def test_read(self):
in_grp = grp.read(os.path.join(FUNCTIONAL_TESTS_DIR, "test.grp"))
self.assertEqual(in_grp, ["r", "d", "e"])
with self.assertRaises(AssertionError) as e:
grp.read("testt.grp")
self.assertIn("The following GRP file", str(e.exception))
def main():
"""Main function
"""
# Get args
parser = build_parser()
try:
args = parser.parse_args()
except:
parser.print_help()
sys.exit(0)
if args.input_glob:
gct_files = glob.glob(args.input_glob)
elif args.input_list:
gct_files = grp.read(args.input_list)
else:
raise Exception('input_glob or input_list must be specified')
gct_list = load_data(gct_files)
setup_logger.setup(verbose=args.verbose)
adj_ds, adj_list = combat_by_group(gct_list,
col_group=args.col_group,
batch_field=args.batch_field,
use_col_group_as_batch=args.use_col_group_as_batch)
save_data(adj_ds, adj_list)
def _read_arg(arg):
"""
If arg is a list with 1 element that corresponds to a valid file path, use
set_io.grp to read the grp file. Otherwise, check that arg is a list of strings.
Args:
arg (list or None)
Returns:
arg_out (list or None)
"""
# If arg is None, just return it back
if arg is None:
arg_out = arg
else:
# If len(arg) == 1 and arg[0] is a valid filepath, read it as a grp file
if len(arg) == 1 and os.path.exists(arg[0]):
arg_out = grp.read(arg[0])
else:
arg_out = arg
# Make sure that arg_out is a list of strings
assert isinstance(arg_out, list), "arg_out must be a list."
assert type(arg_out[0]) == str, "arg_out must be a list of strings."
return arg_out
def test_write(self): example_grp = ["x", "z", "w"] out_path = os.path.join(FUNCTIONAL_TESTS_DIR, "test_write.grp") grp.write(example_grp, out_path) self.assertTrue(os.path.exists(out_path)) read_back_in = grp.read(out_path) self.assertEqual(example_grp, read_back_in) # Cleanup os.remove(out_path)