def test_identify_element_singal_ann_with_tes(self):
gene_list = identify_element("Chr01", 4648477, 4653385, self.ngs,
list(), list(), [("Chr01", 4649000, "-")],
self.ann)
self.assertEqual(len(gene_list), 1)
gene = gene_list[0]
self.assertEqual(str(gene), "Gene: Chr01:4648477-4653385 -")
intron_list = sorted(gene.intron_list, key=lambda x: (x.start, x.end))
self.assertEqual(
str(intron_list),
"[Intron: Chr01:4650078-4650291 -, Intron: Chr01:4650579-4650664 -, "
+
"Intron: Chr01:4650748-4651282 -, Intron: Chr01:4651337-4651429 -, "
+
"Intron: Chr01:4651463-4651566 -, Intron: Chr01:4651660-4651841 -]"
)
internal_exon_list = sorted(gene.internal_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(
str(internal_exon_list),
"[Exon: Chr01:4650291-4650579 -, Exon: Chr01:4650664-4650748 -, " +
"Exon: Chr01:4651282-4651337 -, Exon: Chr01:4651429-4651463 -, " +
"Exon: Chr01:4651566-4651660 -]")
tss_exon_list = sorted(gene.tss_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(str(tss_exon_list), "[Exon: Chr01:4651841-4652385 -]")
tes_exon_list = sorted(gene.tes_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(str(tes_exon_list), "[Exon: Chr01:4649000-4650078 -]")
def test_identify_transcript_singal(self):
gene_list = identify_element("Chr01", 4648477, 4653385, self.ngs,
list(), list(), list(), self.ann)
gene = gene_list[0]
trans = identify_transcript(gene, self.ann)
self.assertEqual(
str(trans.isoA),
"[Isoform: segment array: [1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1]; tss=True; tes=True; invalid=False]"
)
def test_identify_transcript_multi(self):
gene_list = identify_element("Chr01", 795113, 808059, self.ngs, list(),
list(), list(), self.ann)
gene = gene_list[0]
trans = identify_transcript(gene, self.ann)
self.assertEqual(
str(trans.isoA),
"[Isoform: segment array: [1, 0, 1, 0, 1, 0]; tss=True; tes=True; invalid=False, "
+
"Isoform: segment array: [1, 0, 1, 0, 1, 1]; tss=True; tes=True; invalid=False]"
)
def do(self,
out_dir,
ngs_obj_list,
tgs_obj_list,
ext_tss_list,
ext_tes_list,
ann,
f_genome,
paraclu_path=None):
"""Identify isoforms, until receive finish message"""
gene_cluster_indx = 0
with OutputHandle(os.path.join(out_dir,
"node_{0}".format(self.rank))) as f_out:
data = self.recv_data()
while data != self.finish_msg:
chrom, start, end = data
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)
for gene_cluster in gene_cluster_list:
if not gene_cluster.has_element():
continue
gene_cluster_indx += 1
gene_cluster_name = "n_{0}_c_{1}".format(
self.rank + 1, gene_cluster_indx)
gene_cluster.write_element2bed6(*f_out.element_handles(),
gene_cluster_name)
trans = identify_transcript(gene_cluster, ann)
trans.write2bed12(gene_cluster_name,
*f_out.isoform_handles())
self.debug("LBIdentifyIsoWorker: finish identification\n")
self.comm.send((self.rank, self.finish_msg),
dest=self.root,
tag=self.worker_tag)
data = self.recv_data()
self.comm.send((self.rank, self.finish_msg),
dest=self.root,
tag=self.worker_tag)
def test_identify_element_mutil_anns(self):
gene_list = identify_element("Chr01", 795113, 808059, self.ngs, list(),
list(), list(), self.ann)
self.assertEqual(len(gene_list), 1)
gene = gene_list[0]
self.assertEqual(str(gene), "Gene: Chr01:797113-802059 -")
intron_list = sorted(gene.intron_list, key=lambda x: (x.start, x.end))
self.assertEqual(
str(intron_list),
"[Intron: Chr01:799412-799981 -, Intron: Chr01:800328-800876 -]")
internal_exon_list = sorted(gene.internal_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(str(internal_exon_list),
"[Exon: Chr01:799981-800328 -]")
tss_exon_list = sorted(gene.tss_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(
str(tss_exon_list),
"[Exon: Chr01:800876-800959 -, Exon: Chr01:800876-801059 -]")
tes_exon_list = sorted(gene.tes_exon_list,
key=lambda x: (x.start, x.end))
self.assertEqual(str(tes_exon_list), "[Exon: Chr01:798113-799412 -]")
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")
