def test_ChainCollection_numbering_table_shape_pd(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(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(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(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(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(
region='FR1').loc['test'].values[0], 'Q')
def test_ChainCollection_total_charge(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertAlmostEqual(
antibody_collection_1.total_charge[
self.antibody_collection_1_name], 1.3278508)
def test_ChainCollection_molecular_weight_monoisotopic(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertAlmostEqual(
antibody_collection_1.molecular_weights(monoisotopic=True)[0],
20042.1121)
def test_ChainCollection_cdr_regions_part3_cdr(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertCountEqual(
antibody_collection_1.ab_region_index()
[self.antibody_collection_1_name]['CDR'], ['CDR1', 'CDR2', 'CDR3'])
def test_ChainCollection_ec_reduced(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertAlmostEqual(
antibody_collection_1.extinction_coefficients(reduced=True)[0],
52160.0)
def test_ChainCollection_numbering_tableDataFrame(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(
antibody_collection_1.numbering_table(
as_array=False)['CDR1']['H32'].values[0], 'Y')
def test_ChainCollection_Hmatrix_calculation(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_fasta_test.fasta')
antibody_collection_1.load(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))
def test_ChainCollection_igblast_server_query_identity(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_1.igblast_server_query(show_progressbar=False)
self.assertEqual(
antibody_collection_1.germline_identity[
self.antibody_collection_1_name]['Total'], 96.9)
def test_ChainCollection_igblast_server_query_score(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_1.igblast_server_query(show_progressbar=False)
self.assertEqual(
antibody_collection_1.germline[self.antibody_collection_1_name][1],
9.11e-69)
def test_ChainCollection_igblast_parser_germline(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_1.igblast_local_query(
'tests/Data/chain_collection_1_igblast.html')
self.assertEqual(
antibody_collection_1.germline[self.antibody_collection_1_name][0],
'IGHV4-34*01')
def test_ChainCollection_append_1(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_2 = ChainCollection(
path='./tests/Data/chain_collection_2_heavy.json')
antibody_collection_2.load(show_progressbar=False, verbose=False)
antibody_collection_1.append(antibody_collection_2)
self.assertEqual(antibody_collection_1.n_ab, 2)
def test_ChainCollection_append_2(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_2 = ChainCollection(
path='./tests/Data/chain_collection_2_heavy.json')
antibody_collection_2.load(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_json(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_1.save(file_format='json',
file_path='./tests',
file_name='SaveTest')
antibody_collection_2 = ChainCollection(path='./tests/SaveTest.json')
antibody_collection_2.load()
self.assertEqual(antibody_collection_1.sequences[0],
antibody_collection_2.sequences[0])
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(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
antibody_collection_2 = ChainCollection(
path='./tests/Data/chain_collection_2_heavy.json')
antibody_collection_2.load(show_progressbar=False, verbose=False)
antibody_collection_3 = antibody_collection_1 + antibody_collection_2
self.assertEqual(antibody_collection_3.n_ab, 2)
def test_ChainCollection_add_exception_2(self):
# check if adding two ChainCollection objects with one sequence each
# results in a ChainCollection object with two sequences
antibody_chothia = ChainCollection(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia')
antibody_chothia.load(show_progressbar=False, verbose=False)
antibody_kabat = Chain(sequence=read_sequence(
'./tests/Data/chain_collection_fasta_test.fasta'),
numbering_scheme='kabat')
antibody_kabat.load()
self.assertRaises(ValueError, operator.add, antibody_chothia,
antibody_kabat)
def test_ChainCollection_sequence_length(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(len(antibody_collection_1.sequences), 1)
def test_ChainCollection_add_exception_3(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertRaises(ValueError, operator.add, antibody_collection_1, 0)
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(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(antibody_collection_1.get_object('test').name, 'test')
def test_ChainCollection_get_object_1(self):
# check if get_object returns a Chain object
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertIsInstance(antibody_collection_1.get_object('test'), Chain)
def test_ChainCollection_get_object_exception(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertRaises(ValueError, antibody_collection_1.get_object, 'foo')
def test_ChainCollection_charge(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertAlmostEqual(antibody_collection_1.charge.sum(),
1.7497642167513607)
def test_ChainCollection_slicing_2_obj(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_heavy_2_sequences.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
# slicing including multiple sequences returns a ChainCollection object
self.assertIsInstance(antibody_collection_1[[0, 1]], ChainCollection)
def test_ChainCollection_slicing(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertIsInstance(antibody_collection_1.get_object('test'), Chain)
def test_Chain_abysis_parser(self):
antibody = ChainCollection(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='chothia')
antibody.load(verbose=False, show_progressbar=False)
self.assertEqual(antibody.chain, 'heavy')
def test_ChainCollection_slicing_1_obj(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(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_Chain_abysis_parser_kabat(self):
antibody = ChainCollection(
path='./tests/Data/chain_collection_fasta_test.fasta',
numbering_scheme='kabat')
antibody.load(verbose=False, show_progressbar=False)
self.assertEqual(antibody.numbering_table(as_array=True)[0][-1], '-')
def test_ChainCollection_chain(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(antibody_collection_1.chain, 'heavy')
def test_ChainCollection_numbering_scheme_kabat(self):
antibody_collection_1 = ChainCollection(
path='./tests/Data/chain_collection_1_heavy.json',
numbering_scheme='kabat')
antibody_collection_1.load(show_progressbar=False, verbose=False)
self.assertEqual(antibody_collection_1.numbering_scheme, 'kabat')
