def test_operon(self):
op.read_gff = Mock_func().mock_read_gff
out_file = os.path.join(self.test_folder, "test.out")
op.operon("test_ta", "test_tss", "test_gff", "test_term", 3,
5, 5, out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.example.out_file.split("\n")))
def test_operon(self):
op.read_gff = Mock_func().mock_read_gff
out_file = os.path.join(self.test_folder, "test.out")
op.operon("test_ta", "test_tss", "test_gff", "test_term", 3, 5, 5,
out_file)
datas = import_data(out_file)
self.assertEqual(set(datas), set(self.example.out_file.split("\n")))
def _detect_operon(self, prefixs, args_op, log):
log.write("Running detect_operon.py to detect operon.\n")
log.write("The the following files are generated:\n")
for prefix in prefixs:
out_gff = os.path.join(args_op.output_folder, "gffs",
"_".join([prefix, "operon.gff"]))
out_table = os.path.join(self.table_path,
"_".join([prefix, "operon.csv"]))
print("Detecting operons of {0}".format(prefix))
if self.tss_path is None:
tss = False
else:
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)
gff = self.helper.get_correct_file(
args_op.gffs, ".gff", prefix, None, None)
if self.term_path is None:
term = False
else:
term = self.helper.get_correct_file(
self.term_path, "_term.gff", prefix, None, None)
operon(tran, tss, gff, term, args_op.tss_fuzzy,
args_op.term_fuzzy, args_op.length, out_table, out_gff)
log.write("\t" + out_table + "\n")
log.write("\t" + out_gff + "\n")
def _detect_operon(self, prefixs, args_op, log):
log.write("Running detect_operon.py to detect operon.\n")
log.write("The the following files are generated:\n")
for prefix in prefixs:
out_gff = os.path.join(args_op.output_folder, "gffs",
"_".join([prefix, "operon.gff"]))
out_table = os.path.join(self.table_path,
"_".join([prefix, "operon.csv"]))
print("Detecting operons of {0}".format(prefix))
if self.tss_path is None:
tss = False
else:
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)
gff = self.helper.get_correct_file(args_op.gffs, ".gff", prefix,
None, None)
if self.term_path is None:
term = False
else:
term = self.helper.get_correct_file(self.term_path,
"_term.gff", prefix, None,
None)
operon(tran, tss, gff, term, args_op.tss_fuzzy, args_op.term_fuzzy,
args_op.length, out_table, out_gff)
log.write("\t" + out_table + "\n")
log.write("\t" + out_gff + "\n")
def _detect_operon(self, prefixs, args_op):
for prefix in prefixs:
out_table = os.path.join(self.table_path,
"_".join(["operon", prefix + ".csv"]))
print("Detection operons of {0}".format(prefix))
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)
gff = self.helper.get_correct_file(
args_op.gffs, ".gff", prefix, None, None)
if self.term_path is None:
term = False
else:
term = self.helper.get_correct_file(
self.term_path, "_term.gff", prefix, None, None)
operon(tran, tss, gff, term, args_op.tss_fuzzy,
args_op.term_fuzzy, args_op.length, out_table)
def _detect_operon(self, prefixs, args_op):
for prefix in prefixs:
out_table = os.path.join(self.table_path,
"_".join(["operon", prefix + ".csv"]))
print("Detection operons of {0}".format(prefix))
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)
gff = self.helper.get_correct_file(args_op.gffs, ".gff", prefix,
None, None)
if self.term_path is None:
term = False
else:
term = self.helper.get_correct_file(self.term_path,
"_term.gff", prefix, None,
None)
operon(tran, tss, gff, term, args_op.tss_fuzzy, args_op.term_fuzzy,
args_op.length, out_table)