def test_missing_annotations(self):
with self.assertRaises(Exception) as context:
no_meta = "../functional_tests/mini_gctoo_for_testing_nometa.gctx"
added_meta = "../functional_tests/test_gctx2gct_out_annotated.gct"
row_meta = "../functional_tests/test_missing_rowmeta.txt"
args_string = "-f {} -o {} -row_annot_path {}".format(
no_meta, added_meta, row_meta)
args = gctx2gct.build_parser().parse_args(args_string.split())
gctx2gct.gctx2gct_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.gctx"
added_meta = "../functional_tests/test_gctx2gct_out_annotated.gct"
col_meta = "../functional_tests/test_missing_colmeta.txt"
args_string = "-f {} -o {} -col_annot_path {}".format(
no_meta, added_meta, col_meta)
args = gctx2gct.build_parser().parse_args(args_string.split())
gctx2gct.gctx2gct_main(args)
self.assertTrue('Column ids in matrix missing from annotations file' in
context.exception)
def test_gctx2gct_main(self):
in_name = "../functional_tests/mini_gctoo_for_testing.gctx"
out_name = "../functional_tests/test_gctx2gct_out.gct"
args_string = "-f {} -o {}".format(in_name, out_name)
args = gctx2gct.build_parser().parse_args(args_string.split())
gctx2gct.gctx2gct_main(args)
# Make sure the input is identical to output
in_gctx = parse_gctx.parse(in_name)
out_gct = parse_gct.parse(out_name)
pd.util.testing.assert_frame_equal(in_gctx.data_df,
out_gct.data_df,
check_less_precise=3)
pd.util.testing.assert_frame_equal(in_gctx.col_metadata_df,
out_gct.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gctx.row_metadata_df,
out_gct.row_metadata_df)
no_meta = "../functional_tests/mini_gctoo_for_testing_nometa.gctx"
added_meta = "../functional_tests/test_gctx2gct_out_annotated.gct"
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 = gctx2gct.build_parser().parse_args(args_string.split())
gctx2gct.gctx2gct_main(args)
annotated_gct = parse_gct.parse(added_meta)
# Check added annotations are the same as original input GCTX
pd.util.testing.assert_frame_equal(in_gctx.data_df,
annotated_gct.data_df,
check_less_precise=3)
pd.util.testing.assert_frame_equal(in_gctx.col_metadata_df,
annotated_gct.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gctx.row_metadata_df,
annotated_gct.row_metadata_df)
# Clean up
os.remove(out_name)
os.remove(added_meta)
def test_gctx2gct_main(self):
in_name = "functional_tests/mini_gctoo_for_testing.gctx"
out_name = "functional_tests/test_gctx2gct_out.gct"
args_string = "-f {} -o {}".format(in_name, out_name)
args = gctx2gct.build_parser().parse_args(args_string.split())
gctx2gct.gctx2gct_main(args)
# Make sure the input is identical to output
in_gctx = parse_gctx.parse(in_name)
out_gct = parse_gct.parse(out_name)
pd.util.testing.assert_frame_equal(in_gctx.data_df,
out_gct.data_df,
check_less_precise=3)
pd.util.testing.assert_frame_equal(in_gctx.col_metadata_df,
out_gct.col_metadata_df)
pd.util.testing.assert_frame_equal(in_gctx.row_metadata_df,
out_gct.row_metadata_df)
# Clean up
os.remove(out_name)