def main():
parser = argparse.ArgumentParser(description="Reads protein or peptide sequences and predicts peptides "+
"for a specified prediction method and HLA alleles.")
parser.add_argument("-i", "--input",
nargs="+",
required=True,
help="Input data can be RefSeq ID, UniProt ID, fasta file, peptide file (one peptide per line),"
+" or peptide sequences as sequences (max 50)"
)
input_types = parser.add_mutually_exclusive_group(required=True)
input_types.add_argument("-p","--protein",
action="store_true",
help= "Specifies if IDs are protein IDs")
input_types.add_argument("-r","--rna",
action="store_true",
help= "Specifies the input as rna IDs")
input_types.add_argument("-f","--fasta",
action="store_true",
help= "Specifies the input as protein (multi-)Fasta file")
parser.add_argument("-a", "--alleles",
nargs="+",
required=True,
help="Specifies for which alleles prediction should be made. " +
"Input either can be alleles as string (new nomenclature), or a file with one allele per line.")
allele_types = parser.add_mutually_exclusive_group(required=True)
allele_types.add_argument("-af", "--allelefile",
action="store_true",
help="Specifies the allele input as allele file.")
allele_types.add_argument("-as", "--allelestring",
action="store_true",
help="Specifies the allele input as allele string.")
parser.add_argument("-m", "--method",
required=True,
nargs="+",
help="Specifies the method used for prediction.")
parser.add_argument("-l", "--length",
required=False,
type=int,
default=9,
help="Specifies the length of the peptides (default=9).")
parser.add_argument("-o", "--output",
required=True,
help="Specifies the output path. Results will be written to CSV")
parser.add_argument("-am", "--available",
required=False,
action="store_true",
help="Returns all available methods and their allele models.")
#COMMENT: These options are hidden and only used for ETK2
parser.add_argument("-html", "--html",
required=False,
action="store_true",
help=argparse.SUPPRESS)
parser.add_argument("-od", "--outdir",
required=False,
default="",
help=argparse.SUPPRESS)
args = parser.parse_args()
if args.available:
for pred, obj in AEpitopePrediction.registry.iteritems():
if pred not in ["AEpitopePrediction", "APSSMEpitopePredictor", "ANetMHC", "ASVMEpitopePrediction"]:
print "Method: ",pred
print "Supported Alleles: ", " ".join(getattr(obj, "_"+pred+"__alleles" ))
print "Supported Length: ", " ".join(map(str, getattr(obj, "_"+pred+"__supported_length")))
print
sys.exit(0)
mart = MartsAdapter()
#RefSeq
transcripts = []
if args.protein:
for pid in args.input:
ids = mart.get_transcript_information_from_protein_id(pid)
#UniProt
elif args.uniprot:
pass
