Mercurial > repos > bgruening > openbabel_obgrep

comparison change_title_to_metadata_value.py @ 0:b0311f002a5f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 8350bb3a632722c33bc91ec5238d47a536903729
author bgruening
date Sat, 20 May 2017 08:59:45 -0400
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children 8b23033ff72c
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-1:000000000000 0:b0311f002a5f
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