def verify(self, input_ts, cmd):
with tempfile.TemporaryDirectory() as tmpdir:
input_filename = pathlib.Path(tmpdir) / "input.trees"
input_ts.dump(input_filename)
output_filename = pathlib.Path(tmpdir) / "output.trees"
full_cmd = str(input_filename) + f" {output_filename} " + cmd
cli.tsdate_main(full_cmd.split())
output_ts = tskit.load(output_filename)
self.assertEqual(input_ts.num_samples, output_ts.num_samples)
self.ts_equal_except_times(input_ts, output_ts)
def preprocess_compare_python_api(self, input_ts):
with tempfile.TemporaryDirectory() as tmpdir:
input_filename = pathlib.Path(tmpdir) / "input.trees"
input_ts.dump(input_filename)
output_filename = pathlib.Path(tmpdir) / "output.trees"
full_cmd = "preprocess " + str(input_filename) + f" {output_filename}"
print(full_cmd)
cli.tsdate_main(full_cmd.split())
output_ts = tskit.load(output_filename)
preprocessed_ts = tsdate.preprocess_ts(input_ts)
self.ts_equal(output_ts, preprocessed_ts, times_equal=True)
def compare_python_api(self, input_ts, cmd, Ne, mutation_rate, method):
with tempfile.TemporaryDirectory() as tmpdir:
input_filename = pathlib.Path(tmpdir) / "input.trees"
input_ts.dump(input_filename)
output_filename = pathlib.Path(tmpdir) / "output.trees"
full_cmd = "date " + str(input_filename) + f" {output_filename} " + cmd
cli.tsdate_main(full_cmd.split())
output_ts = tskit.load(output_filename)
dated_ts = tsdate.date(input_ts, Ne=Ne, mutation_rate=mutation_rate,
method=method)
print(dated_ts.tables.nodes.time, output_ts.tables.nodes.time)
self.assertTrue(np.array_equal(dated_ts.tables.nodes.time,
output_ts.tables.nodes.time))
def main():
cli.tsdate_main()