Mercurial > repos > bgruening > openbabel_remduplicates
comparison change_title_to_metadata_value.py @ 0:112341e4fc94 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:34:54 -0400 |
| parents | |
| children | e185dfd1dfea |
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| -1:000000000000 | 0:112341e4fc94 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 # -*- coding: UTF-8 -*- | |
| 3 | |
| 4 """ | |
| 5 Change the title from a molecule file to metadata | |
| 6 value of a given-id of the same molecule file. | |
| 7 """ | |
| 8 | |
| 9 import os | |
| 10 import sys | |
| 11 import argparse | |
| 12 import openbabel | |
| 13 openbabel.obErrorLog.StopLogging() | |
| 14 import pybel | |
| 15 | |
| 16 | |
| 17 def main(): | |
| 18 parser = argparse.ArgumentParser( | |
| 19 description="Change the title from a molecule file to metadata \ | |
| 20 value of a given-id of the same molecule file.", | |
| 21 ) | |
| 22 parser.add_argument('--infile', '-i', | |
| 23 required=True, help="path to the input file") | |
| 24 parser.add_argument('--outfile', '-o', | |
| 25 required=True, help="path to the output file") | |
| 26 parser.add_argument('--key', '-k', | |
| 27 required=True, help="the metadata key from the sdf file which should inlcude the new title") | |
| 28 | |
| 29 args = parser.parse_args() | |
| 30 | |
| 31 output = pybel.Outputfile("sdf", args.outfile, overwrite=True) | |
| 32 | |
| 33 for mol in pybel.readfile("sdf", args.infile): | |
| 34 if args.key in mol.data: | |
| 35 mol.title = mol.data[args.key] | |
| 36 output.write( mol ) | |
| 37 | |
| 38 output.close() | |
| 39 | |
| 40 | |
| 41 if __name__ == "__main__": | |
| 42 main() | |
| 43 |