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))