[-known_path_length:] in Hp:
forward_extension_bins += Hp[
forward_extension_bins[-known_path_length:]]
break
else:
break
while True:
extended_sequence = backward_extension + initial_sequence
extension = longest_path(extended_sequence[:k], H, W, False)
if extension:
backward_extension = extension[0] + backward_extension
backward_extension_bins = extension[1] + backward_extension_bins
if backward_extension_bins[:known_path_length] in Hp:
backward_extension_bins = Hp[
backward_extension_bins[:known_path_length]] + backward_extension_bins
break
else:
break
return forward_extension_bins, backward_extension_bins
def rand_kmer_coords(f, nodes):
N = {}
while len(N) < nodes:
rk = rand_kmer(f, nodes)
if rk['q'].count(2) < 3:
N[len(N)] = list(letters_to_coords(rk))
return N
for a in range(len(A)):
if H.get(B[0][a],False):
E.append(([A[a]],(B[0][a],)))
# POSSIBLE TO USE MULTIPLE WHEELS HERE
#extension_bins = ()
#for b in range(len(B)):
# if H.get(B[b][a],False):
# extension_bins += (B[b][a],)
# else:
# break
#if len(extension_bins) == len(B):
# E.append(([A[a]],(extension_bins,)))
return E
Alphabet = {'s': 'ATCG'}
Mapped_Alphabet = letters_to_coords(Alphabet)
def extend_kmer(s,forward=True):
A = []
C = []
for a in Mapped_Alphabet:
if forward:
C.append(s[1:] + [a])
else:
C.append([a] + s[:-1])
A.append(a)
return A,C
def longest_path(s0,H,W,fb):
k = len(s0)
P = extend_path(s0,H,W,fb)
while len(P) > 1:
if H.get(B[0][a], False):
E.append(([A[a]], (B[0][a], )))
# POSSIBLE TO USE MULTIPLE WHEELS HERE
#extension_bins = ()
#for b in range(len(B)):
# if H.get(B[b][a],False):
# extension_bins += (B[b][a],)
# else:
# break
#if len(extension_bins) == len(B):
# E.append(([A[a]],(extension_bins,)))
return E
Alphabet = {'s': 'ATCG'}
Mapped_Alphabet = letters_to_coords(Alphabet)
def extend_kmer(s, forward=True):
A = []
C = []
for a in Mapped_Alphabet:
if forward:
C.append(s[1:] + [a])
else:
C.append([a] + s[:-1])
A.append(a)
return A, C
def longest_path(s0, H, W, fb):