def get_aln_data(t_seq, q_seq):
aln_data = []
K = 8
seq0 = t_seq
lk_ptr = kup.allocate_kmer_lookup( 1 << (K * 2) )
sa_ptr = kup.allocate_seq( len(seq0) )
sda_ptr = kup.allocate_seq_addr( len(seq0) )
kup.add_sequence( 0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
q_id = "dummy"
kmer_match_ptr = kup.find_kmer_pos_for_seq(q_seq, len(q_seq), K, sda_ptr, lk_ptr)
kmer_match = kmer_match_ptr[0]
aln_range_ptr = kup.find_best_aln_range(kmer_match_ptr, K, K*5, 12)
aln_range = aln_range_ptr[0]
x,y = zip( * [ (kmer_match.query_pos[i], kmer_match.target_pos[i]) for i in range(kmer_match.count)] )
kup.free_kmer_match(kmer_match_ptr)
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
if e1 - s1 > 100:
alignment = DWA.align(q_seq[s1:e1], e1-s1,
seq0[s2:e2], e2-s2,
1500,1)
if alignment[0].aln_str_size > 100:
aln_data.append( ( q_id, 0, s1, e1, len(q_seq), s2, e2, len(seq0), alignment[0].aln_str_size, alignment[0].dist ) )
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data, x, y
def get_aln_data(t_seq, q_seq):
aln_data = []
#x = []
#y = []
K = 8
seq0 = t_seq
lk_ptr = kup.allocate_kmer_lookup(1 << (K * 2))
sa_ptr = kup.allocate_seq(len(seq0))
sda_ptr = kup.allocate_seq_addr(len(seq0))
kup.add_sequence(0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
q_id = "dummy"
kmer_match_ptr = kup.find_kmer_pos_for_seq(
q_seq, len(q_seq), K, sda_ptr, lk_ptr)
kmer_match = kmer_match_ptr[0]
if kmer_match.count != 0:
aln_range_ptr = kup.find_best_aln_range(kmer_match_ptr, K, K * 5, 12)
aln_range = aln_range_ptr[0]
#x, y = list(zip(* [(kmer_match.query_pos[i], kmer_match.target_pos[i])
# for i in range(kmer_match.count)]))
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
log('Mapped (q, s1 = {}, e1 = {}, len1 = {}, (e1 - s1) = {}, t, s2 = {}, e2 = {}, (e2 - s2) = {}, len2 = {})'.format(
s1, e1, e1 - s1, len(q_seq), s2, e2, e2 - s2, len(t_seq)))
max_len = 250000 # to keep allocations < 16GB, given band_tol=1500
if (e1 - s1) >= max_len or (e2 - s2) >= max_len:
# DW.align() would crash, so raise here.
# (500000 is the approx. upper bound for int overflow,
# but some users run out of memory anyway.)
raise TooLongError('q_len={} or t_len={} are too big, over 500k'.format(
(e1-s1), (e2-s2)))
if e1 - s1 > 100:
log('Calling DW_banded.align(q, s1 = {}, e1 = {}, len1 = {}, (e1 - s1) = {}, t, s2 = {}, e2 = {}, (e2 - s2) = {}, len2 = {})'.format(
s1, e1, e1 - s1, len(q_seq), s2, e2, e2 - s2, len(t_seq)))
alignment = DWA.align(q_seq[s1:e1], e1 - s1,
seq0[s2:e2], e2 - s2,
1500, 1)
if alignment[0].aln_str_size > 100:
aln_data.append((q_id, 0, s1, e1, len(q_seq), s2, e2, len(
seq0), alignment[0].aln_str_size, alignment[0].dist))
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_aln_range(aln_range_ptr)
kup.free_kmer_match(kmer_match_ptr)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data #, x, y
def get_aln_data(t_seq, q_seq):
aln_data = []
#x = []
#y = []
K = 8
seq0 = t_seq
lk_ptr = kup.allocate_kmer_lookup(1 << (K * 2))
sa_ptr = kup.allocate_seq(len(seq0))
sda_ptr = kup.allocate_seq_addr(len(seq0))
kup.add_sequence(0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
q_id = "dummy"
kmer_match_ptr = kup.find_kmer_pos_for_seq(q_seq, len(q_seq), K, sda_ptr,
lk_ptr)
kmer_match = kmer_match_ptr[0]
if kmer_match.count != 0:
aln_range_ptr = kup.find_best_aln_range(kmer_match_ptr, K, K * 5, 12)
aln_range = aln_range_ptr[0]
#x, y = list(zip(* [(kmer_match.query_pos[i], kmer_match.target_pos[i])
# for i in range(kmer_match.count)]))
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
max_len = 250000 # to keep allocations < 16GB, given band_tol=1500
if (e1 - s1) >= max_len or (e2 - s2) >= max_len:
