def test_ardnmf_poisson(self):
spectra = file_loader(SPECTRA_ARROW)
np.random.seed(0)
res = ardnmf(spectra, K0=10, max_iter=50, verbose=False)
for i, _ in enumerate(LAM_TRUE_1):
self.assertAlmostEqual(list(res['lam'])[i],
LAM_TRUE_1[i],
places=7)
def test_cosmic_dbs(self):
"""
Test doublet-base substitution mappers.
"""
maf_df = file_loader(MAF_TEST_FILE)
spectra_ref = pd.read_parquet("refs/test_cosmic3dbs_spectra.parquet")
_, spectra = get_spectra_from_maf(maf_df, cosmic='cosmic3_DBS')
self.assertEqual(np.linalg.norm(spectra.values - spectra_ref.values),
0)
def test_cosmic_id(self):
"""
Test insertion-deletion mappers.
"""
maf_df = file_loader(MAF_TEST_FILE)
spectra_ref = pd.read_parquet("refs/test_cosmic3id_spectra.parquet")
_, spectra = get_spectra_from_maf(maf_df,
cosmic='cosmic3_ID',
hgfile=HG_FILE)
self.assertEqual(np.linalg.norm(spectra.values - spectra_ref.values),
0)
def test_cosmic_sbs(self):
"""
Test single-base substituion mappers.
"""
maf_df = file_loader(MAF_TEST_FILE)
spectra_ref = pd.read_parquet("refs/test_cosmic2_spectra.parquet")
_, spectra = get_spectra_from_maf(maf_df,
cosmic='cosmic2',
hgfile=HG_FILE)
self.assertEqual(np.linalg.norm(spectra.values - spectra_ref.values),
0)
def test_sbs_cosmic3exome(self):
"""Test SBS Cosmic3 Exome"""
dirpath = tempfile.mkdtemp()
np.random.seed(0)
spectra = file_loader(SPECTRA_ARROW)
run_spectra(spectra,
outdir=dirpath,
cosmic='cosmic3_exome',
nruns=1,
K0=10,
max_iter=100,
plot_results=False)
cosine_df_arrow = pd.read_hdf(os.path.join(dirpath, 'nmf_output.h5'),
"cosine")
shutil.rmtree(dirpath)
ref_cosine = np.load("refs/test_mapping_cosmic3_exome.npy")
self.assertEqual(
np.linalg.norm(ref_cosine - cosine_df_arrow.sum(1).values), 0)
np.random.seed(0)
spectra = file_loader(SPECTRA_WORD)
run_spectra(spectra,
outdir=dirpath,
cosmic='cosmic3_exome',
nruns=1,
K0=10,
max_iter=100,
plot_results=False)
cosine_df_word = pd.read_hdf(os.path.join(dirpath, 'nmf_output.h5'),
"cosine")
shutil.rmtree(dirpath)
self.assertEqual(
np.linalg.norm(cosine_df_arrow.values - cosine_df_word.values), 0)