def main(args):
in_gctoo = parse_gct.parse(args.filename, convert_neg_666=False)
logger.debug("Original out name: {}".format(in_gctoo.src))
if args.output_filepath == None:
out_name = str.split(in_gctoo.src, "/")[-1].split(".")[0]
else:
out_name = args.output_filepath
write_gctx.write(in_gctoo, out_name)
def main():
args = build_parser().parse_args(sys.argv[1:])
setup_logger.setup(verbose=args.verbose)
in_gctoo = parse_gct.parse(args.filename, convert_neg_666=False)
logger.debug("Original out name: {}".format(in_gctoo.src))
if args.output_filepath == None:
out_name = str.split(in_gctoo.src, "/")[-1].split(".")[0]
else:
out_name = args.output_filepath
write_gctx.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_write_src(self):
# case 1: gctoo obj doesn't have src
mini1 = mini_gctoo_for_testing.make()
mini1.src = None
write_gctx.write(mini1, "no_src_example")
hdf5_file = h5py.File("no_src_example.gctx")
hdf5_src1 = hdf5_file.attrs[write_gctx.src_attr]
hdf5_file.close()
self.assertEqual(hdf5_src1, "no_src_example.gctx")
os.remove("no_src_example.gctx")
# case 2: gctoo obj does have src
mini2 = mini_gctoo_for_testing.make()
write_gctx.write(mini2, "with_src_example.gctx")
hdf5_file = h5py.File("with_src_example.gctx")
hdf5_src2 = hdf5_file.attrs[write_gctx.src_attr]
hdf5_file.close()
self.assertEqual(hdf5_src2, "mini_gctoo.gctx")
os.remove("with_src_example.gctx")
def test_write_version(self):
#TODO @oana refactor this test so it just calls the write_version method
# case 1: gctoo obj doesn't have version
mini1 = mini_gctoo_for_testing.make()
mini1.version = None
fn = "no_version_provided_example.gctx"
write_gctx.write(mini1, fn)
hdf5_file = h5py.File(fn)
hdf5_v1 = hdf5_file.attrs[write_gctx.version_attr]
hdf5_file.close()
self.assertEqual(hdf5_v1, write_gctx.version_number)
os.remove(fn)
# case 2: gctoo obj does have version, but it is not used when writing
mini2 = mini_gctoo_for_testing.make()
mini2.version = "MY_VERSION"
fn = "with_version_provided_example.gctx"
write_gctx.write(mini2, fn)
hdf5_file = h5py.File(fn)
hdf5_v2 = hdf5_file.attrs[write_gctx.version_attr]
hdf5_file.close()
self.assertEqual(hdf5_v2, write_gctx.version_number)
os.remove(fn)
def test_parse(self):
# parse whole thing
mg1 = mini_gctoo_for_testing.make()
mg2 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx")
assert_frame_equal(mg1.data_df, mg2.data_df)
assert_frame_equal(mg1.row_metadata_df, mg2.row_metadata_df)
assert_frame_equal(mg1.col_metadata_df, mg2.col_metadata_df)
# test with string rid/cid
test_rids = [
'LJP007_MCF10A_24H:TRT_CP:BRD-K93918653:3.33',
'LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'
]
test_cids = ['LJP007_MCF7_24H:TRT_POSCON:BRD-A61304759:10']
mg3 = slice_gct.slice_gctoo(mg1, rid=test_rids, cid=test_cids)
mg4 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
rid=test_rids,
cid=test_cids)
assert_frame_equal(mg3.data_df, mg4.data_df)
assert_frame_equal(mg3.row_metadata_df, mg4.row_metadata_df)
assert_frame_equal(mg3.col_metadata_df, mg4.col_metadata_df)
# first, make & write out temp version of mini_gctoo with int rids/cids
new_mg = mini_gctoo_for_testing.make(convert_neg_666=False)
int_indexed_data_df = new_mg.data_df.copy()
int_indexed_data_df.index = range(0, 6)
int_indexed_data_df.columns = range(10, 16)
int_indexed_row_meta = new_mg.row_metadata_df.copy()
int_indexed_row_meta.index = range(0, 6)
int_indexed_col_meta = new_mg.col_metadata_df.copy()
int_indexed_col_meta.index = range(10, 16)
int_indexed_gctoo = GCToo.GCToo(data_df=int_indexed_data_df,
row_metadata_df=int_indexed_row_meta,
col_metadata_df=int_indexed_col_meta)
write_gctx.write(int_indexed_gctoo, "int_indexed_mini_gctoo.gctx")
# test with numeric (repr as string) rid/cid
mg5 = GCToo.GCToo(data_df=int_indexed_data_df,
row_metadata_df=int_indexed_row_meta,
col_metadata_df=int_indexed_col_meta)
mg5 = slice_gct.slice_gctoo(
mg5,
row_bool=[True, False, True, False, True, False],
col_bool=[True, False, False, True, True, True])
mg5.data_df.index.name = "rid"
mg5.data_df.columns.name = "cid"
mg5.row_metadata_df.index.name = "rid"
mg5.row_metadata_df.columns.name = "rhd"
mg5.col_metadata_df.index.name = "cid"
mg5.col_metadata_df.columns.name = "chd"
mg6 = parse_gctx.parse("int_indexed_mini_gctoo.gctx",
rid=[0, 2, 4],
cid=[10, 13, 14, 15],
convert_neg_666=False)
os.remove("int_indexed_mini_gctoo.gctx")
assert_frame_equal(mg5.data_df, mg6.data_df)
assert_frame_equal(mg5.row_metadata_df, mg6.row_metadata_df)
assert_frame_equal(mg5.col_metadata_df, mg6.col_metadata_df)
# test with ridx/cidx
mg7 = slice_gct.slice_gctoo(
mg1,
rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
cid='LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666')
mg8 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
ridx=[4],
cidx=[4])
assert_frame_equal(mg7.data_df, mg8.data_df)
assert_frame_equal(mg7.row_metadata_df, mg8.row_metadata_df)
assert_frame_equal(mg7.col_metadata_df, mg8.col_metadata_df)
# test with rid/cidx
mg9 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
rid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'],
cidx=[4])
assert_frame_equal(mg7.data_df, mg9.data_df)
assert_frame_equal(mg7.row_metadata_df, mg9.row_metadata_df)
assert_frame_equal(mg7.col_metadata_df, mg9.col_metadata_df)
# test with ridx/cid
mg10 = parse_gctx.parse("functional_tests/mini_gctoo_for_testing.gctx",
ridx=[4],
cid=['LJP007_MCF7_24H:CTL_VEHICLE:DMSO:-666'])
assert_frame_equal(mg7.data_df, mg10.data_df)
assert_frame_equal(mg7.row_metadata_df, mg10.row_metadata_df)
assert_frame_equal(mg7.col_metadata_df, mg10.col_metadata_df)