Mercurial > repos > bgruening > openbabel_genprop
view change_title_to_metadata_value.py @ 6:ebe0654a8b85 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 3ba9268697beb4827bd9e8e639e70166f224cb8b
author | bgruening |
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date | Mon, 03 Sep 2018 16:40:42 -0400 |
parents | df6d948e95ba |
children | c427987b54fd |
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#!/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 os import sys import argparse import openbabel openbabel.obErrorLog.StopLogging() import pybel 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") 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] output.write( mol ) output.close() if __name__ == "__main__": main()