parser=argparse.ArgumentParser(description='Make bioinformatic observations on aminoacid sequences')
parser.set_defaults(func=help)
subparsers=parser.add_subparsers()
info_parser=subparsers.add_parser('info')
info_parser.add_argument('--listanalyses','-l',action='store_true',help='Show available analysis steps')
info_parser.set_defaults(func=info)
analyze_parser=subparsers.add_parser('analyze')
analyze_parser.add_argument('--fasta','-f',required=True,help='A fasta file with aminoacid sequences')
analyze_parser.add_argument('--output','-o',required=True,help='The output directory for the json documents')
analyze_parser.add_argument('--profile','-p',default='fast',help='The profile to use')
analyze_parser.add_argument('--live','-l',action='store_true',help='Report results as they are computed, not only at the end of the computation. The live results will be available in the $output/live.')
analyze_parser.add_argument('--config','-c',help='The config to use')
analyze_parser.add_argument('--debug','-d',action='store_true',help='Debug mode, computation directory will not be removed after computation')
analyze_parser.add_argument('--execution_dir','-e',help='Use the specified execution directory and do not delete it after the computation')
parser=argparse.ArgumentParser(description='Make bioinformatic observations on aminoacid sequences')
parser.set_defaults(func=help)
subparsers=parser.add_subparsers()
info_parser=subparsers.add_parser('info')
info_parser.add_argument('--listanalyses','-l',action='store_true',help='Show available analysis steps')
info_parser.set_defaults(func=info)
analyze_parser=subparsers.add_parser('analyze')
analyze_parser.add_argument('--fasta','-f',required=True,help='A fasta file with aminoacid sequences')
analyze_parser.add_argument('--output','-o',required=True,help='The output directory for the json documents')
analyze_parser.add_argument('--profile','-p',default='fast',help='The profile to use')
analyze_parser.add_argument('--live','-l',action='store_true',help='Report results as they are computed, not only at the end of the computation. The live results will be available in the $output/live.')
analyze_parser.add_argument('--config','-c',help='The config to use')
analyze_parser.add_argument('--debug','-d',action='store_true',help='Debug mode, computation directory will not be removed after computation')
analyze_parser.add_argument('--execution_dir','-e',help='Use the specified execution directory and do not delete it after the computation')