def _compute_utr(self, args_utr):
for gff in os.listdir(args_utr.gffs):
if gff.endswith(".gff"):
prefix = gff[:-4]
tss = self.helper.get_correct_file(self.tss_path, "_TSS.gff",
prefix, None, None)
tran = self.helper.get_correct_file(self.tran_path,
"_transcript.gff", prefix,
None, None)
if args_utr.terms:
term = self.helper.get_correct_file(
os.path.join(args_utr.terms, "tmp"), "_term.gff",
prefix, None, None)
else:
term = None
print("Computing 5'UTR of {0}".format(prefix))
detect_5utr(
tss, os.path.join(args_utr.gffs, gff), tran,
os.path.join(self.utr5_path, "gffs",
"_".join([prefix, "5UTR.gff"])), args_utr)
print("Computing 3'UTR of {0}".format(prefix))
detect_3utr(
tran, os.path.join(args_utr.gffs, gff), term,
os.path.join(self.utr3_path, "gffs",
"_".join([prefix, "3UTR.gff"])), args_utr)
self.helper.move_all_content(os.getcwd(), self.utr5_stat_path,
["_5utr_length.png"])
self.helper.move_all_content(os.getcwd(), self.utr3_stat_path,
["_3utr_length.png"])
def _compute_utr(self, args_utr):
for gff in os.listdir(args_utr.gffs):
if gff.endswith(".gff"):
prefix = gff[:-4]
tss = self.helper.get_correct_file(
self.tss_path, "_TSS.gff", prefix, None, None)
tran = self.helper.get_correct_file(
self.tran_path, "_transcript.gff", prefix, None, None)
if args_utr.terms:
term = self.helper.get_correct_file(
os.path.join(args_utr.terms, "tmp"),
"_term.gff", prefix, None, None)
else:
term = None
print("computing 5'UTR of {0} .....".format(prefix))
detect_5utr(tss, os.path.join(args_utr.gffs, gff),
tran, os.path.join(self.utr5_path, "gffs",
"_".join([prefix, "5UTR.gff"])), args_utr)
print("computing 3'UTR of {0} .....".format(prefix))
detect_3utr(tran, os.path.join(args_utr.gffs, gff),
term, os.path.join(self.utr3_path, "gffs",
"_".join([prefix, "3UTR.gff"])), args_utr)
self.helper.move_all_content(
os.getcwd(), self.utr5_stat_path, ["_5utr_length.png"])
self.helper.move_all_content(
os.getcwd(), self.utr3_stat_path, ["_3utr_length.png"])
def _compute_utr(self, args_utr, log):
log.write("Running detect_utr.py to detect UTRs.\n")
for gff in os.listdir(args_utr.gffs):
if gff.endswith(".gff"):
prefix = gff[:-4]
tss = self.helper.get_correct_file(
self.tss_path, "_TSS.gff", prefix, None, None)
tran = self.helper.get_correct_file(
self.tran_path, "_transcript.gff", prefix, None, None)
if args_utr.terms:
term = self.helper.get_correct_file(
os.path.join(args_utr.terms, "tmp"),
"_term.gff", prefix, None, None)
else:
term = None
print("Computing 5'UTRs of {0}".format(prefix))
detect_5utr(tss, os.path.join(args_utr.gffs, gff),
tran, os.path.join(self.utr5_path, "gffs",
"_".join([prefix, "5UTR.gff"])), args_utr)
print("Computing 3'UTRs of {0}".format(prefix))
detect_3utr(tran, os.path.join(args_utr.gffs, gff),
term, os.path.join(self.utr3_path, "gffs",
"_".join([prefix, "3UTR.gff"])), args_utr)
self.helper.move_all_content(
os.getcwd(), self.utr5_stat_path, ["_5utr_length.png"])
self.helper.move_all_content(
os.getcwd(), self.utr3_stat_path, ["_3utr_length.png"])
log.write("The following files are generated:\n")
for folder in (os.path.join(self.utr5_path, "gffs"),
os.path.join(self.utr3_path, "gffs"),
self.utr5_stat_path, self.utr3_stat_path):
for file_ in os.listdir(folder):
log.write("\t" + os.path.join(folder, file_) + "\n")
def test_detect_5utr(self):
args = self.mock_args.mock()
du.read_file = Mock_func().mock_read_file
du.plot = Mock_func().mock_plot
out_file = os.path.join(self.test_folder, "5utr.gff")
args.source = True
args.base_5utr = "both"
args.length = 300
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
header = ["##gff-version 3"]
args.source = False
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_other]
self.assertEqual(datas[1], ref[1])
args.base_5utr = "transcript"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
self.assertEqual(set(datas), set(ref))
args.source = True
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_tsspredator]
self.assertListEqual(datas, ref)
def test_detect_5utr(self):
args = self.mock_args.mock()
du.read_file = Mock_func().mock_read_file
du.plot = Mock_func().mock_plot
out_file = os.path.join(self.test_folder, "5utr.gff")
args.source = True
args.base_5utr = "both"
args.length = 300
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
header = ["##gff-version 3"]
args.source = False
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_other]
self.assertEqual(datas[1], ref[1])
args.base_5utr = "transcript"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
self.assertEqual(set(datas), set(ref))
args.source = True
args.base_5utr = "both"
du.detect_5utr("test.tss", "test.gff", "test.ta", out_file, args)
datas = import_data(out_file)
ref = header + [self.example.out_5utr_tsspredator]
self.assertListEqual(datas, ref)
def _compute_utr(self, args_utr, log):
log.write("Running detect_utr.py to detect UTRs.\n")
for gff in os.listdir(args_utr.gffs):
if gff.endswith(".gff"):
prefix = gff[:-4]
tss = self.helper.get_correct_file(self.tss_path, "_TSS.gff",
prefix, None, None)
tran = self.helper.get_correct_file(self.tran_path,
"_transcript.gff", prefix,
None, None)
if args_utr.terms:
term = self.helper.get_correct_file(
os.path.join(args_utr.terms, "tmp"), "_term.gff",
prefix, None, None)
else:
term = None
print("Computing 5'UTRs of {0}".format(prefix))
detect_5utr(
tss, os.path.join(args_utr.gffs, gff), tran,
os.path.join(self.utr5_path, "gffs",
"_".join([prefix, "5UTR.gff"])), args_utr)
print("Computing 3'UTRs of {0}".format(prefix))
detect_3utr(
tran, os.path.join(args_utr.gffs, gff), term,
os.path.join(self.utr3_path, "gffs",
"_".join([prefix, "3UTR.gff"])), args_utr)
self.helper.move_all_content(os.getcwd(), self.utr5_stat_path,
["_5utr_length.png"])
self.helper.move_all_content(os.getcwd(), self.utr3_stat_path,
["_3utr_length.png"])
log.write("The following files are generated:\n")
for folder in (os.path.join(self.utr5_path, "gffs"),
os.path.join(self.utr3_path, "gffs"),
self.utr5_stat_path, self.utr3_stat_path):
for file_ in os.listdir(folder):
log.write("\t" + os.path.join(folder, file_) + "\n")