# DW.align() would crash, so raise here.
# (500000 is the approx. upper bound for int overflow,
# but some users run out of memory anyway.)
raise TooLongError(
'q_len={} or t_len={} are too big, over 500k'.format(
(e1 - s1), (e2 - s2)))
if e1 - s1 > 100:
log('Calling DW_banded.align(q, {}, t, {}, 1500, 1)'.format(
e1 - s1, e2 - s2))
alignment = DWA.align(q_seq[s1:e1], e1 - s1, seq0[s2:e2], e2 - s2,
1500, 1)
if alignment[0].aln_str_size > 100:
aln_data.append(
(q_id, 0, s1, e1, len(q_seq), s2, e2, len(seq0),
alignment[0].aln_str_size, alignment[0].dist))
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_aln_range(aln_range_ptr)
kup.free_kmer_match(kmer_match_ptr)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data #, x, y
def get_alignment(seq1, seq0):
K = 8
lk_ptr = kup.allocate_kmer_lookup(1 << (K * 2))
sa_ptr = kup.allocate_seq(len(seq0))
sda_ptr = kup.allocate_seq_addr(len(seq0))
kup.add_sequence(0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
kmer_match_ptr = kup.find_kmer_pos_for_seq(seq1, len(seq1), K, sda_ptr,
lk_ptr)
kmer_match = kmer_match_ptr[0]
aln_range = kup.find_best_aln_range(kmer_match_ptr, K, K * 5, 50)
#x,y = zip( * [ (kmer_match.query_pos[i], kmer_match.target_pos[i]) for i in range(kmer_match.count )] )
kup.free_kmer_match(kmer_match_ptr)
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
if e1 - s1 > 500:
#s1 = 0 if s1 < 14 else s1 - 14
#s2 = 0 if s2 < 14 else s2 - 14
e1 = len(seq1) if e1 >= len(seq1) - 2 * K else e1 + K * 2
e2 = len(seq0) if e2 >= len(seq0) - 2 * K else e2 + K * 2
alignment = DWA.align(seq1[s1:e1], e1 - s1, seq0[s2:e2], e2 - s2, 100,
0)
#print seq1[s1:e1]
#print seq0[s2:e2]
#if alignment[0].aln_str_size > 500:
#aln_str1 = alignment[0].q_aln_str
#aln_str0 = alignment[0].t_aln_str
aln_size = alignment[0].aln_str_size
aln_dist = alignment[0].dist
aln_q_s = alignment[0].aln_q_s
aln_q_e = alignment[0].aln_q_e
aln_t_s = alignment[0].aln_t_s
aln_t_e = alignment[0].aln_t_e
assert aln_q_e - aln_q_s <= alignment[
0].aln_str_size or aln_t_e - aln_t_s <= alignment[0].aln_str_size
#print aln_str1
#print aln_str0
DWA.free_alignment(alignment)
kup.free_seq_addr_array(sda_ptr)
kup.free_seq_array(sa_ptr)
kup.free_kmer_lookup(lk_ptr)
if e1 - s1 > 500 and aln_size > 500:
return s1, s1 + aln_q_e - aln_q_s, s2, s2 + aln_t_e - aln_t_s, aln_size, aln_dist
else:
return None
def get_alignment(seq1, seq0):
K = 8
lk_ptr = kup.allocate_kmer_lookup( 1 << (K * 2) )
sa_ptr = kup.allocate_seq( len(seq0) )
sda_ptr = kup.allocate_seq_addr( len(seq0) )
kup.add_sequence( 0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
kmer_match_ptr = kup.find_kmer_pos_for_seq(seq1, len(seq1), K, sda_ptr, lk_ptr)
