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')