def setUp(self):
self.ann_dir = "tests/data/ann.bed12"
self.size = "tests/data/chrom.sizes"
names = ('Bract', 'Cotyledon')
ngs = [
os.path.join('tests/data', "%s.sort.bam" % name) for name in names
]
self.ngs = [SeqFile(fname, 'NGS') for fname in ngs]
self.ann = SeqFile(bed2bam(self.ann_dir, self.size, "/tmp/igia"),
'ANN')
load_seqinfo(self.ngs)
def setUp(self):
names = ('Bract', 'Cotyledon')
ngs = [
os.path.join('tests/data', "%s.sort.bam" % name) for name in names
]
self.ngs = [SeqFile(fname, 'NGS') for fname in ngs]
load_seqinfo(self.ngs)
self.tgs = [SeqFile('tests/data/all_fixed_star.sort.bam', 'TGS')]
self.ival_rev = Interval("Chr01", 93000, 96500, "-")
self.ival_rev.build_cov(self.ngs)
jgn_rev = JunctionGraphNgs(self.ival_rev)
self.rev_intron = jgn_rev.identify_intron(self.ngs)
self.ival_fwd = Interval("Chr01", 485500, 493000, "+")
self.ival_fwd.build_cov(self.ngs)
jgn_fwd = JunctionGraphNgs(self.ival_fwd)
self.fwd_intron = jgn_fwd.identify_intron(self.ngs)
self.genome = GenomeFile(os.path.join("tests", "data", "genome.fa"))
def main(args):
"""Main entry point allowing external calls
Args:
args ([str]): command line parameter list
"""
args = parse_args(args)
setup_logging(args.loglevel)
check_paraclu(args)
_logger.debug("Starting IGIA ...")
ngs_obj_list = [SeqFile(x, "NGS") for x in args.ngs_file]
tgs_obj_list = [SeqFile(x, "TGS") for x in args.tgs_file]
ext_tss_list = load_txs(args.tss)
ext_tes_list = load_txs(args.tes)
out_dir = args.out_dir
ann = load_ann(args.ann, args.size, out_dir, "ANN")
# Update Global variables.
GVAR.RULE = args.rule
GVAR.TXS_DIFF = args.dtxs
GVAR.SPLICED_INTRON_PIR_CUTOFF = args.pir
f_genome = args.f_genome
paraclu_path = args.paraclu_path
load_seqinfo(ngs_obj_list)
_logger.info("Start building linkage ...")
bam_list = ngs_obj_list + tgs_obj_list
if ann is not None:
bam_list += [ann]
linkage = find_linkage(bam_list)
_logger.info("Finish building linkage")
cluster_indx = 0
with OutputHandle(out_dir) as f_out:
for chrom, start, end in linkage.iterlinkage():
try:
if args.time_out is not None:
signal.signal(signal.SIGALRM, time_out_handler)
signal.alarm(args.time_out)
_logger.debug(
"Start identifying elements in {0}:{1}-{2}".format(
chrom, start, end))
gene_cluster_list = identify_element(
chrom, start, end, ngs_obj_list, tgs_obj_list,
ext_tss_list, ext_tes_list, ann, f_genome, paraclu_path)
_logger.debug(
"Finish identifying elements in {0}:{1}-{2}".format(
chrom, start, end))
for gene_cluster in gene_cluster_list: # list of gene cluster without any common exon
if not gene_cluster.has_element():
continue
cluster_indx += 1
cluster_name = "c_{0}".format(cluster_indx)
gene_cluster.write_element2bed6(*f_out.element_handles(),
cluster_name)
_logger.debug(
"Start identifying transcript for {0}".format(
gene_cluster))
trans = identify_transcript(gene_cluster, ann)
trans.write2bed12(cluster_name, *f_out.isoform_handles())
_logger.debug(
"Finish identifying transcript for {0}".format(
gene_cluster))
if args.time_out is not None:
signal.alarm(0)
except TimeOutError:
print("TimeOut: {0}\t{1}\t{2}\n".format(chrom, start, end))
with open(os.path.join(args.out_dir, "igia_debug_timeout.log"),
"a") as f:
f.write("TimeOut ({0}s): {1}\t{2}\t{3}\n".format(
args.time_out, chrom, start, end))
_logger.info("End")
def main(args):
"""Main entry point allowing external calls
Args:
args ([str]): command line parameter list
"""
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
rank_size = comm.Get_size()
if rank == 0:
args = parse_args(args)
check_paraclu(args)
out_dir = args.out_dir
rand_seq = str(hash(time.time() * 100000 + random.random()))
tmp_dir = os.path.join(out_dir, rand_seq)
args.tmp_dir = tmp_dir
setup_logging(args.loglevel)
_logger.info("Starting IGIA in MPI mode ...")
