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