class BWAIterator(object):
def __init__(self, root, gopt, popt, max_isize, pairing_batch_size,
visitor=None, mmap_enabled=False):
if visitor is None:
self.visitor = QuietMonitor()
else:
self.visitor = visitor
self.root = root
self.gopt = gopt
self.popt = popt
self.max_isize = max_isize
self.pairing_batch_size = pairing_batch_size
self.mmap_enabled = mmap_enabled
# reference structures, loaded on demand
self.__bwts = None # the reference index
# the reference itself
self.__pacseq = None
self.__bnsp = None
self.__last_ii = None
self.clean_isize_statistics()
def clean_isize_statistics(self):
self.__last_ii = bwa.isize_info_t()
self.__last_ii.avg = -1.0
def reference_loaded(self):
# we use a single variable (__bwts) to determine whether
# the ref has been loaded.
return self.__bwts is not None
def load_reference(self):
"""
Load the reference at self.root.
Remember to deallocate it when unload_reference() once finished!"""
if self.reference_loaded():
raise RuntimeError("A reference is already loaded!")
try:
with self.visitor.time_block("restore_index"):
self.__bwts = bwa.restore_index(self.root, self.mmap_enabled)
with self.visitor.time_block("restore_reference"):
self.__bnsp, self.__pacseq = bwa.restore_reference(self.root,
self.mmap_enabled)
except:
self.unload_reference()
raise
def unload_reference(self):
"""Free an allocated reference, if any.
Sets __bwts, __pacseq, and __bnsp to None.
"""
if self.__bwts:
for j in 0, 1:
bwa.bwt_destroy(self.__bwts[j], self.mmap_enabled)
self.__bwts = None
if self.__pacseq:
del self.__pacseq
self.__pacseq = None
if self.__bnsp:
bwa.bns_destroy(self.__bnsp, self.mmap_enabled)
self.__bnsp = None
def __analyze(self, bwsa, seq_pairs_read):
##################################################
# This method performs the actual analysis work.
# BWA writes its results directly into the bwsa structures.
##################################################
if not self.reference_loaded():
self.load_reference()
ii = bwa.isize_info_t()
self.visitor.start("cal_sa_reg_gap")
for i in 0, 1:
bwa.cal_sa_reg_gap_mt(self.__bwts, seq_pairs_read, bwsa[i], self.gopt)
self.visitor.stop("cal_sa_reg_gap")
self.visitor.start("cal_pac_pos_pe")
bwa.cal_pac_pos_pe(self.__bwts, seq_pairs_read, bwsa, ii,
self.popt, self.gopt, self.__last_ii)
self.visitor.stop("cal_pac_pos_pe")
self.__last_ii = ii
if ii.avg > self.max_isize:
self.visitor.log_warning("skipping S-W, isize is too big (%.3f)" % ii.avg)
else:
self.visitor.start("paired_sw")
if 0 < self.pairing_batch_size < seq_pairs_read:
for offset in xrange(0, seq_pairs_read, self.pairing_batch_size):
nseq = min(self.pairing_batch_size, seq_pairs_read - offset)
self.visitor.start("paired_sw_batch")
bwa.paired_sw(self.__bnsp, self.__pacseq, nseq, bwsa, self.popt, ii, offset)
self.visitor.stop_batch("paired_sw_batch", offset, nseq)
else:
bwa.paired_sw(self.__bnsp, self.__pacseq, seq_pairs_read, bwsa, self.popt, ii)
self.visitor.stop("paired_sw")
self.visitor.start("refine_gapped")
for i in 0, 1:
bwa.refine_gapped(self.__bnsp, seq_pairs_read, bwsa[i], self.__pacseq)
self.visitor.stop("refine_gapped")
def analyze(self, bwsa, seq_pairs_read):
"""
Align the seq_pairs_read sequence pairs in bwsa and iterate
through the matches one read at a time. For each read
in each pair in bwsa, this method will yield
pairs of BwaMapping objects (mread1, mread2) and (mread2, mread1).
"""
self.__analyze(bwsa, seq_pairs_read)
for i in xrange(seq_pairs_read):
for j in 0, 1:
yield BwaMapping(self.gopt[0], self.__bnsp[0], bwsa[j][i], bwsa[j^1][i])
def analyze_pairs(self, bwsa, seq_pairs_read):
"""
Align the seq_pairs_read sequence pairs in bwsa and iterate
through the matches two reads at a time. For each pair
in bwsa this method will yield a
pairs of BwaMapping objects (mread1, mread2) and (mread2, mread1).
