def __init__(self, ctx):
super(type(self), self).__init__(ctx)
self.__get_configuration(ctx)
logging.basicConfig(level=self.log_level)
self.event_monitor = HadoopEventMonitor(self.COUNTER_CLASS,
logging.getLogger("mapper"),
ctx)
self.aligner = BwaAligner()
self.aligner.event_monitor = self.event_monitor
self.aligner.qformat = self.format
self.aligner.max_isize = self.max_isize
self.aligner.nthreads = self.nthreads
self.aligner.trim_qual = self.trim_qual
self.aligner.mmap_enabled = True
######## assemble hit processor chain
chain = FilterLink(self.event_monitor)
chain.remove_unmapped = self.remove_unmapped
chain.min_hit_quality = self.min_hit_quality
if self.__map_only:
chain.set_next(EmitSamLink(ctx, self.event_monitor))
else:
chain.set_next(MarkDuplicatesEmitter(ctx, self.event_monitor))
self.aligner.hit_visitor = chain
######## set the path to the reference index
self.ref_archive = utils.get_ref_archive(ctx.getJobConf())
self.aligner.reference = self.get_reference_root(self.ref_archive)
# part of the code is a workaround for accumulating records, see #331
isplit = InputSplit(ctx.getInputSplit())
self.split_end = isplit.offset + isplit.length
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname,
log_level=logging.INFO, pairing_batch_size=None,
seq_list_len=None, fastq_subfmt="fastq-illumina"):
logger = logging.getLogger("PY")
logger.setLevel(log_level)
logger.info("RUNNING PYTHON VERSION")
def debug_dump(seq, state):
logger.debug("%s: name=%s" % (state, seq.get_name()))
logger.debug("%s: qual=%s" % (state, seq.get_qual_string()))
logger.debug("%s: strand=%d" % (state, seq.strand))
logger.debug("%s: pos=%d" % (state, seq.pos))
logger.debug("%s: mapQ=%d" % (state, seq.mapQ))
read_flow = Bio.SeqIO.parse(open(read_fname), fastq_subfmt)
mate_flow = Bio.SeqIO.parse(open(mate_fname), fastq_subfmt)
pairs_flow = it.izip(read_flow, mate_flow)
class ResultCollector(object):
def __init__(self):
self.result = []
def process(self, pair):
self.result.append(pair[0])
self.result.append(pair[1])
result = ResultCollector()
while 1:
start = time.time()
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
# turn the biopython SeqRecords into simple tuples
tuples = map(lambda t: (t[0].name, t[0].seq.tostring(), None, t[1].seq.tostring(), None), pairs[0:5])
for t in tuples:
print t
logger.info('reading seqs %f sec' % (time.time() - start))
start = time.time()
aligner = BwaAligner()
aligner.reference = refseq_fname
aligner.hit_visitor = result
for t in tuples[0:5]:
aligner.load_pair_record(t)
aligner.run_alignment()
aligner.clear_batch()
logger.info('alignment %f sec' % (time.time() - start))
# map bwa mappings to dictionaries
def bwam_to_hash(bwa_m):
h = dict(
name=bwa_m.name,
aux=bwa_m.tags,
seq=bwa_m.get_seq_5()
)
return h
return map(bwam_to_hash, result.result)
def setUp(self):
utils.build_ref_index()
self.aligner = BwaAligner()
self.aligner.reference = utils.reference
self.aligner.hit_visitor = type(self).SimpleVisitor()
self.pairs = []
with open(utils.get_fixture_path("pairs.txt")) as f:
for line in f:
if not line.startswith("#"): # leave #-lines for comments
self.pairs.append(line.rstrip("\r\n").split("\t"))
def setUp(self):
self.aligner = BwaAligner()
test_dir = os.path.abspath(
os.path.join(os.path.dirname(__file__), '..', '..', '..'))
self.aligner.reference = os.path.join(test_dir, 'seal',
'mini_ref_fixture',
'mini_ref.fasta')
self.aligner.hit_visitor = MappingsCollector()
self.aligner.qformat = "fastq-sanger"
self.pair = (
"HWI-ST301L:236:C0EJ5ACXX:1:1101:18292:2904",
"GGGAGGTGTTAGGGACAAGCCTGGAGGCAGCATGCGTCACTCCCATGCAGAGTCCATTGGCCAATGCTGGCTCCGATGGCCACATCTCACTCCAGGGGCAG",
"?@@B?<=AADFCFH@FB?EFEGAAFGEEGEGHCGEGIGH?B?CGEFHGIIGAEEEEHEAEEEH937;;@3=;>@8;?8;9A:<A#################",
"AATAGAATGTAATATAATATATGTAAAACACCAGGTGCCTAACCTGGCACAGAGCAGGAGGGCTAAGCATGACATCCAGCACGTGGTCAGTGGAATCCAGT",
"@@@DFDDDBHDD<EHEHIFEEB<IHIEGHDFEH?B:CBEHICEGCGGIIGFGCFCE@FAFEGAAGHIIHF;A?DBDFB);@@35;?,;@35(:5:ACCC<>"
)
