#!/usr/bin/env python3
import argparse
from os import system

parser = argparse.ArgumentParser(description='Find signal peptides in amino acid sequences')
parser.add_argument('--fasta', '-f', required=True, help='A fasta file with aminoacid sequences')
parser.add_argument('--organism', '-o', choices=['euk', 'gram+', 'gram-'], default='euk', help='The organism type')
args = parser.parse_args()

system("/vol/biotools/bin/signalp -t " + args.organism + " " + args.fasta)