def test_train(self, mocked_do_eval):
cli.main(f"train {self.config_file}".split())
cache_dirs = list(self.conf.dir.glob("zarrcache_*"))
models = list(self.conf.dir.glob("*.hdf5"))
self.assertEqual(len(cache_dirs), 1)
self.assertEqual(len(models), 1)
self.assertEqual(mocked_do_eval.call_count, 1)
def test_apply_creates_predictions(self):
cli.main(f"apply {self.config_file} {self.nn_hdf5_file}".split())
plot_dir = pathlib.Path(self.nn_hdf5_file[:-len(".hdf5")])
for pred_file in [
"predictions.txt",
"predictions.pdf",
]:
self.assertTrue((plot_dir / pred_file).exists())
def test_eval_creates_plots(self):
cli.main(f"eval {self.config_file} {self.nn_hdf5_file}".split())
plot_dir = pathlib.Path(self.nn_hdf5_file[:-len(".hdf5")])
for plot_file in [
"genotype_matrices.pdf",
"roc.pdf",
"accuracy.pdf",
"confusion.pdf",
"reliability.pdf",
]:
self.assertTrue((plot_dir / plot_file).exists())
def setUpClass(cls):
cls.temp_dir = tempfile.TemporaryDirectory()
cls.config_file = pathlib.Path(cls.temp_dir.name) / "config.toml"
# load the example toml, patch it, then write it back out
d = toml.load("examples/test-example.toml")
d["dir"] = cls.temp_dir.name
d["vcf"]["phased"] = cls.phased
with open(cls.config_file, "w") as f:
toml.dump(d, f)
cls.conf = config.Config(cls.config_file)
if cls.need_sim_data:
with mock.patch("genomatnn.sim._models", new=sim__models()):
cli.main(f"sim -n 10 --seed 1 {cls.config_file}".split())
if cls.need_trained_model:
cli.main(f"train --seed 1 {cls.config_file}".split())
models = list(cls.conf.dir.glob("*.hdf5"))
assert len(models) == 1
cls.nn_hdf5_file = str(models[0])
def test_sim(self):
cli.main(f"sim -n 2 {self.config_file}".split())
path = pathlib.Path(self.temp_dir.name)
ts_files = list(path.glob("**/*.trees"))
self.assertEqual(len(ts_files), 2 * 3)
def test_missing_config_file(self):
with self.assertRaises(FileNotFoundError):
cli.main(["sim", "nonexistent.toml"])
def test_vcfplot_creates_plot(self):
plot_file = pathlib.Path(self.temp_dir.name) / "plot.pdf"
cli.main(
f"vcfplot {self.config_file} {plot_file} {self.region}".split())
self.assertTrue(plot_file.exists())
def test_missing_config_file(self):
plot_file = pathlib.Path(self.temp_dir.name) / "plot.pdf"
with self.assertRaises(FileNotFoundError):
cli.main(
f"vcfplot nonexistent.toml {plot_file} {self.region}".split())
def test_missing_nn_hdf5_file(self):
with self.assertRaises((FileNotFoundError, IOError)):
cli.main(f"apply {self.config_file} nonexistent.hdf5".split())
def test_missing_config_file(self):
with self.assertRaises(FileNotFoundError):
cli.main(f"apply nonexistent.toml {self.nn_hdf5_file}".split())