def run_alignment(self):
if not self.reference:
raise ValueError(
"You must set the reference path before calling run_alignment")
if not self.hit_visitor:
raise ValueError(
"You must set the hit_visitor before calling run_alignment (else you'll lose the alignment results)"
)
self.__check_reference()
# update __gopt to reflect any changes to our public attributes.
self.__gopt.contents.n_threads = self.nthreads
self.event_monitor.log_debug("BWA using %d threads",
self.__gopt.contents.n_threads)
if self.__iterator is None:
self.__iterator = BWAIterator(self.reference,
self.__gopt,
self.__popt,
self.max_isize,
len(self.__batch),
visitor=self.event_monitor,
mmap_enabled=self.mmap_enabled)
status = "aligning against %s" % os.path.basename(self.reference)
self.event_monitor.new_status(status)
self.event_monitor.log_debug(status)
self.event_monitor.count("reads processed", 2 * len(self.__batch))
with self.event_monitor.time_block("build_bwsa"):
# we need to rebuild sequences each time, bwa functions modify them.
bwsa = bwa.build_bws_array(self.__batch,
qtype=self.qformat,
trim_qual=self.trim_qual)
self.__count_bases(bwsa, len(self.__batch))
# bwa_iterator.analyze_pairs performs the alignment, then lets you iterate
# over the results
with self.event_monitor.time_block(
"analyze_pairs (cal_+sw+refgap+process)"):
# The python speed optimization tips suggest removing non-local variable look-ups
# from loops.
# http://wiki.python.org/moin/PythonSpeed/PerformanceTips
h_proc = self.hit_visitor.process
for hit1, hit2 in self.__iterator.analyze_pairs(
bwsa, len(self.__batch)):
h_proc((hit1, hit2))
with self.event_monitor.time_block("destroy_sequences"):
for j in 0, 1:
bwa.free_seq(len(self.__batch), bwsa[j])
def run_alignment(self):
if not self.reference:
raise ValueError("You must set the reference path before calling run_alignment")
if not self.hit_visitor:
raise ValueError("You must set the hit_visitor before calling run_alignment (else you'll lose the alignment results)")
self.__check_reference()
# update __gopt to reflect any changes to our public attributes.
self.__gopt.contents.n_threads = self.nthreads
self.event_monitor.log_debug("BWA using %d threads", self.__gopt.contents.n_threads)
if self.__iterator is None:
self.__iterator = BWAIterator(self.reference, self.__gopt, self.__popt,
self.max_isize, len(self.__batch),
visitor=self.event_monitor,
mmap_enabled=self.mmap_enabled)
status = "aligning against %s" % os.path.basename(self.reference)
self.event_monitor.new_status(status)
self.event_monitor.log_debug(status)
self.event_monitor.count("reads processed", 2*len(self.__batch))
with self.event_monitor.time_block("build_bwsa"):
# we need to rebuild sequences each time, bwa functions modify them.
bwsa = bwa.build_bws_array(self.__batch, qtype=self.qformat, trim_qual=self.trim_qual)
self.__count_bases(bwsa, len(self.__batch))
# bwa_iterator.analyze_pairs performs the alignment, then lets you iterate
# over the results
with self.event_monitor.time_block("analyze_pairs (cal_+sw+refgap+process)"):
# The python speed optimization tips suggest removing non-local variable look-ups
# from loops.
# http://wiki.python.org/moin/PythonSpeed/PerformanceTips
h_proc = self.hit_visitor.process
for hit1, hit2 in self.__iterator.analyze_pairs(bwsa, len(self.__batch)):
h_proc( (hit1, hit2) )
with self.event_monitor.time_block("destroy_sequences"):
for j in 0, 1:
bwa.free_seq(len(self.__batch), bwsa[j])
class BwaAligner510(object):
"""
Object oriented interface to perform bwa aln + bwa sampe
using libbwa and the bwa module.
"""
def __init__(self):
self.event_monitor = QuietMonitor()
self.logger = QuietMonitor()
self.__gopt = bwa.gap_init_opt()
self.__popt = bwa.pe_init_opt()
self.__batch = []
self.qformat = "fastq-illumina"
self.max_isize = 1000
self.nthreads = 1
self.trim_qual = 0
self.mmap_enabled = False
# .reference is the path to the indexed BWA reference to use. Include the
# "root name" of the reference files--i.e. the names without the file extensions.
# The trailing dot, if included, will be removed.
# e.g. my_references/hg_18.bwt
# my_references/hg_18.rsax
# my_references/hg_18.sax => "my_references/hg_18"
# my_references/hg_18.pac
# ...
self.reference = None
self.hit_visitor = None
self.__iterator = None
def load_pair_record(self, record):
"""
Append a tuple of the format (id, seq1, qual1, seq2, qual2) to this aligner's work batch.
