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)