kmer_match = kmer_match_ptr[0]
aln_range = kup.find_best_aln_range(kmer_match_ptr, K, K*5, 50)
#x,y = zip( * [ (kmer_match.query_pos[i], kmer_match.target_pos[i]) for i in range(kmer_match.count )] )
kup.free_kmer_match(kmer_match_ptr)
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
if e1 - s1 > 500:
#s1 = 0 if s1 < 14 else s1 - 14
#s2 = 0 if s2 < 14 else s2 - 14
e1 = len(seq1) if e1 >= len(seq1)-2*K else e1 + K*2
e2 = len(seq0) if e2 >= len(seq0)-2*K else e2 + K*2
alignment = DWA.align(seq1[s1:e1], e1-s1,
seq0[s2:e2], e2-s2,
100, 0)
#print seq1[s1:e1]
#print seq0[s2:e2]
#if alignment[0].aln_str_size > 500:
#aln_str1 = alignment[0].q_aln_str
#aln_str0 = alignment[0].t_aln_str
aln_size = alignment[0].aln_str_size
aln_dist = alignment[0].dist
aln_q_s = alignment[0].aln_q_s
aln_q_e = alignment[0].aln_q_e
aln_t_s = alignment[0].aln_t_s
aln_t_e = alignment[0].aln_t_e
assert aln_q_e- aln_q_s <= alignment[0].aln_str_size or aln_t_e- aln_t_s <= alignment[0].aln_str_size
#print aln_str1
#print aln_str0
DWA.free_alignment(alignment)
kup.free_seq_addr_array(sda_ptr)
kup.free_seq_array(sa_ptr)
kup.free_kmer_lookup(lk_ptr)
if e1 - s1 > 500 and aln_size > 500:
return s1, s1+aln_q_e-aln_q_s, s2, s2+aln_t_e-aln_t_s, aln_size, aln_dist
else:
return None
def get_aln_data(t_seq, q_seq):
aln_data = []
x = []
y = []
K = 8
seq0 = t_seq
lk_ptr = kup.allocate_kmer_lookup(1 << (K * 2))
sa_ptr = kup.allocate_seq(len(seq0))
sda_ptr = kup.allocate_seq_addr(len(seq0))
kup.add_sequence(0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
q_id = "dummy"
kmer_match_ptr = kup.find_kmer_pos_for_seq(q_seq, len(q_seq), K, sda_ptr,
lk_ptr)
kmer_match = kmer_match_ptr[0]
if kmer_match.count != 0:
aln_range_ptr = kup.find_best_aln_range(kmer_match_ptr, K, K * 5, 12)
aln_range = aln_range_ptr[0]
x, y = zip(*[(kmer_match.query_pos[i], kmer_match.target_pos[i])
for i in range(kmer_match.count)])
s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
if e1 - s1 > 100:
alignment = DWA.align(q_seq[s1:e1], e1 - s1, seq0[s2:e2], e2 - s2,
1500, 1)
if alignment[0].aln_str_size > 100:
aln_data.append(
(q_id, 0, s1, e1, len(q_seq), s2, e2, len(seq0),
alignment[0].aln_str_size, alignment[0].dist))
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_aln_range(aln_range_ptr)
kup.free_kmer_match(kmer_match_ptr)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data, x, y
monomer_db[rid].append((rng, r.sequence, orientation))
print len(seq_db), " sequences read.",\
"Reads with monomers:", len(monomer_db.keys())
# RUN OVER ALL READS THAT CONTAIN MONOMERS #
for rid, monomers in monomer_db.items():
aln_data = []
range_list = []
