annotate change_title_to_metadata_value.py @ 16:a638d8d13bb3 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit d9c51279c061a1da948a2582d5b502ca7573adbf

#!/usr/bin/env python
# -*- coding: UTF-8 -*-

"""
    Change the title from a molecule file to metadata
    value of a given-id of the same molecule file.
"""

import argparse
import random
import string

from openbabel import openbabel, pybel

openbabel.obErrorLog.StopLogging()


def main():
    parser = argparse.ArgumentParser(
        description="Change the title from a molecule file to metadata \
                     value of a given-id of the same molecule file.",
    )
    parser.add_argument("--infile", "-i", required=True, help="path to the input file")
    parser.add_argument(
        "--outfile", "-o", required=True, help="path to the output file"
    )
    parser.add_argument(
        "--key",
        "-k",
        required=True,
        help="the metadata key from the sdf file which should inlcude the new title",
    )
    parser.add_argument(
        "--random", "-r", action="store_true", help="Add random suffix to the title."
    )

    args = parser.parse_args()

    output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
    for mol in pybel.readfile("sdf", args.infile):
        if args.key in mol.data:
            mol.title = mol.data[args.key]
            if args.random:
                suffix = "".join(
                    random.choice(string.ascii_lowercase + string.digits)
                    for _ in range(13)
                )
                mol.title += "__%s" % suffix
        output.write(mol)

    output.close()


if __name__ == "__main__":
    main()