def test_FabCollection_igblast_query_1(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
fab_collection.igblast_server_query()
self.assertAlmostEqual(
fab_collection.germline_identity['Heavy', 'Total'].iloc[0], 93.8)
def test_FabCollection_igblast_query_1(self):
# check germline assignment score
fab_collection = FabCollection(light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
fab_collection.igblast_server_query()
self.assertAlmostEqual(fab_collection.germline['Heavy', 'Score'].loc['Fab1'], 1.82e-66)
def test_FabCollection_ec_2(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertAlmostEqual(
fab_collection.extinction_coefficients(normalise=True)[0],
2.1082102969136987)
def test_FabCollection_input4(self):
light_chain_collection = ChainCollection(path='./tests/Data/chain_collection_light_2_sequences.json')
heavy_chain_collection = ChainCollection(path='./tests/Data/chain_collection_heavy_2_sequences.json')
fab_collection = FabCollection(light_chains=light_chain_collection,
heavy_chains=heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertEqual(fab_collection.numbering_table()['Light']['CDR3']['L89'].loc['Fab1'], 'Q')
def test_FabCollection_igblast_query_1(self):
# check germline assignment
fab_collection = FabCollection(light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
fab_collection.igblast_server_query()
self.assertEqual(fab_collection.germline['Heavy', 'Assignment']['Fab1'], 'IGHV1-8*01')
def test_FabCollection_json1(self):
light_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_light_2_sequences.json')
heavy_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_heavy_2_sequences.json')
fab_collection = FabCollection(light_chains=light_chain_collection,
heavy_chains=heavy_chain_collection,
names=['Fab1', 'Fab2'])
fab_collection.save(file_format='json', path='./tests/fab_1')
self.assertTrue(os.path.isfile('./tests/fab_1.json'))
def test_FabCollection_slicing_5(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertEqual(fab_collection[[0, 1]]._light_chains.names,
['LightSeq1', 'LightSeq2'])
def test_FabCollection_input_3(self):
# check if input with a list of Chain objects
self.assertIsInstance(
FabCollection(
heavy_chains=[self.heavy_chain_1, self.heavy_chain_2],
light_chains=[self.light_chain_1, self.light_chain_2]),
FabCollection)
def test_FabCollection_germline_identity(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertAlmostEqual(
fab_collection.germline_identity['Average']['CDR3'].loc['Fab1'],
78.55)
def test_FabCollection_json2(self):
fab_collection = FabCollection.load_from_file(
path='./tests/fab_1.json', show_progressbar=False, verbose=False)
light_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_light_2_sequences.json')
heavy_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_heavy_2_sequences.json')
self.assertEqual(fab_collection._light_chains.sequences[0],
light_chain_collection.sequences[0])
self.assertEqual(fab_collection._heavy_chains.sequences[0],
heavy_chain_collection.sequences[0])
def test_FabCollection_input_2(self):
# check if input with a list with fab objects works
self.assertIsInstance(FabCollection(fab=[self.fab_1, self.fab_2]),
FabCollection)
def test_FabCollection_input_1(self):
self.assertIsInstance(
FabCollection(light_chains=self.light_chain_collection,
heavy_chains=self.light_chain_collection),
FabCollection)
def test_FabCollection_slicing_2(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertEqual(fab_collection[0].name, 'Fab1')
def test_FabCollection_slicing_1(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertIsInstance(fab_collection[0], Fab)
def test_FabCollection_charge(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertAlmostEqual(fab_collection.charge().sum(),
-2.0354649111988743)
def test_FabCollection_n_ab(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(fab_collection.n_ab, 2)
def test_FabCollection_names(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection,
names=['Fab1', 'Fab2'])
self.assertEqual(fab_collection.names[0], 'Fab1')
def test_FabCollection_MW(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertAlmostEqual(fab_collection.molecular_weights()[0],
25078.143331999992)
def test_FabCollection_name_4(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(fab_collection._light_chains.names[1], 'LightSeq2')
def test_FabCollection_name_1(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(fab_collection._heavy_chains.names[0], 'Seq1')
def test_FabCollection_total_charge(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertAlmostEqual(fab_collection.total_charge()[0],
3.3658691836339365)
def test_FabCollection_len(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(len(fab_collection), 2)
def test_FabCollection_HMatrix(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(fab_collection.hydrophobicity_matrix().shape,
(2, 296))
def test_FabCollection_ec_1(self):
fab_collection = FabCollection(
light_chains=self.light_chain_collection,
heavy_chains=self.heavy_chain_collection)
self.assertEqual(fab_collection.extinction_coefficients()[0], 52870)
