/
assembler.py
216 lines (204 loc) · 5.87 KB
/
assembler.py
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from hyper_sequences import set_wheels,get_wheels,generator_to_bins,coords_to_bins,letters_to_coords
from pymongo import Connection
from random import randint
import itertools
from collections import defaultdict
from operator import itemgetter
conn = Connection()
# PROBABLY FINE FOR TESTING, NOT OPTIMIZED FOR PRODUCTION PERFORMANCE
# RUN LIKE THIS:
# >>> S = generate_test_genome(n=100000,read_size=75,k=31)
# >>> W = do_wheels(41)
# choose spokes based on memory requirements
# >>> W = get_wheels('/mnt/test_Wheels.txt',spoke_limit=30)
# >>> H = hash_test_kmers(W)
# >>> PR = read_many_sequences(H,W,31,3)
def generate_test_genome(n=10000,read_size=50,repeats=10,k=20):
L = {0: 'A',1: 'T',2: 'C',3: 'G'}
S = ''.join([L[randint(0,3)] for _ in xrange(n)])
db = conn['test_genome']
db.kmers.drop()
db.reads.drop()
T = 0
for c in range(repeats):
i = 0
while i < len(S):
r = randint(-read_size/5,read_size/5) + read_size
s = S[i:i+r]
q = []
for _ in s:
r0 = randint(0,100)
if r0 <= 5:
q.append(randint(10,40))
elif r0 <= 20:
q.append(randint(31,35))
else:
q.append(34)
db.reads.insert({"_id": i,"s": s,"q": q})
i += r
l = 0
while l < len(s)-k:
db.kmers.insert({'_id': T,'s': s[l:l+k],'q': q[l:l+k]})
T += 1
l += 1
return S
def do_wheels(s,w=1):
db = conn['test_genome']
d = len(db.kmers.find_one()['s'])
set_wheels(d,realm='test_genome',spokes=s,wheels=w,out_path='/mnt/test_')
W = get_wheels('/mnt/test_Wheels.txt')
return W
def hash_test_kmers(W):
db = conn['test_genome']
docs = db.kmers.find({},timeout=False)
A,B = generator_to_bins(docs,W,return_terminals=True)
H = defaultdict()
for j in range(len(B)):
for i in xrange(len(A)):
H[B[j][i]] = True
return H
def update_known_paths(Hp,Pb,pl,forward=True):
# not storing the full sequence path or bin path.
# will only return terminal bins to conserve memory
if forward:
for i in range(len(Pb)-pl):
if Pb[i:i+pl] not in Hp:
Hp[Pb[i:i+pl]] = Pb[-2:]
else:
for i in range(len(Pb),pl,-1):
if Pb[i-pl:i] not in Hp:
H[Pb[i-pl:i]] = Pb[:2]
return Hp
def read_many_sequences(H,W,kmer_size,path_length):
db = conn['test_genome']
Read_Terminals = defaultdict(list)
Known_Paths = {}
docs = db.reads.find({},timeout=False)
for doc in docs:
if len(doc['s']) > kmer_size:
f,b = read_sequence(doc,H,Known_Paths,W,k=kmer_size,known_path_length=path_length)
Known_Paths = update_known_paths(Known_Paths,f,path_length)
Known_Paths = update_known_paths(Known_Paths,b,path_length,forward=False)
for x in f[-2:] + b[:2]:
Read_Terminals[x].append(doc['_id'])
Read_Terminals = [(len(v),k,v) for k,v in Read_Terminals.iteritems()]
Read_Terminals.sort(reverse=True)
Partitioned_Reads = {}
for rt in Read_Terminals:
partition_counts = defaultdict(int)
for r in rt[2]:
partition_counts[Partitioned_Reads.get(r,None)] += 1
partition_counts[None] = 0
partition_counts = sorted(partition_counts.iteritems(),key=itemgetter(1),reverse=True)
if partition_counts[0][1] > rt[0]*.25:
p0 = partition_counts[0][0]
else:
p0 = rt[1]
for r in rt[2]:
if r not in Partitioned_Reads:
Partitioned_Reads[r] = p0
return Partitioned_Reads
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 extend_path(s0,H,W,fb):
k = len(s0)
A,C = extend_kmer(s0,forward=fb)
A,B = coords_to_bins(A,C,W)
E = []
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:
did_extension = False
for i in range(len(P)):
p = P[i][0]
if fb:
sp = s0[len(p):] + p[-k:]
else:
sp = p[:k] + s0[:max(0,k-len(p))]
for e in extend_path(sp,H,W,fb):
if fb:
P.append((p+e[0],P[i][1]+e[1]))
else:
P.append((e[0]+p,e[1]+P[i][1]))
did_extension = True
P = [(len(p[0]),p) for p in P]
P = sorted(P,key=itemgetter(0),reverse=True)
P = [p[1] for p in P if p[0]==P[0][0]]
if not did_extension:
P = P[:1]
if P:
return P[0]
else:
return None
def test_false_positives(S,H,W,k=20):
i = 0
fp = 0
fn = 0
while i < len(S)-k:
Ef = extend_path(S[i:i+k],H,W,True)
if len(Ef) == 0:
fn += 1
elif len(Ef) > 1:
fp += 1
Eb = extend_path(S[i:i+k],H,W,False)
if len(Eb) == 0:
fn += 1
elif len(Eb) > 1:
fp += 1
i += 1
return fp,fn