def get_binding_value():
peptides_string = request.forms.get('peptide')
if peptides_string is None:
return "ERROR: no peptide given"
peptides_list = split_uppercase_sequences(peptides_string)
alleles_string = request.forms.get('allele')
if alleles_string is None:
return "ERROR: no allele given"
alleles_list = split_allele_names(alleles_string)
try:
result_df = predict(alleles=alleles_list, peptides=peptides_list)
except ValueError as e:
return "ERROR: %s" % e.args[0]
return result_df.to_csv(sep="\t", index=False, float_format="%0.4f")
from mhcflurry.class1 import predict
parser = argparse.ArgumentParser()
parser.add_argument(
"--mhc",
default="HLA-A*02:01",
type=split_allele_names,
help="Comma separated list of MHC alleles")
parser.add_argument(
"--sequence",
required=True,
type=split_uppercase_sequences,
help="Comma separated list of protein sequences")
parser.add_argument(
"--fasta-file",
help="FASTA file of protein sequences to chop up into peptides")
parser.add_argument(
"--peptide-lengths",
default=[9],
type=parse_int_list,
help="Comma separated list of peptide length, e.g. 8,9,10,11")
if __name__ == "__main__":
args = parser.parse_args()
df = predict(alleles=args.mhc, peptides=args.sequence)
print(df.to_csv(sep="\t", index=False), end="")