total_monomer_len = 0
# Align all monomers on the read to each other.
for i in range(len(monomers)):
for j in range(i + 1, len(monomers)):
t_seq = monomers[i][1]
q_seq = monomers[j][1]
alignment = DWA.align(q_seq, len(q_seq), t_seq, len(t_seq), 50, 1)
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
aln_size = alignment[0].aln_str_size
aln_dist = alignment[0].dist
aln_q_s = alignment[0].aln_q_s
aln_q_e = alignment[0].aln_q_e
aln_t_s = alignment[0].aln_t_s
aln_t_e = alignment[0].aln_t_e
# Skip if no alignment
if aln_size != 0:
# Store the alignment score for the monomer pair: (i, j, score)
aln_data.append((i, j, 1 - (1.0*aln_dist/aln_size)))
DWA.free_alignment(alignment)
def get_ovelap_alignment(seq1, seq0):
K = 8
lk_ptr = kup.allocate_kmer_lookup( 1 << (K * 2) )
sa_ptr = kup.allocate_seq( len(seq0) )
sda_ptr = kup.allocate_seq_addr( len(seq0) )
kup.add_sequence( 0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)
kmer_match_ptr = kup.find_kmer_pos_for_seq(seq1, len(seq1), K, sda_ptr, lk_ptr)
kmer_match = kmer_match_ptr[0]
aln_range = kup.find_best_aln_range(kmer_match_ptr, K, K*5, 50)
#x,y = zip( * [ (kmer_match.query_pos[i], kmer_match.target_pos[i]) for i in range(kmer_match.count )] )
kup.free_kmer_match(kmer_match_ptr)
s1, e1, s0, e0 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
len_1 = len(seq1)
len_0 = len(seq0)
do_aln = False
contain_status = "none"
if e1 - s1 > 500:
if s1 < 100 and len_1 - e1 < 100:
do_aln = False
contain_status = "contains"
elif s0 < 100 and len_0 - e0 < 100:
do_aln = False
contain_status = "contained"
else:
do_aln = True
if s0 < s1:
s1 -= s0 #assert s1 > 0
s0 = 0
e1 = len_1
e0 = len_1 - s1 if len_1 - s1 < len_0 else len_0
if e0 == len_0:
do_aln = False
contain_status = "contained"
if s1 <= s0:
s0 -= s1 #assert s1 > 0
s1 = 0
e0 = len_0
e1 = len_0 - s0 if len_0 - s0 < len_1 else len_1
if e1 == len_1:
do_aln = False
contain_status = "contains"
if do_aln:
alignment = DWA.align(seq1[s1:e1], e1-s1,
seq0[s0:e0], e0-s0,
500, 0)
#print seq1[s1:e1]
#print seq0[s2:e2]
#if alignment[0].aln_str_size > 500:
#aln_str1 = alignment[0].q_aln_str
#aln_str0 = alignment[0].t_aln_str
aln_size = alignment[0].aln_str_size
aln_dist = alignment[0].dist
aln_q_s = alignment[0].aln_q_s
aln_q_e = alignment[0].aln_q_e
aln_t_s = alignment[0].aln_t_s
aln_t_e = alignment[0].aln_t_e
assert aln_q_e- aln_q_s <= alignment[0].aln_str_size or aln_t_e- aln_t_s <= alignment[0].aln_str_size
#print aln_str1
#print aln_str0
if aln_size > 500:
contain_status = "overlap"
DWA.free_alignment(alignment)
kup.free_seq_addr_array(sda_ptr)
kup.free_seq_array(sa_ptr)
kup.free_kmer_lookup(lk_ptr)
if e1 - s1 > 500 and do_aln and aln_size > 500:
#return s1, s1+aln_q_e-aln_q_s, s2, s2+aln_t_e-aln_t_s, aln_size, aln_dist, x, y
return s1, s1+aln_q_e-aln_q_s, s0, s0+aln_t_e-aln_t_s, aln_size, aln_dist, contain_status
else:
return 0, 0, 0, 0, 0, 0, contain_status
monomer_db[rid].append((rng, r.sequence, orientation))
print len(seq_db), " sequences read.",\
"Reads with monomers:", len(monomer_db.keys())
# RUN OVER ALL READS THAT CONTAIN MONOMERS #
for rid, monomers in monomer_db.items():
aln_data = []
range_list = []
total_monomer_len = 0
# Align all monomers on the read to each other.
for i in range(len(monomers)):
for j in range(i + 1, len(monomers)):
t_seq = monomers[i][1]
q_seq = monomers[j][1]
alignment = DWA.align(q_seq, len(q_seq), t_seq, len(t_seq), 50, 1)
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
aln_size = alignment[0].aln_str_size
aln_dist = alignment[0].dist
aln_q_s = alignment[0].aln_q_s
aln_q_e = alignment[0].aln_q_e
aln_t_s = alignment[0].aln_t_s
aln_t_e = alignment[0].aln_t_e
# Skip if no alignment
if aln_size != 0:
# Store the alignment score for the monomer pair: (i, j, score)
aln_data.append((i, j, 1 - (1.0 * aln_dist / aln_size)))
DWA.free_alignment(alignment)