diff options
Diffstat (limited to 'tests')
| -rw-r--r-- | tests/test_domagi.py | 32 |
1 files changed, 32 insertions, 0 deletions
diff --git a/tests/test_domagi.py b/tests/test_domagi.py index c65b87e..1ce5fc0 100644 --- a/tests/test_domagi.py +++ b/tests/test_domagi.py @@ -19,6 +19,7 @@ import io from click.testing import CliRunner +import duckdb import pandas as pd from pandas.testing import assert_frame_equal from pathlib import Path @@ -185,6 +186,37 @@ def test_domagi_matrix(tmp_path, test_data_file, expected_output): @pytest.mark.parametrize("test_data_file, expected_output", [(Path("test-data/test1.gfa"), + Path("test-data/expected-output/test1-overlap")), + (Path("test-data/test2.gfa"), + Path("test-data/expected-output/test2-overlap")), + (Path("test-data/test3.gfa"), + Path("test-data/expected-output/test3-overlap"))]) +def test_domagi_overlap(tmp_path, test_data_file, expected_output): + duckdb_path = tmp_path / f"{test_data_file.stem}.db" + runner = CliRunner() + result = runner.invoke(main, ["build", + "--gfa", test_data_file, + "--out", duckdb_path]) + assert result.exit_code == 0 + paths = [path for path, in (duckdb.connect(duckdb_path, True) + .execute("SELECT name FROM path") + .fetchall())] + result = runner.invoke(main, ["overlap", + "--db", duckdb_path, + *sum([["--path", path] for path in paths], + [])]) + assert result.exit_code == 0 + assert_frame_equal(pd.read_csv(expected_output, sep="\t") + .sort_values(by=["#path", "path.touched"], + ignore_index=True), + pd.read_csv(io.StringIO(result.stdout), + sep="\t") + .sort_values(by=["#path", "path.touched"], + ignore_index=True), + check_dtype=False) + +@pytest.mark.parametrize("test_data_file, expected_output", + [(Path("test-data/test1.gfa"), Path("test-data/expected-output/test1-paths")), (Path("test-data/test2.gfa"), Path("test-data/expected-output/test2-paths")), |