def test_netmhcii_pan_multiple_alleles(): alleles = [ normalize_allele_name("HLA-DPA1*01:05-DPB1*100:01"), normalize_allele_name("HLA-DQA1*05:11-DQB1*03:02"), normalize_allele_name("HLA-DRA1*01:01-DRB1*01:01") ] ii_pan_predictor = NetMHCIIpan(alleles=alleles) fasta_dictionary = {"TP53-001": "SQAMDDLMLSPDDIEQWFTED"} binding_predictions = ii_pan_predictor.predict_subsequences( sequence_dict=fasta_dictionary, peptide_lengths=[15, 16]) unique_lengths = {x.length for x in binding_predictions} eq_(unique_lengths, {15, 16}) unique_alleles = {x.allele for x in binding_predictions} eq_( unique_alleles, { "HLA-DPA1*01:05-DPB1*100:01", "HLA-DQA1*05:11-DQB1*03:02", "HLA-DRA1*01:01-DRB1*01:01" }) # length of "SQAMDDLMLSPDDIEQWFTED" is 21 # Expect 3 * ((21-15+1) + (21-16+1)) = 39 entries assert len(binding_predictions) == 39, \ "Expected 39 epitopes from %s" % (binding_predictions,)
def test_netmhcii_pan_mouse(): alleles = [normalize_allele_name("H2-IAb")] ii_pan_predictor = NetMHCIIpan(alleles=alleles) fasta_dictionary = { "SMAD4-001": "PAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGT", "TP53-001": "SQAMDDLMLSPDDIEQWFTED" } binding_predictions = ii_pan_predictor.predict_subsequences( sequence_dict=fasta_dictionary, peptide_lengths=[15, 16]) unique_lengths = {x.length for x in binding_predictions} eq_(unique_lengths, {15, 16}) unique_alleles = {x.allele for x in binding_predictions} eq_(unique_alleles, {"H-2-IAb"}) # length of "PAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGT" is 34 # length of "SQAMDDLMLSPDDIEQWFTED" is 21 # Expect (34-15+1) + (34-16+1) + (21-15+1) + (21-16+1) = 52 entries assert len(binding_predictions) == 52, \ "Expected 52 epitopes from %s" % (binding_predictions,)