def test_read_write_h5ad(self):
adata = scc.read_input(
"tests/scCloud-test-data/input/hgmm_1k_v3_filtered_feature_bc_matrix/"
)
scc.write_output(adata, "test.h5ad")
adata2 = scc.read_input("test.h5ad")
assert_adata_equal(self, adata, adata2)
def test_read_write_old_5ad_backed_whitelist(self):
shutil.copy(
"tests/scCloud-test-data/input/test_obsm_compound.h5ad",
"test_obsm_compound.h5ad",
)
adata = scc.read_input("test_obsm_compound.h5ad", h5ad_mode="r+")
scc.write_output(adata, "test_obsm_compound.h5ad", whitelist=['obs'])
adata2 = scc.read_input("test_obsm_compound.h5ad")
assert_adata_equal(self, adata, adata2)
def test_aggregate_10x_matrices(self):
m1 = scc.read_input(
"tests/scCloud-test-data/input/heart_1k_v3/filtered_feature_bc_matrix.h5",
genome="mm10",
)
m2 = scc.read_input(
"tests/scCloud-test-data/input/heart_1k_v2/filtered_gene_bc_matrices_h5.h5",
genome="mm10",
)
scc.aggregate_matrices(
"tests/scCloud-test-data/input/aggregate_test.csv",
restrictions=[],
attributes=["Version"],
what_to_return="aggregate_test",
google_cloud=False,
select_singlets=False,
ngene=None,
)
result = scc.read_input("aggregate_test.h5sc", genome="mm10")
self.assertEqual(m1.shape[0] + m2.shape[0], result.shape[0],
"Cell dimension is incorrect")
self.assertEqual(m1.shape[1], result.shape[1],
"Gene dimension is incorrect")
self.assertTrue(
result.obs.get("Version") is not None, "Version not added")
m1_result = result[list(range(m1.shape[0])), :]
m2_result = result[list(range(m1.shape[0], m1.shape[0] +
m2.shape[0])), :]
self.assertEqual((m1_result.X != m1.X).sum(), 0, "Values differ")
self.assertEqual((m2_result.X != m2.X).sum(), 0, "Values differ")
self.assertTrue(
m1_result.obs.index.values[0].startswith("heart_1k_v3"),
"Prefix not added")
self.assertTrue(
m2_result.obs.index.values[0].startswith("heart_1k_v2"),
"Prefix not added")
def test_read_write_old_5ad(self):
adata = scc.read_input(
"tests/scCloud-test-data/input/test_obsm_compound.h5ad")
scc.write_output(adata, "test.h5ad")
adata2 = scc.read_input("test.h5ad")
assert_adata_equal(self, adata, adata2)
def test_mtx_v3_dir(self):
adata = scc.read_input(
"tests/scCloud-test-data/input/hgmm_1k_v3_filtered_feature_bc_matrix/"
)
self.assertEqual(adata.shape[0], 1046)
def test_mtx_v2_dir(self):
adata = scc.read_input(
"tests/scCloud-test-data/input/hgmm_1k_filtered_gene_bc_matrices/hg19/"
)
self.assertEqual(adata.shape[0], 504)