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, 2).split()
scHicClusterCompartments.main(args)
assert are_files_equal(
ROOT + "scHicClusterCompartments/cluster_spectral.txt", outfile.name)
def test_kmeans_norm_clustering():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} --binarization --norm".format(
ROOT + 'test_matrix.mcool', 3, 'kmeans', outfile.name, 2).split()
scHicClusterCompartments.main(args)
assert are_files_equal_clustering(
ROOT + "scHicClusterCompartments/cluster_kmeans_binarization_norm.txt",
outfile.name)
def test_spectral_extraTrack_clustering():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} --binarization --extraTrack {} --norm".format(
ROOT + 'test_matrix.mcool', 3, 'spectral', outfile.name, 2,
ROOT + 'scHicClusterCompartments/mm9_gene.bed.gz').split()
scHicClusterCompartments.main(args)
assert are_files_equal_clustering(
ROOT +
"scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt",
outfile.name)
def test_kmeans_histonmark():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} --histonMarkType {} --binarization --norm".format(
ROOT + 'test_matrix.mcool', 3, 'kmeans', outfile.name, 2,
ROOT + 'scHicClusterCompartments/mm9_H3K36me3.bed.gz').split()
scHicClusterCompartments.main(args)
assert are_files_equal(
ROOT +
"scHicClusterCompartments/cluster_kmeans_binarization_norm_histon_track.txt",
outfile.name)
def test_help():
args = "--help".split()
with pytest.raises(SystemExit) as pytest_wrapped_e:
scHicClusterCompartments.main(args)
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 0
