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,)
