def setUpClass(cls):
cls.ab_collection_1 = ChainCollection.load_from_file(path='./tests/Data/sequence_alignment_seq_1.json',
show_progressbar=False, verbose=False)
cls.ab_collection_2 = ChainCollection.load_from_file(path='./tests/Data/sequence_alignment_seq_2.json',
show_progressbar=False, verbose=False)
cls.seq2_aligned = read_sequence_from_file('./tests/Data/BLOSUM62_aligned_sequence')
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_input4(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'])
self.assertEqual(
fab_collection.numbering_table()['Light']['CDR3']
['L89'].loc['Fab1'], 'Q')
def test_ChainCollection_append_1(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_2 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_2_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_1.append(antibody_collection_2)
self.assertEqual(antibody_collection_1.n_ab, 2)
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 setUpClass(cls):
cls.light_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_light.json',
verbose=False,
show_progressbar=False)
cls.heavy_chain_collection = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
verbose=False,
show_progressbar=False)
cls.heavy_chain = cls.heavy_chain_collection[0]
cls.light_chain = cls.light_chain_collection[0]
def test_ChainCollection_json(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_1.save(file_format='json', path='./tests/SaveTest')
antibody_collection_2 = ChainCollection.load_from_file(
path='./tests/SaveTest.json',
show_progressbar=False,
verbose=False)
self.assertEqual(antibody_collection_1.sequences[0],
antibody_collection_2.sequences[0])
def test_ChainCollection_append_2(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_2 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_2_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_1.append(antibody_collection_2)
self.assertEqual(antibody_collection_1.hydrophobicity_matrix().shape,
(2, 158))
def test_ChainCollection_add(self):
# check if adding two ChainCollection objects with one sequence each
# results in a ChainCollection object with two sequences
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_2 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_2_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_3 = antibody_collection_1 + antibody_collection_2
self.assertEqual(antibody_collection_3.n_ab, 2)
def setUpClass(cls):
cls.test_sequence = read_sequence(
'./tests/Data/chain_collection_fasta_test.fasta')
cls.heavy_chain_collection_object = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
cls.heavy_chain_object = cls.heavy_chain_collection_object[0]
cls.light_chain_collection_object = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_light.json',
show_progressbar=False,
verbose=False)
cls.light_chain_object = cls.light_chain_collection_object[0]
def test_ChainCollection_add_exception_1(self):
# check if adding two ChainCollection objects with one sequence each
# results in a ChainCollection object with two sequences
antibody_chothia = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia',
show_progressbar=False,
verbose=False)
antibody_kabat = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='kabat',
show_progressbar=False,
verbose=False)
self.assertRaises(ValueError, operator.add, antibody_chothia,
antibody_kabat)
def test_ChainCollection_get_object_2(self):
# check if get_object returns a Chain object and keeps the information (i.e. name)
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertEqual(antibody_collection_1.get_object('test').name, 'test')
def test_ChainCollection_charge(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertAlmostEqual(antibody_collection_1.charge.sum(),
1.7497642167513607)
def test_ChainCollection_slicing_1_obj(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
# if returning a single chain abpytools automatically creates a new Chain object
self.assertIsInstance(antibody_collection_1[0], Chain)
def test_ChainCollection_slicing_2_obj(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_heavy_2_sequences.json',
show_progressbar=False,
verbose=False)
# slicing multiple sequences returns a ChainCollection object
self.assertIsInstance(antibody_collection_1[[0, 1]], ChainCollection)
def test_ChainCollection_cdr_regions_part1(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertCountEqual(antibody_collection_1.ab_region_index().keys(),
[self.antibody_collection_1_name])
def test_Chain_abysis_parser_kabat(self):
antibody = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='kabat',
verbose=False,
show_progressbar=False)
self.assertEqual(antibody.numbering_table(as_array=True)[0][-1], '-')
def test_Chain_abysis_parser(self):
antibody = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia',
verbose=False,
show_progressbar=False)
self.assertEqual(antibody.chain, 'heavy')
def test_ChainCollection_get_object_1(self):
# check if get_object returns a Chain object
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertIsInstance(antibody_collection_1.get_object('test'), Chain)
def test_Chain_set_name(self):
heavy_chain_object = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
heavy_chain_object[0].set_name("new_name")
self.assertEqual(heavy_chain_object[0].name, "new_name")
def test_ChainCollection_numbering_scheme_kabat(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_1.set_numbering_scheme('kabat', realign=False)
self.assertEqual(antibody_collection_1.numbering_scheme, 'kabat')
def test_ChainCollection_total_charge(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertAlmostEqual(
antibody_collection_1.total_charge[
self.antibody_collection_1_name], 1.3278508)
def test_ChainCollection_numbering_tableDataFrame(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(
as_array=False)['CDR1']['H32'].values[0], 'Y')
def test_ChainCollection_numbering_table_shape_pd(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(as_array=False).shape,
(1, 158))
def test_ChainCollection_numbering_table_region_np(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(as_array=True,
region='CDR1')[0][-1], 'Y')
def test_ChainCollection_numbering_table_fr_region(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(
region='FR1').loc['test'].values[0], 'Q')
def test_ChainCollection_proto_io_1(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
antibody_collection_1.save(file_format='pb2',
path='./tests/chain_collection_1_heavy')
self.assertTrue(os.path.isfile('./tests/chain_collection_1_heavy.pb2'))
def test_ChainCollection_molecular_weight_monoisotopic(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertAlmostEqual(
antibody_collection_1.molecular_weights(monoisotopic=True)[0],
20042.1121)
def test_ChainCollection_ec_reduced(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
self.assertAlmostEqual(
antibody_collection_1.extinction_coefficients(reduced=True)[0],
52160.0)
def test_ChainCollection_Hmatrix_shape(self):
antibody_collection_1 = ChainCollection.load_from_file(
path='./tests/Data/chain_collection_1_heavy.json',
show_progressbar=False,
verbose=False)
# if this fails it means that abysis has been updated
self.assertEqual(antibody_collection_1.hydrophobicity_matrix().shape,
(1, 158))
