def test_featureMatch2(self): goodcsi = self.goodcsi.view(CSIDirFmt) tablefp = collate_fingerprint(goodcsi) smiles = get_feature_smiles(goodcsi, tablefp) fpfeatrs = set(tablefp.index) smlfeatrs = set(smiles.index) self.assertEqual(fpfeatrs == smlfeatrs, True)
def test_featureMatch1(self): goodcsi = self.goodcsi.view(CSIDirFmt) tablefp = collate_fingerprint(goodcsi) features = load_table(self.featureTable) allfeatrs = set(features.ids(axis='observation')) fpfeatrs = set(tablefp.index) self.assertEqual(fpfeatrs <= allfeatrs, True)
def setUp(self): THIS_DIR = os.path.dirname(os.path.abspath(__file__)) table = pd.DataFrame() self.emptyfps = table table = pd.DataFrame(index=['a', 'b', 'c'], data=['a', 'b', 'c']) self.wrongtips = table goodtable = os.path.join(THIS_DIR, 'data/features_formated.biom') self.features = load_table(goodtable) goodsmiles = os.path.join(THIS_DIR, 'data/features_smiles.txt') self.smiles = pd.read_csv(goodsmiles, dtype=str, sep='\t') self.smiles = self.smiles.set_index('#featureID') goodcsi = os.path.join(THIS_DIR, 'data/goodcsi') self.tablefp = collate_fingerprint(goodcsi)
def test_pubchemFalse(self): goodcsi = self.goodcsi.view(CSIDirFmt) tablefp = collate_fingerprint(goodcsi) indx = self.properties.index self.assertEqual(set(tablefp.columns) == set(indx), True)
def test_fingerprintOut(self): msg = "Fingerprint file is empty!" with self.assertRaisesRegex(ValueError, msg): collate_fingerprint(self.emptycsi)
def test_pubchemTrue(self): goodcsi = self.goodcsi.view(CSIDirFmt) tablefp = collate_fingerprint(goodcsi, qc_properties=True) indx = self.properties.loc[self.properties.type == 'PUBCHEM'].index self.assertEqual(set(tablefp.columns) == set(indx), True)