To analyze the match objects use bwa.analyze_hit
"""
self.__analyze(bwsa, seq_pairs_read)
for i in xrange(seq_pairs_read):
# XXX LP: if we leave in this check our filtered map counts will be wrong.
# since it doesn't seem to make much of a difference in speed I'll leave it in.
#if bwsa[0][i].type == bwa.BWA_TYPE_NO_MATCH or bwsa[1][i].type == bwa.BWA_TYPE_NO_MATCH:
yield BwaMapping(self.gopt[0], self.__bnsp[0], bwsa[0][i], bwsa[1][i]), BwaMapping(self.gopt[0], self.__bnsp[0], bwsa[1][i], bwsa[0][i])
class BWAIterator(object):
def __init__(self,
root,
gopt,
popt,
max_isize,
pairing_batch_size,
visitor=None,
mmap_enabled=False):
if visitor is None:
self.visitor = QuietMonitor()
else:
self.visitor = visitor
self.root = root
self.gopt = gopt
self.popt = popt
self.max_isize = max_isize
self.pairing_batch_size = pairing_batch_size
self.mmap_enabled = mmap_enabled
# reference structures, loaded on demand
self.__bwts = None # the reference index
# the reference itself
self.__pacseq = None
self.__bnsp = None
self.__last_ii = None
self.clean_isize_statistics()
def clean_isize_statistics(self):
self.__last_ii = bwa.isize_info_t()
self.__last_ii.avg = -1.0
def reference_loaded(self):
# we use a single variable (__bwts) to determine whether
# the ref has been loaded.
return self.__bwts is not None
def load_reference(self):
"""
Load the reference at self.root.
Remember to deallocate it when unload_reference() once finished!"""
if self.reference_loaded():
raise RuntimeError("A reference is already loaded!")
try:
with self.visitor.time_block("restore_index"):
self.__bwts = bwa.restore_index(self.root, self.mmap_enabled)
with self.visitor.time_block("restore_reference"):
self.__bnsp, self.__pacseq = bwa.restore_reference(
self.root, self.mmap_enabled)
except:
self.unload_reference()
raise
def unload_reference(self):
"""Free an allocated reference, if any.
Sets __bwts, __pacseq, and __bnsp to None.
"""
if self.__bwts:
for j in 0, 1:
bwa.bwt_destroy(self.__bwts[j], self.mmap_enabled)
self.__bwts = None
if self.__pacseq:
del self.__pacseq
self.__pacseq = None
if self.__bnsp:
bwa.bns_destroy(self.__bnsp, self.mmap_enabled)
self.__bnsp = None
def __analyze(self, bwsa, seq_pairs_read):
##################################################
# This method performs the actual analysis work.
# BWA writes its results directly into the bwsa structures.
##################################################
if not self.reference_loaded():
self.load_reference()
ii = bwa.isize_info_t()
self.visitor.start("cal_sa_reg_gap")
for i in 0, 1:
bwa.cal_sa_reg_gap_mt(self.__bwts, seq_pairs_read, bwsa[i],
self.gopt)
self.visitor.stop("cal_sa_reg_gap")
self.visitor.start("cal_pac_pos_pe")
bwa.cal_pac_pos_pe(self.__bwts, seq_pairs_read, bwsa, ii, self.popt,
self.gopt, self.__last_ii)
self.visitor.stop("cal_pac_pos_pe")
self.__last_ii = ii
if ii.avg > self.max_isize:
self.visitor.log_warning("skipping S-W, isize is too big (%.3f)" %
ii.avg)
else:
self.visitor.start("paired_sw")
if 0 < self.pairing_batch_size < seq_pairs_read:
for offset in xrange(0, seq_pairs_read,
self.pairing_batch_size):
nseq = min(self.pairing_batch_size,
seq_pairs_read - offset)
self.visitor.start("paired_sw_batch")
bwa.paired_sw(self.__bnsp, self.__pacseq, nseq, bwsa,
self.popt, ii, offset)
self.visitor.stop_batch("paired_sw_batch", offset, nseq)
else:
bwa.paired_sw(self.__bnsp, self.__pacseq, seq_pairs_read, bwsa,
self.popt, ii)
self.visitor.stop("paired_sw")
self.visitor.start("refine_gapped")
for i in 0, 1:
bwa.refine_gapped(self.__bnsp, seq_pairs_read, bwsa[i],
self.__pacseq)
self.visitor.stop("refine_gapped")
def analyze(self, bwsa, seq_pairs_read):
"""
Align the seq_pairs_read sequence pairs in bwsa and iterate
through the matches one read at a time. For each read
in each pair in bwsa, this method will yield
pairs of BwaMapping objects (mread1, mread2) and (mread2, mread1).
"""
self.__analyze(bwsa, seq_pairs_read)
for i in xrange(seq_pairs_read):
for j in 0, 1:
yield BwaMapping(self.gopt[0], self.__bnsp[0], bwsa[j][i],
bwsa[j ^ 1][i])
def analyze_pairs(self, bwsa, seq_pairs_read):
"""
Align the seq_pairs_read sequence pairs in bwsa and iterate
through the matches two reads at a time. For each pair
in bwsa this method will yield a
pairs of BwaMapping objects (mread1, mread2) and (mread2, mread1).
To analyze the match objects use bwa.analyze_hit
"""
self.__analyze(bwsa, seq_pairs_read)
for i in xrange(seq_pairs_read):
# XXX LP: if we leave in this check our filtered map counts will be wrong.
# since it doesn't seem to make much of a difference in speed I'll leave it in.
#if bwsa[0][i].type == bwa.BWA_TYPE_NO_MATCH or bwsa[1][i].type == bwa.BWA_TYPE_NO_MATCH:
yield BwaMapping(self.gopt[0], self.__bnsp[0], bwsa[0][i],
bwsa[1][i]), BwaMapping(self.gopt[0],
self.__bnsp[0],
bwsa[1][i], bwsa[0][i])
