def test_featureMatch(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__)) tablefp = Table({}, [], []) self.emptyfeatures = tablefp goodtable = os.path.join(THIS_DIR, 'data/features_formated.biom') self.features = load_table(goodtable) goodtable = os.path.join(THIS_DIR, 'data/features2_formated.biom') self.features2 = load_table(goodtable) self.goodcsi = qiime2.Artifact.load( os.path.join(THIS_DIR, 'data/csiFolder.qza')) goodcsi = self.goodcsi.view(CSIDirFmt) self.collated = collate_fingerprint(goodcsi) self.goodcsi2 = qiime2.Artifact.load( os.path.join(THIS_DIR, 'data/csiFolder2.qza')) goodcsi = self.goodcsi2.view(CSIDirFmt) self.collated2 = collate_fingerprint(goodcsi)
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) 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, qc_properties=False) indx = self.properties.index self.assertEqual(set(tablefp.columns) == set(indx), True)
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)
def test_fingerprintOut(self): msg = "Fingerprint file is empty!" with self.assertRaisesRegex(ValueError, msg): collate_fingerprint(self.emptycsi)