Mercurial > repos > bgruening > openbabel_remions

comparison change_title_to_metadata_value.py @ 13:3153b6f3087c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 1fe240ef0064a1a4a66d9be1ccace53824280b75"
author bgruening
date Mon, 19 Oct 2020 14:43:01 +0000
parents 354c048550f7
children f70b83b730ac
comparison
equal deleted inserted replaced
12:354c048550f7 13:3153b6f3087c
4 """ 4 """
5 Change the title from a molecule file to metadata 5 Change the title from a molecule file to metadata
6 value of a given-id of the same molecule file. 6 value of a given-id of the same molecule file.
7 """ 7 """
8 8
9 import os
10 import sys
11 import argparse 9 import argparse
12 import random 10 import random
13 import string 11 import string
14 12
15
16 from openbabel import openbabel, pybel 13 from openbabel import openbabel, pybel
17 openbabel.obErrorLog.StopLogging() 14 openbabel.obErrorLog.StopLogging()
15
18 16
19 def main(): 17 def main():
20 parser = argparse.ArgumentParser( 18 parser = argparse.ArgumentParser(
21 description="Change the title from a molecule file to metadata \ 19 description="Change the title from a molecule file to metadata \
22 value of a given-id of the same molecule file.", 20 value of a given-id of the same molecule file.",
23 ) 21 )
24 parser.add_argument('--infile', '-i', 22 parser.add_argument('--infile', '-i', required=True,
25 required=True, help="path to the input file") 23 help="path to the input file")
26 parser.add_argument('--outfile', '-o', 24 parser.add_argument('--outfile', '-o', required=True,
27 required=True, help="path to the output file") 25 help="path to the output file")
28 parser.add_argument('--key', '-k', 26 parser.add_argument('--key', '-k', required=True,
29 required=True, help="the metadata key from the sdf file which should inlcude the new title") 27 help="the metadata key from the sdf file which should inlcude the new title")
30 parser.add_argument('--random', '-r', 28 parser.add_argument('--random', '-r', action="store_true",
31 action="store_true", help="Add random suffix to the title.") 29 help="Add random suffix to the title.")
32 30
33 args = parser.parse_args() 31 args = parser.parse_args()
34 32
35 output = pybel.Outputfile("sdf", args.outfile, overwrite=True) 33 output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
36 for mol in pybel.readfile("sdf", args.infile): 34 for mol in pybel.readfile("sdf", args.infile):
37 if args.key in mol.data: 35 if args.key in mol.data:
38 mol.title = mol.data[args.key] 36 mol.title = mol.data[args.key]
39 if args.random: 37 if args.random:
40 suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13)) 38 suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13))
41 mol.title += '__%s' % suffix 39 mol.title += '__%s' % suffix
42 output.write( mol ) 40 output.write(mol)
43 41
44 output.close() 42 output.close()
45 43
46 44
47 if __name__ == "__main__": 45 if __name__ == "__main__":
48 main() 46 main()
49