def test_spectral():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {}".format(ROOT + 'test_matrix.mcool', 3,
'spectral', outfile.name, 1).split()
scHicCluster.main(args)
assert are_files_equal(ROOT + "scHicCluster/cluster_spectral.txt",
outfile.name)
def test_kmeans_chromosomes():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} --chromosomes {}".format(
ROOT + 'test_matrix.mcool', 3, 'kmeans', outfile.name, 1,
"chr1 chr2").split()
scHicCluster.main(args)
assert are_files_equal(
ROOT + "scHicCluster/cluster_kmeans_chromosomes.txt", outfile.name)
def test_help():
args = "--help".split()
with pytest.raises(SystemExit) as pytest_wrapped_e:
scHicCluster.main(args)
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 0
