def test_save_tsv(matrix, tmpdir):
output_file = tmpdir.join('expression.tsv').strpath
matrix.save_tsv(output_file)
recovered_matrix = ExpMatrix.load_tsv(output_file)
assert recovered_matrix.equals(matrix)
def test_run(expression_tsv_file, tmpdir, denoised_matrix):
output_file = tmpdir.join('denoised_expression.tsv').strpath
os.system('enhance.py -f %s -o %s' % (expression_tsv_file, output_file))
denoised_matrix_test = ExpMatrix.load_tsv(output_file).astype(np.float32)
assert np.allclose(denoised_matrix_test, denoised_matrix, atol=1e-4)
def denoised_matrix():
expression_file = resource_filename(
'monet', 'data/test/pbmc_100_denoised_expression.npz')
return ExpMatrix.load_npz(expression_file)
def test_load_tsv(expression_tsv_file):
matrix = ExpMatrix.load_tsv(expression_tsv_file)
assert matrix.values.dtype == np.uint32
assert matrix.num_genes == 14384
assert matrix.num_cells == 100
def matrix(expression_npz_file):
matrix = ExpMatrix.load_npz(expression_npz_file)
return matrix