else:
args = None
args = comm.bcast(args, root=0)
out_dir = args.out_dir
tmp_dir = args.tmp_dir
ngs_obj_list = [SeqFile(x, "NGS") for x in args.ngs_file]
tgs_obj_list = [SeqFile(x, "TGS") for x in args.tgs_file]
ext_tss_list = load_txs(args.tss)
ext_tes_list = load_txs(args.tes)
f_ann = args.ann
size = args.size
f_genome = args.f_genome
paraclu_path = args.paraclu_path
ann = None
if f_ann:
if rank == 0:
_logger.info("Loading annotation transcripts ...")
if not size:
raise ValueError("Error: missing Chrom Size file")
ann_bam = bed2bam(f_ann, size, tmp_dir)
else:
ann_bam = None
ann_bam = comm.bcast(ann_bam, root=0)
ann = SeqFile(ann_bam, "ANN")
# Update Global variables
GVAR.RULE = args.rule
GVAR.TXS_DIFF = args.dtxs
GVAR.SPLICED_INTRON_PIR_CUTOFF = args.pir
load_seqinfo(ngs_obj_list)
_logger.info("Start building linkage ... ")
bam_list = ngs_obj_list + tgs_obj_list
if ann is not None:
bam_list += [ann]
# Scatter linkage scan tasks
if rank == 0:
chrom_size_list = bam_list[0].chromsize()
scan_linkage_infos = [(chrom_size, seq_obj_indx)
for chrom_size in chrom_size_list
for seq_obj_indx in range(len(bam_list))]
master = LBMaster(comm,
GVAR.MAX_QUEUE_LEN,
master_tag=0,
worker_tag=1,
sleep=GVAR.SLEEP_TIME)
linkages = master.do(scan_linkage_infos)
linkage = Linkage()
for sub_linkage in linkages:
linkage.add_linkage(sub_linkage)
else:
worker = LBScanLinkageWorker(comm, master_tag=0, worker_tag=1)
worker.do(bam_list)
linkage = None
_logger.info("Finish building linkage ... ")
# with open("node_{0}.log".format(rank), "a") as f:
# f.write("finish building linkage\n")
if rank == 0:
data = "do"
else:
data = None
data = comm.bcast(data, root=0)
assert data == "do"
# Identify transcripts
if rank == 0:
_logger.info("Start identifying transcripts")
linkage_region_list = list(linkage.iterlinkage())
master = LBMaster(comm,
GVAR.MAX_QUEUE_LEN,
master_tag=2,
worker_tag=3,
sleep=GVAR.SLEEP_TIME)
master.do(linkage_region_list)
else:
worker = LBIdentifyIsoWorker(comm, master_tag=2, worker_tag=3)
worker.do(tmp_dir, ngs_obj_list, tgs_obj_list, ext_tss_list,
ext_tes_list, ann, f_genome, paraclu_path)
# Merge results
if rank == 0:
_logger.info("Finish identifying transcripts")
outfiles = [
"intron.bed6", "internal_exon.bed6", "tss_exon.bed6",
"tes_exon.bed6", "isoF.bed12", "isoA.bed12", "isoR.bed12",
"isoM.bed12", "isoC.bed12", "isoP.bed12"
]
res_dirs = [
os.path.join(tmp_dir, "node_{0}".format(x))
for x in range(1, rank_size)
]
for name in outfiles:
out_files = [os.path.join(res_dir, name) for res_dir in res_dirs]
code = "cat " + " ".join(out_files) + " > " + os.path.join(
out_dir, name)
subprocess.call(code, shell=True)
for res_dir in res_dirs:
code = "rm -r {0}".format(res_dir)
subprocess.call(code, shell=True)
_logger.info("End")