def test_missing_annotations(self):
with self.assertRaises(Exception) as context:
no_meta = "../functional_tests/mini_gctoo_for_testing_nometa.gct"
added_meta = "../functional_tests/test_gctx2gct_out_annotated.gctx"
row_meta = "../functional_tests/test_missing_rowmeta.txt"
args_string = "-f {} -o {} -row_annot_path {}".format(
no_meta, added_meta, row_meta)
args = gct2gctx.build_parser().parse_args(args_string.split())
gct2gctx.gct2gctx_main(args)
self.assertTrue('Row ids in matrix missing from annotations file' in
context.exception)
with self.assertRaises(Exception) as context:
no_meta = "../functional_tests/mini_gctoo_for_testing_nometa.gct"
added_meta = "../functional_tests/test_gctx2gct_out_annotated.gctx"
col_meta = "../functional_tests/test_missing_colmeta.txt"
args_string = "-f {} -o {} -col_annot_path {}".format(
no_meta, added_meta, col_meta)
args = gct2gctx.build_parser().parse_args(args_string.split())
gct2gctx.gct2gctx_main(args)
self.assertTrue('Column ids in matrix missing from annotations file' in
context.exception)
def test_gct2gctx_main(self):
in_name = "../functional_tests/mini_gctoo_for_testing.gct"
out_name = "../functional_tests/test_gct2gctx_out.gctx"
args_string = "-f {} -o {}".format(in_name, out_name)
args = gct2gctx.build_parser().parse_args(args_string.split())
gct2gctx.gct2gctx_main(args)
# Make sure the input is identical to output
in_gct = parse_gct.parse(in_name)
out_gctx = parse_gctx.parse(out_name)
pd.util.testing.assert_frame_equal(in_gct.data_df, out_gctx.data_df)
pd.util.testing.assert_frame_equal(in_gct.col_metadata_df,
out_gctx.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gct.row_metadata_df,
out_gctx.row_metadata_df)
no_meta = "../functional_tests/mini_gctoo_for_testing_nometa.gct"
added_meta = "../functional_tests/test_gct2gctx_out_annotated.gctx"
row_meta = "../functional_tests/test_rowmeta_n6.txt"
col_meta = "../functional_tests/test_colmeta_n6.txt"
args_string = "-f {} -o {} -row_annot_path {} -col_annot_path {}".format(
no_meta, added_meta, row_meta, col_meta)
args = gct2gctx.build_parser().parse_args(args_string.split())
gct2gctx.gct2gctx_main(args)
annotated_gctx = parse_gctx.parse(added_meta)
# Check added annotations are the same as original input GCTX
pd.util.testing.assert_frame_equal(in_gct.data_df,
annotated_gctx.data_df,
check_less_precise=3)
pd.util.testing.assert_frame_equal(in_gct.col_metadata_df,
annotated_gctx.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gct.row_metadata_df,
annotated_gctx.row_metadata_df)
# Clean up
os.remove(out_name)
os.remove(added_meta)
def test_gct2gctx_main(self):
in_name = "functional_tests/mini_gctoo_for_testing.gct"
out_name = "functional_tests/test_gct2gctx_out.gctx"
args_string = "-f {} -o {}".format(in_name, out_name)
args = gct2gctx.build_parser().parse_args(args_string.split())
gct2gctx.gct2gctx_main(args)
# Make sure the input is identical to output
in_gct = parse_gct.parse(in_name)
out_gctx = parse_gctx.parse(out_name)
pd.util.testing.assert_frame_equal(in_gct.data_df, out_gctx.data_df)
pd.util.testing.assert_frame_equal(in_gct.col_metadata_df,
out_gctx.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gct.row_metadata_df,
out_gctx.row_metadata_df)
# Clean up
os.remove(out_name)