def setUp(self):
self.peptides_mhcI = [Peptide("SYFPEITHI"), Peptide("IHTIEPFYS")]
self.peptides_mhcII = [Peptide("AAAAAASYFPEITHI"), Peptide("IHTIEPFYSAAAAAA")]
self.mhcI = [Allele("HLA-B*07:02"), Allele("HLA-A*02:01")]
self.mhcII = [Allele("HLA-DRB1*07:01"), Allele("HLA-DRB1*15:01")]
self.mhcII_combined_alleles = [CombinedAllele("DPA1*01:03-DPB1*01:01"), CombinedAllele("DQA1*06:02-DQB1*06:31")]
self.transcript = Transcript("")
def parse_external_result(self, output):
"""
Searches within the defined dir _file for the newest dir and reads
the prediction file from there
:param str output: The path to the output dir
:return: The predicted HLA genotype
:rtype: list(:class:`~Fred2.Core.Allele.Allele`)
"""
alleles = []
try:
with open(output + "-ClassI.HLAgenotype4digits") as c1:
for row in csv.DictReader(c1, delimiter="\t"):
alleles.extend([
Allele("HLA-" + row["Allele 1"].replace("'", "")),
Allele("HLA-" + row["Allele 2"].replace("'", ""))
])
except IOError as e:
warnings.warn(
"Output file {c1} for HLA-I could not be found. {error}".
format(c1=output + "-ClassI.HLAgenotype4digits"),
error=e)
try:
with open(output + "-ClassII.HLAgenotype4digits") as c2:
DQA = []
DQB = []
for row in csv.DictReader(c2, delimiter="\t"):
a1, a2 = row["Allele 1"], row["Allele 2"]
if "DRB" in a1 or "DRB" in a2:
alleles.extend([
Allele("HLA-" + a1.replace("'", "")),
Allele("HLA-" + a2.replace("'", ""))
])
elif "DQA" in a1 or "DQA" in a2:
DQA.extend([a1.replace("'", ""), a2.replace("'", "")])
else:
DQB.extend([a1.replace("'", ""), a2.replace("'", "")])
for dq in itertools.product(DQA, DQB):
alleles.append(CombinedAllele("HLA-" + "-".join(dq)))
except IOError as e:
warnings.warn(
"Output file {c2} for HLA-I could not be found. {error}".
format(c2=output + "-ClassII.HLAgenotype4digits"),
error=e)
return alleles
def test_combined_allele(self):
comb = CombinedAllele("HLA-DPA1*01:03-DPB1*01:01")
self.assertTrue(repr(comb) == "HLA-DPA1*01:03-DPB1*01:01")
self.assertEqual(comb, CombinedAllele("HLA-DPA1*01:03-DPB1*01:01"))
self.assertNotEqual(comb, CombinedAllele("HLA-DPA1*01:03-DPB1*01:02"))