"""
self.__batch.append(record)
return len(self.__batch)
def get_batch_size(self):
return len(self.__batch)
def clear_batch(self):
self.__batch = []
def run_alignment(self):
if not self.reference:
raise ValueError(
"You must set the reference path before calling run_alignment")
if not self.hit_visitor:
raise ValueError(
"You must set the hit_visitor before calling run_alignment (else you'll lose the alignment results)"
)
self.__check_reference()
# update __gopt to reflect any changes to our public attributes.
self.__gopt.contents.n_threads = self.nthreads
self.event_monitor.log_debug("BWA using %d threads",
self.__gopt.contents.n_threads)
if self.__iterator is None:
self.__iterator = BWAIterator(self.reference,
self.__gopt,
self.__popt,
self.max_isize,
len(self.__batch),
visitor=self.event_monitor,
mmap_enabled=self.mmap_enabled)
status = "aligning against %s" % os.path.basename(self.reference)
self.event_monitor.new_status(status)
self.event_monitor.log_debug(status)
self.event_monitor.count("reads processed", 2 * len(self.__batch))
with self.event_monitor.time_block("build_bwsa"):
# we need to rebuild sequences each time, bwa functions modify them.
bwsa = bwa.build_bws_array(self.__batch,
qtype=self.qformat,
trim_qual=self.trim_qual)
self.__count_bases(bwsa, len(self.__batch))
# bwa_iterator.analyze_pairs performs the alignment, then lets you iterate
# over the results
with self.event_monitor.time_block(
"analyze_pairs (cal_+sw+refgap+process)"):
# The python speed optimization tips suggest removing non-local variable look-ups
# from loops.
# http://wiki.python.org/moin/PythonSpeed/PerformanceTips
h_proc = self.hit_visitor.process
for hit1, hit2 in self.__iterator.analyze_pairs(
bwsa, len(self.__batch)):
h_proc((hit1, hit2))
with self.event_monitor.time_block("destroy_sequences"):
for j in 0, 1:
bwa.free_seq(len(self.__batch), bwsa[j])
def release_resources(self):
if self.__iterator:
self.__iterator.unload_reference()
def __count_bases(self, bwsa, bwsa_size):
self.event_monitor.start("count_bases")
for r in 0, 1:
for i in xrange(bwsa_size):
seq = bwsa[r][i]
self.event_monitor.count("total bases", seq.full_len)
self.event_monitor.count("trimmed bases",
seq.full_len - seq.clip_len)
self.event_monitor.stop("count_bases")
def __check_reference(self):
"""
Checks that the indexed referenced at path self.reference includes
files with all the expected extensions.
Raises ValueError if something is missing.
"""
if self.reference[-1] == '.':
self.reference = self.reference[
0:-1] # remove the trailing '.', if any
ref_extensions = set([
os.path.splitext(path)[1].lstrip('.')
for path in glob.iglob(self.reference + ".*")
])
index_extensions = set([
e for e in ref_extensions if e in BWA_INDEX_EXT
]) # only extensions pertaining to index
missing = BWA_INDEX_MANDATORY_EXT - index_extensions
if missing:
raise ValueError("Missing BWA index file types: %s" %
', '.join(missing))
if self.mmap_enabled and (BWA_INDEX_MMAP_EXT - index_extensions):
raise ValueError("Missing BWA mmap index files: %s" %
', '.join(BWA_INDEX_MMAP_EXT - index_extensions))
elif not self.mmap_enabled and (BWA_INDEX_NORM_EXT - index_extensions):
raise ValueError("Missing BWA index files: %s" %
', '.join(BWA_INDEX_NORM_EXT - index_extensions))
class BwaAligner510(object):
"""
Object oriented interface to perform bwa aln + bwa sampe
using libbwa and the bwa module.
