def test_11_hla(install_test_files, data_dir):
"""Test HLA typing with OptiType.
"""
from bcbio.hla import optitype
hla_dir = os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX", "hla")
with make_workdir() as workdir:
data = {"dirs": {"work": workdir},
"rgnames": {"sample": "test"},
"config": {},
"hla": {"fastq": glob.glob(os.path.join(hla_dir, "*"))}}
out = optitype.run(data)
with open(out["hla"]["call_file"]) as in_handle:
header = in_handle.readline().strip().split(",")
hla_a = dict(zip(header, in_handle.readline().strip().split(",")))
assert hla_a["alleles"] == "HLA-A*11:01;HLA-A*24:02", hla_a
def test_11_hla(install_test_files, data_dir):
"""Test HLA typing with OptiType.
"""
from bcbio.hla import optitype
hla_dir = os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX", "hla")
with make_workdir() as workdir:
data = {"dirs": {"work": workdir},
"rgnames": {"sample": "test"},
"config": {},
"hla": {"fastq": glob.glob(os.path.join(hla_dir, "*"))}}
out = optitype.run(data)
with open(out["hla"]["call_file"]) as in_handle:
header = in_handle.readline().strip().split(",")
hla_a = dict(zip(header), in_handle.readline().strip().split(","))
assert hla_a["alleles"] == "HLA-A*11:01;HLA-A*24:02", hla_a