def test_fasta_best():
args = [
data_path("example.fasta"),
"--alleles",
"HLA-A*02:01,HLA-A*03:01,HLA-B*57:01,HLA-B*45:01,HLA-C*02:02,HLA-C*07:02",
"--results-best",
"affinity_percentile",
]
deletes = []
try:
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_scan_command.run(full_args)
result = read_output_csv(fd_out.name)
print(result)
assert not result.isnull().any().any()
finally:
for delete in deletes:
os.unlink(delete)
assert len(result) > 0
assert_array_equal(
result.groupby(["sequence_name"]).peptide.count().values, 1)
def test_fasta():
args = [
data_path("example.fasta"),
"--alleles",
"HLA-A*02:01,HLA-A*03:01,HLA-B*57:01,HLA-B*45:01,HLA-C*02:03,HLA-C*07:02",
]
deletes = []
try:
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_scan_command.run(full_args)
result = read_output_csv(fd_out.name)
print(result)
assert not result.isnull().any().any()
finally:
for delete in deletes:
os.unlink(delete)
assert_equal(result.best_allele.nunique(),
6,
err_msg=str(list(result.best_allele.unique())))
assert_equal(result.sequence_name.nunique(), 3)
assert_array_less(result.affinity_percentile, 2.0)
def test_fasta_50nm():
args = [
data_path("example.fasta"),
"--alleles",
"HLA-A*02:01,HLA-A*03:01,HLA-B*57:01,HLA-B*45:01,HLA-C*02:02,HLA-C*07:02",
"--results-filtered",
"affinity",
"--threshold-affinity",
"50",
]
deletes = []
try:
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_scan_command.run(full_args)
result = read_output_csv(fd_out.name)
print(result)
assert not result.isnull().any().any()
finally:
for delete in deletes:
os.unlink(delete)
assert len(result) > 0
assert_array_less(result.affinity, 50)
def test_commandline_sequences():
args = [
"--sequences",
"ASDFGHKL",
"QWERTYIPCVNM",
"--alleles",
"HLA-A0201,HLA-A0301",
"H-2-Kb",
"--peptide-lengths",
"8",
"--results-all",
]
deletes = []
try:
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_scan_command.run(full_args)
result = read_output_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
print(result)
assert_equal(result.sequence_name.nunique(), 2)
assert_equal(result.best_allele.nunique(), 3)
assert_equal(result.sample_name.nunique(), 2)
assert_equal((result.peptide == "ASDFGHKL").sum(), 2)
assert_equal((result.peptide != "ASDFGHKL").sum(), 10)