def test_unequalMS2MatchesFtables(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
goodcsi2 = self.goodcsi2.view(CSIDirFmt)
ms2_match1 = pd.DataFrame(index=['2', '4'], columns=['Smiles'])
msg = ("The MS2 match tables should have a one-to-one "
"correspondance with feature tables and CSI results.")
with self.assertRaisesRegex(ValueError, msg):
make_hierarchy([goodcsi, goodcsi2],
[self.features, self.features2], [ms2_match1])
def test_MS2NoSmiles(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
goodcsi2 = self.goodcsi2.view(CSIDirFmt)
ms2_match1 = pd.DataFrame(index=['2', '4'], columns=[])
ms2_match2 = pd.DataFrame(index=['10', '12'], columns=['Smiles'])
msg = "MS2 match tables must contain the column `Smiles`"
with self.assertRaisesRegex(ValueError, msg):
make_hierarchy([goodcsi, goodcsi2],
[self.features, self.features2],
[ms2_match1, ms2_match2])
def test_MS2NoSmiles(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
goodcsi2 = self.goodcsi2.view(CSIDirFmt)
ms2_match1 = pd.DataFrame(index=['2', '4'], columns=[])
ms2_match2 = pd.DataFrame(index=['10', '12'], columns=['Smiles'])
msg = ("MS2 match tables must contain the column `Smiles`. Please "
"check if you have the correct input file for this command.")
with self.assertRaisesRegex(ValueError, msg):
make_hierarchy([goodcsi, goodcsi2],
[self.features, self.features2],
[ms2_match1, ms2_match2])
def test_Pipeline(self):
goodcsi1 = self.goodcsi.view(CSIDirFmt)
goodcsi2 = self.goodcsi2.view(CSIDirFmt)
treeout, merged_fts, merged_fdata = make_hierarchy(
[goodcsi1, goodcsi2], [self.features, self.features2])
tip_names = {node.name for node in treeout.tips()}
self.assertEqual(tip_names, set(merged_fts._observation_ids))
def test_mergeFeatureDataSingle(self):
goodcsi1 = self.goodcsi.view(CSIDirFmt)
treeout, merged_fts, merged_fdata = make_hierarchy([goodcsi1],
[self.features])
featrs = sorted(list(merged_fts.ids(axis='observation')))
fdata_featrs = sorted(list(merged_fdata.index))
self.assertEqual(len(featrs) == 3, True)
self.assertEqual(fdata_featrs, featrs)
def test_mergeFeatureDataSingle(self):
goodcsi1 = self.goodcsi.view(CSIDirFmt)
treeout, merged_fts, merged_fdata = make_hierarchy(
[goodcsi1], [self.features], [self.ms2_match])
featrs = sorted(list(merged_fts.ids(axis='observation')))
fdata_featrs = sorted(list(merged_fdata.index))
self.assertEqual('csi_smiles' in merged_fdata.columns, True)
self.assertEqual('ms2_smiles' in merged_fdata.columns, True)
self.assertEqual(len(merged_fdata[pd.notna(
merged_fdata.ms2_smiles)]), 1)
self.assertEqual(len(featrs) == 3, True)
self.assertEqual(fdata_featrs, featrs)
def test_unequalFtablesCSI(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
msg = ("The feature tables and CSI results should have a one-to-one"
" correspondance.")
with self.assertRaisesRegex(ValueError, msg):
make_hierarchy([goodcsi], [self.features, self.features2])
def test_tipMatchSingle(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
treeout, merged_fts, merged_fdata = make_hierarchy(
[goodcsi], [self.features])
tip_names = {node.name for node in treeout.tips()}
self.assertEqual(tip_names, set(merged_fts._observation_ids))
def test_emptyFeatures(self):
goodcsi = self.goodcsi.view(CSIDirFmt)
with self.assertRaises(ValueError):
make_hierarchy([goodcsi], [self.emptyfeatures])
