comparison ob_filter.py @ 10:c427987b54fd draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"

9:a26f96c1f061

        help='Output file name',
        required=True)
    parser.add_argument('--filters', 
        help="Specify the filters to apply",
        required=True,
        )
    return parser.parse_args()

def filter_precalculated_compounds(args, filters):
    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)

        sys.stderr.write("%s\n" % cmd)
    else:
        sys.stdout.write(stdout.decode('utf-8'))
        sys.stdout.write(stderr.decode('utf-8'))


def __main__():
    """
        Select compounds with certain properties from a small library
    """
    args = parse_command_line()
    # Its a small trick to get the parameters in an easy way from the xml file.
    # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
    # Also the last loop creates a ',{' that is not an valid jason expression.
    filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
    if args.iformat == 'sdf':

10:c427987b54fd

        help='Output file name',
        required=True)
    parser.add_argument('--filters', 
        help="Specify the filters to apply",
        required=True,
        )
    parser.add_argument('--list_of_names', 
        help="A file with list of molecule names to extract. Every name is in one line.",
        required=False,
        )
    return parser.parse_args()

def filter_precalculated_compounds(args, filters):
    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)

        sys.stderr.write("%s\n" % cmd)
    else:
        sys.stdout.write(stdout.decode('utf-8'))
        sys.stdout.write(stderr.decode('utf-8'))

def filter_by_name(args):
    outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
    for mol in pybel.readfile('sdf', args.input):
        for name in open(args.list_of_names):
            if mol.title.strip() == name.strip():
                outfile.write(mol)
    outfile.close()

def __main__():
    """
        Select compounds with certain properties from a small library
    """
    args = parse_command_line()
    
    if args.filters == '__filter_by_name__':
        filter_by_name(args)
        return
    
    # Its a small trick to get the parameters in an easy way from the xml file.
    # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
    # Also the last loop creates a ',{' that is not an valid jason expression.
    filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
    if args.iformat == 'sdf':