Mercurial > repos > bgruening > openbabel_spectrophore_search
view change_title_to_metadata_value.py @ 8:aedce3959676 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 72df8ae9b8fd9910b3d24aa0836b9b3c9d43f4fb
author | bgruening |
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date | Fri, 10 May 2019 08:10:28 -0400 |
parents | 7133973beaf0 |
children | 3d91d24e89c5 |
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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()