def objective(pArgs):
if pArgs['dimensionsPCA'] <= pArgs['umap_n_components']:
return 1
intraChromosomalContactsOnly = ''
noPCA = ''
noUMAP = ''
if pArgs['intraChromosomalContactsOnly']:
intraChromosomalContactsOnly = '-ic'
if pArgs['noPCA']:
noPCA = '--noPCA'
args = "-m {} -c {} -cm {} -o ramani_1mb_kmeans_c5.txt -t {} -k {} -nh {} -dim_pca {} " \
" -cct {} --colorMap glasbey_dark {} {} {} "\
"--umap_n_neighbors {} " \
"--umap_n_components {} " \
"--umap_min_dist {}".format(
pArgs['matrixFile'], pArgs['numberOfClusters'], pArgs['clusterMethod'], pArgs['threads'],
pArgs['numberOfNearestNeighbors'], pArgs['numberOfHashFunctions'],
pArgs['dimensionsPCA'], pArgs['cell_coloring_type'],
intraChromosomalContactsOnly, noPCA, noUMAP,
pArgs['umap_n_neighbors'], pArgs['umap_n_components'], pArgs['umap_min_dist']).split()
scHicClusterMinHash.main(args)
with open('correct_associated', 'r') as file:
error_score = 1 - float(file.readline().strip())
print('Error score: {}'.format(error_score))
return error_score
def test_kmeans_exact():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} -nh {} --exactModeMinHash".format(
ROOT + 'test_matrix.mcool', 3, 'kmeans', outfile.name, 2, 800).split()
scHicClusterMinHash.main(args)
assert are_files_equal(
ROOT + "scHicClusterMinHash/cluster_kmeans_exact.txt", outfile.name)
def test_spectral_chromosomes():
outfile = NamedTemporaryFile(suffix='.txt', delete=False)
outfile.close()
args = "--matrix {} --numberOfClusters {} --clusterMethod {} \
--outFileName {} -t {} -nh {} --chromosomes {} ".format(
ROOT + 'test_matrix.mcool', 3, 'spectral', outfile.name, 2, 800,
"chr1 chr2").split()
scHicClusterMinHash.main(args)
assert are_files_equal(
ROOT + "scHicClusterMinHash/cluster_spectral_chromosomes.txt",
outfile.name)
def test_version():
args = "--version".split()
with pytest.raises(SystemExit) as pytest_wrapped_e:
scHicClusterMinHash.main(args)
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 0