def test_no_csv():
args = [
"--alleles",
"HLA-A0201",
"H-2-Kb",
"--peptides",
"SIINFEKL",
"DENDREKLLL",
"PICKLEEE",
"--prediction-column-prefix",
"mhcflurry1_",
"--affinity-only",
]
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_command.run(full_args)
result = pandas.read_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
print(result)
assert_equal(len(result), 6)
sub_result1 = result.loc[result.peptide == "SIINFEKL"].set_index("allele")
print(sub_result1)
assert (sub_result1.loc["H-2-Kb"].mhcflurry1_affinity <
sub_result1.loc["HLA-A0201"].mhcflurry1_affinity)
def test_no_csv():
args = [
"--alleles", "HLA-A0201", "H-2Kb",
"--peptides", "SIINFEKL", "DENDREKLLL", "PICKLE",
"--prediction-column", "prediction",
]
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_command.run(full_args)
result = pandas.read_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
assert_equal(result.shape, (6, 3))
sub_result1 = result.ix[result.peptide == "SIINFEKL"].set_index("allele")
assert (
sub_result1.ix["H-2Kb"].prediction <
sub_result1.ix["HLA-A0201"].prediction)
def test_no_csv():
args = [
"--alleles",
"HLA-A0201",
"H-2Kb",
"--peptides",
"SIINFEKL",
"DENDREKLLL",
"PICKLE",
"--prediction-column",
"prediction",
]
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_command.run(full_args)
result = pandas.read_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
assert_equal(result.shape, (6, 3))
sub_result1 = result.ix[result.peptide == "SIINFEKL"].set_index("allele")
assert (sub_result1.ix["H-2Kb"].prediction <
sub_result1.ix["HLA-A0201"].prediction)
def test_csv():
args = ["--allele-column", "Allele", "--peptide-column", "Peptide"]
deletes = []
try:
with tempfile.NamedTemporaryFile(delete=False, suffix=".csv") as fd:
fd.write(TEST_CSV.encode())
deletes.append(fd.name)
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = [fd.name] + args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_command.run(full_args)
result = pandas.read_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
assert_equal(result.shape, (3, 6))
def test_csv():
args = ["--allele-column", "Allele", "--peptide-column", "Peptide"]
deletes = []
try:
with tempfile.NamedTemporaryFile(delete=False, suffix=".csv") as fd:
fd.write(TEST_CSV.encode())
deletes.append(fd.name)
fd_out = tempfile.NamedTemporaryFile(delete=False, suffix=".csv")
deletes.append(fd_out.name)
full_args = [fd.name] + args + ["--out", fd_out.name]
print("Running with args: %s" % full_args)
predict_command.run(full_args)
result = pandas.read_csv(fd_out.name)
print(result)
finally:
for delete in deletes:
os.unlink(delete)
assert_equal(result.shape, (3, 4))