"""
def __init__(self):
self.event_monitor = QuietMonitor()
self.logger = QuietMonitor()
self.__gopt = bwa.gap_init_opt()
self.__popt = bwa.pe_init_opt()
self.__batch = []
self.qformat = "fastq-illumina"
self.max_isize = 1000
self.nthreads = 1
self.trim_qual = 0
self.mmap_enabled = False
# .reference is the path to the indexed BWA reference to use. Include the
# "root name" of the reference files--i.e. the names without the file extensions.
# The trailing dot, if included, will be removed.
# e.g. my_references/hg_18.bwt
# my_references/hg_18.rsax
# my_references/hg_18.sax => "my_references/hg_18"
# my_references/hg_18.pac
# ...
self.reference = None
self.hit_visitor = None
self.__iterator = None
def load_pair_record(self, record):
"""
Append a tuple of the format (id, seq1, qual1, seq2, qual2) to this aligner's work batch.
"""
self.__batch.append(record)
return len(self.__batch)
def get_batch_size(self):
return len(self.__batch)
def clear_batch(self):
self.__batch = []
def run_alignment(self):
if not self.reference:
raise ValueError("You must set the reference path before calling run_alignment")
if not self.hit_visitor:
raise ValueError("You must set the hit_visitor before calling run_alignment (else you'll lose the alignment results)")
self.__check_reference()
# update __gopt to reflect any changes to our public attributes.
self.__gopt.contents.n_threads = self.nthreads
self.event_monitor.log_debug("BWA using %d threads", self.__gopt.contents.n_threads)
if self.__iterator is None:
self.__iterator = BWAIterator(self.reference, self.__gopt, self.__popt,
self.max_isize, len(self.__batch),
visitor=self.event_monitor,
mmap_enabled=self.mmap_enabled)
status = "aligning against %s" % os.path.basename(self.reference)
self.event_monitor.new_status(status)
self.event_monitor.log_debug(status)
self.event_monitor.count("reads processed", 2*len(self.__batch))
with self.event_monitor.time_block("build_bwsa"):
# we need to rebuild sequences each time, bwa functions modify them.
bwsa = bwa.build_bws_array(self.__batch, qtype=self.qformat, trim_qual=self.trim_qual)
self.__count_bases(bwsa, len(self.__batch))
# bwa_iterator.analyze_pairs performs the alignment, then lets you iterate
# over the results
with self.event_monitor.time_block("analyze_pairs (cal_+sw+refgap+process)"):
# The python speed optimization tips suggest removing non-local variable look-ups
# from loops.
# http://wiki.python.org/moin/PythonSpeed/PerformanceTips
h_proc = self.hit_visitor.process
for hit1, hit2 in self.__iterator.analyze_pairs(bwsa, len(self.__batch)):
h_proc( (hit1, hit2) )
with self.event_monitor.time_block("destroy_sequences"):
for j in 0, 1:
bwa.free_seq(len(self.__batch), bwsa[j])
def release_resources(self):
if self.__iterator:
self.__iterator.unload_reference()
def __count_bases(self, bwsa, bwsa_size):
self.event_monitor.start("count_bases")
for r in 0,1:
for i in xrange(bwsa_size):
seq = bwsa[r][i]
self.event_monitor.count("total bases", seq.full_len)
self.event_monitor.count("trimmed bases", seq.full_len - seq.clip_len)
self.event_monitor.stop("count_bases")
def __check_reference(self):
"""
Checks that the indexed referenced at path self.reference includes
files with all the expected extensions.
Raises ValueError if something is missing.
"""
if self.reference[-1] == '.':
self.reference = self.reference[0:-1] # remove the trailing '.', if any
ref_extensions = set([ os.path.splitext(path)[1].lstrip('.') for path in glob.iglob(self.reference + ".*") ])
index_extensions = set([ e for e in ref_extensions if e in BWA_INDEX_EXT ]) # only extensions pertaining to index
missing = BWA_INDEX_MANDATORY_EXT - index_extensions
if missing:
raise ValueError("Missing BWA index file types: %s" % ', '.join(missing))
if self.mmap_enabled and (BWA_INDEX_MMAP_EXT - index_extensions):
raise ValueError("Missing BWA mmap index files: %s" % ', '.join(BWA_INDEX_MMAP_EXT - index_extensions))
elif not self.mmap_enabled and (BWA_INDEX_NORM_EXT - index_extensions):
raise ValueError("Missing BWA index files: %s" % ', '.join(BWA_INDEX_NORM_EXT - index_extensions))