def main(args):
in_gctoo = parse_gctx.parse(args.filename, convert_neg_666=False)
if args.output_filepath == None:
out_name = str.split(in_gctoo.src, "/")[-1].split(".")[0]
else:
out_name = args.output_filepath
write_gct.write(in_gctoo, out_name)
def main():
args = build_parser().parse_args(sys.argv[1:])
setup_logger.setup(verbose=args.verbose)
in_gctoo = parse_gctx.parse(args.filename, convert_neg_666=False)
if args.output_filepath == None:
out_name = str.split(in_gctoo.src, "/")[-1].split(".")[0]
else:
out_name = args.output_filepath
write_gct.write(in_gctoo, out_name)
def main():
# get args
args = build_parser().parse_args(sys.argv[1:])
setup_logger.setup(verbose=args.verbose)
# Get files directly
if args.input_filepaths is not None:
files = args.input_filepaths
# Or find them
else:
files = get_file_list(args.file_wildcard)
# No files found
if len(files) == 0:
msg = "No files were found. args.file_wildcard: {}".format(
args.file_wildcard)
logger.error(msg)
raise Exception(msg)
# Only 1 file found
if len(files) == 1:
logger.warning(
"Only 1 file found. No concatenation needs to be done, exiting")
return
# More than 1 file found
else:
# Parse each file and append to a list
gctoos = []
for f in files:
gctoos.append(parse.parse(f))
# Create concatenated gctoo object
if args.concat_direction == "horiz":
out_gctoo = hstack(gctoos, args.fields_to_remove, args.reset_ids)
elif args.concat_direction == "vert":
out_gctoo = vstack(gctoos, args.fields_to_remove, args.reset_ids)
# Write out_gctoo to file
logger.info("Writing to output file args.out_name: {}".format(
args.out_name))
if args.out_type == "gctx":
write_gctx.write(out_gctoo, args.out_name)
elif args.out_type == "gct":
write_gct.write(out_gctoo,
args.out_name,
filler_null=args.filler_null,
metadata_null=args.metadata_null,
data_null=args.data_null)
def test_p100_functional(self):
p100_in_path = os.path.join(FUNCTIONAL_TESTS_PATH, "test_p100.gct")
p100_out_path = os.path.join(FUNCTIONAL_TESTS_PATH, "test_p100_writing.gct")
# Read in original gct file
p100_in_gct = pg.parse(p100_in_path)
# Read in new gct file
wg.write(p100_in_gct, p100_out_path)
p100_out_gct = pg.parse(p100_out_path)
self.assertTrue(p100_in_gct.data_df.equals(p100_out_gct.data_df))
self.assertTrue(p100_in_gct.row_metadata_df.equals(p100_out_gct.row_metadata_df))
self.assertTrue(p100_in_gct.col_metadata_df.equals(p100_out_gct.col_metadata_df))
# Clean up
os.remove(p100_out_path)
def test_main(self):
out_name = os.path.join(FUNCTIONAL_TESTS_PATH, "test_main_out.gct")
gctoo = GCToo.GCToo(data_df=self.data_df,
row_metadata_df=self.row_metadata_df,
col_metadata_df=self.col_metadata_df)
wg.write(gctoo, out_name, data_null="NaN",
metadata_null="-666", filler_null="-666")
# Read in the gct and verify that it's the same as gctoo
new_gct = pg.parse(out_name)
pd.util.testing.assert_frame_equal(new_gct.data_df, gctoo.data_df)
pd.util.testing.assert_frame_equal(new_gct.row_metadata_df, gctoo.row_metadata_df)
pd.util.testing.assert_frame_equal(new_gct.col_metadata_df, gctoo.col_metadata_df)
# Also check that missing values were written to the file as expected
in_df = pd.read_csv(out_name, sep="\t", skiprows=2, keep_default_na=False)
self.assertEqual(in_df.iloc[0, 1], "-666")
self.assertEqual(in_df.iloc[5, 6], "NaN")
# Cleanup
os.remove(out_name)
def main(args):
# Read the input gct
in_gct = pg.parse(args.in_gct_path)
# Read in each of the command line arguments
rid = _read_arg(args.rid)
cid = _read_arg(args.cid)
exclude_rid = _read_arg(args.exclude_rid)
exclude_cid = _read_arg(args.exclude_cid)
# Slice the gct
out_gct = slice_gctoo(in_gct,
rid=rid,
cid=cid,
exclude_rid=exclude_rid,
exclude_cid=exclude_cid)
assert out_gct.data_df.size > 0, "Slicing yielded an empty gct!"
# Write the output gct
wg.write(out_gct,
args.out_name,
data_null="NaN",
metadata_null="NA",
filler_null="NA")