def run_bwa_py_sampe_alloc_only(refseq_fname, read_fname, mate_fname):
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs = [x for x in it.izip(read_flow, mate_flow)]
print_meminfo("AFTER READING PAIRS")
bwsa = bwa.build_bws_array(pairs)
print_meminfo("AFTER BUILDING BWSA")
bwts = bwa.restore_index(refseq_fname)
print_meminfo("AFTER RESTORING INDEX")
bnsp, pacseq = bwa.restore_reference(refseq_fname)
print_meminfo("AFTER RESTORING REFERENCE")
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
print_meminfo("AFTER INIT OPT & II")
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
print_meminfo("AFTER DEALLOC")
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PACSEQ")
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PAIRS")
def main(argv):
try:
hit_fn = argv[1]
except IndexError:
hit_fn = 'hit_pairs.fastq'
N = 10
root_name = 'refseq'
generate_ref(root_name)
bwts = bwa.restore_index(root_name)
bnsp, pacseq = bwa.restore_reference(root_name)
sys.stderr.write(str(bnsp[0]))
seq_reader = Bio.SeqIO.parse(open(hit_fn), 'fastq-illumina')
process_sequences(bwts, bnsp, pacseq, seq_reader, N, print_sams)
u.clean_up_aux_files(root_name)
def main(argv):
try:
hit_fn = argv[1]
except IndexError:
hit_fn = 'hit_pairs.fastq'
N = 10
root_name = 'refseq'
generate_ref(root_name)
bwts = bwa.restore_index(root_name)
bnsp, pacseq = bwa.restore_reference(root_name)
sys.stderr.write(str(bnsp[0]))
seq_reader = Bio.SeqIO.parse(open(hit_fn), 'fastq-illumina')
process_sequences(bwts, bnsp, pacseq, seq_reader, N, print_sams)
u.clean_up_aux_files(root_name)
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 5000
max_isize = pairing_batch_size = 1000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
res = []
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
logger = logging.getLogger("test")
logger.setLevel(logging.DEBUG)
counters = get_counters()
ctx = ContextStub()
visitor = MRVisitor(logger, ctx, counters)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size, visitor)
for read, mate in bwa_iterator.analyze(bwsa, l):
print read.get_name(), mate.get_name()
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
for cn, c in counters.iteritems():
sys.stderr.write("%s = %d\n" % (cn, c.value))
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 5000
max_isize = pairing_batch_size = 1000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
res = []
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
logger = logging.getLogger("test")
logger.setLevel(logging.DEBUG)
counters = get_counters()
ctx = ContextStub()
visitor = MRVisitor(logger, ctx, counters)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size, visitor)
for read, mate in bwa_iterator.analyze(bwsa, l):
print read.get_name(), mate.get_name()
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
for cn, c in counters.iteritems():
sys.stderr.write("%s = %d\n" % (cn, c.value))
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname):
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs = [x for x in it.izip(read_flow, mate_flow)]
print_meminfo("AFTER READING PAIRS")
bwsa = bwa.build_bws_array(pairs)
print_meminfo("AFTER BUILDING BWSA")
bwts = bwa.restore_index(refseq_fname)
print_meminfo("AFTER RESTORING INDEX")
bnsp, pacseq = bwa.restore_reference(refseq_fname)
print_meminfo("AFTER RESTORING REFERENCE")
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
print_meminfo("AFTER INIT OPT & II")
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
print_meminfo("AFTER CAL_SA_REG_GAP")
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
print_meminfo("AFTER CAL_PAC_POS_PE")
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
print_meminfo("AFTER PAIRED_SW")
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
print_meminfo("AFTER REFINE_GAPPED")
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
print_meminfo("AFTER ANALYZE_HIT")
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
print_meminfo("AFTER DEALLOC")
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PACSEQ")
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PAIRS")
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 10000
max_isize = pairing_batch_size = 10000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size)
pairs = [p for p in bwa_iterator.analyze(bwsa, l)]
print "READ POS GAPO GAPE MM STRAND SCORE CIGAR"
for read, mate in pairs:
if read.n_multi > 0:
print
multi_list = [m for m in read.itermulti()]
for m in multi_list:
print read.get_name(), m.pos, m.n_gapo, m.n_gape, m.n_mm, m.strand, \
m.score, m.get_cigar(read.len)
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 10000
max_isize = pairing_batch_size = 10000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size)
pairs = [p for p in bwa_iterator.analyze(bwsa, l)]
print "READ POS GAPO GAPE MM STRAND SCORE CIGAR"
for read, mate in pairs:
if read.n_multi > 0:
print
multi_list = [m for m in read.itermulti()]
for m in multi_list:
print read.get_name(), m.pos, m.n_gapo, m.n_gape, m.n_mm, m.strand, \
m.score, m.get_cigar(read.len)
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname, seq_list_len=None):
size_list = []
resident_list = []
failed_ii = 0
read_flow = Bio.SeqIO.parse(open(read_fname), "fastq-illumina")
mate_flow = Bio.SeqIO.parse(open(mate_fname), "fastq-illumina")
# pairs = [x for x in it.izip(read_flow, mate_flow)]
pairs_flow = it.izip(read_flow, mate_flow)
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
size, resident = print_meminfo("AFTER READING PAIRS")
size_list.append(size)
resident_list.append(resident)
bwsa = bwa.build_bws_array(pairs)
size, resident = print_meminfo("AFTER BUILDING BWSA")
size_list.append(size)
resident_list.append(resident)
bwts = bwa.restore_index(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING INDEX")
size_list.append(size)
resident_list.append(resident)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING REFERENCE")
size_list.append(size)
resident_list.append(resident)
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
size, resident = print_meminfo("AFTER INIT OPT & II")
size_list.append(size)
resident_list.append(resident)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
size, resident = print_meminfo("AFTER CAL_SA_REG_GAP")
size_list.append(size)
resident_list.append(resident)
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
size, resident = print_meminfo("AFTER CAL_PAC_POS_PE")
size_list.append(size)
resident_list.append(resident)
# sys.stderr.write("ii=%f\n" % ii.avg)
if ii.avg < 0.0:
failed_ii += 1
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
size, resident = print_meminfo("AFTER PAIRED_SW")
size_list.append(size)
resident_list.append(resident)
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
size, resident = print_meminfo("AFTER REFINE_GAPPED")
size_list.append(size)
resident_list.append(resident)
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
size, resident = print_meminfo("AFTER ANALYZE_HIT")
size_list.append(size)
resident_list.append(resident)
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
size, resident = print_meminfo("AFTER DEALLOC")
size_list.append(size)
resident_list.append(resident)
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PACSEQ")
size_list.append(size)
resident_list.append(resident)
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PAIRS")
size_list.append(size)
resident_list.append(resident)
return max(size_list), max(resident_list), failed_ii
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname, seq_list_len=None):
size_list = []
resident_list = []
failed_ii = 0
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
#pairs = [x for x in it.izip(read_flow, mate_flow)]
pairs_flow = it.izip(read_flow, mate_flow)
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
size, resident = print_meminfo("AFTER READING PAIRS")
size_list.append(size)
resident_list.append(resident)
bwsa = bwa.build_bws_array(pairs)
size, resident = print_meminfo("AFTER BUILDING BWSA")
size_list.append(size)
resident_list.append(resident)
bwts = bwa.restore_index(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING INDEX")
size_list.append(size)
resident_list.append(resident)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING REFERENCE")
size_list.append(size)
resident_list.append(resident)
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
size, resident = print_meminfo("AFTER INIT OPT & II")
size_list.append(size)
resident_list.append(resident)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
size, resident = print_meminfo("AFTER CAL_SA_REG_GAP")
size_list.append(size)
resident_list.append(resident)
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
size, resident = print_meminfo("AFTER CAL_PAC_POS_PE")
size_list.append(size)
resident_list.append(resident)
#sys.stderr.write("ii=%f\n" % ii.avg)
if ii.avg < 0.0:
failed_ii += 1
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
size, resident = print_meminfo("AFTER PAIRED_SW")
size_list.append(size)
resident_list.append(resident)
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
size, resident = print_meminfo("AFTER REFINE_GAPPED")
size_list.append(size)
resident_list.append(resident)
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
size, resident = print_meminfo("AFTER ANALYZE_HIT")
size_list.append(size)
resident_list.append(resident)
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
size, resident = print_meminfo("AFTER DEALLOC")
size_list.append(size)
resident_list.append(resident)
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PACSEQ")
size_list.append(size)
resident_list.append(resident)
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PAIRS")
size_list.append(size)
resident_list.append(resident)
return max(size_list), max(resident_list), failed_ii