Mercurial > repos > bgruening > openbabel_filter

annotate change_title_to_metadata_value.py @ 10:da03b00048b1 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
author bgruening
date Sat, 21 Mar 2020 10:26:39 -0400
parents 0d6e836460be
children ff2dd4b7d918
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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1 #!/usr/bin/env python
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2 # -*- coding: UTF-8 -*-
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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4 """
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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5 Change the title from a molecule file to metadata
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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6 value of a given-id of the same molecule file.
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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7 """
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9 import os
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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10 import sys
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11 import argparse
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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12 import openbabel
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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13 openbabel.obErrorLog.StopLogging()
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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14 import pybel
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15 import random
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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16 import string
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19 def main():
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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20 parser = argparse.ArgumentParser(
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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21 description="Change the title from a molecule file to metadata \
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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22 value of a given-id of the same molecule file.",
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23 )
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24 parser.add_argument('--infile', '-i',
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25 required=True, help="path to the input file")
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26 parser.add_argument('--outfile', '-o',
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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27 required=True, help="path to the output file")
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28 parser.add_argument('--key', '-k',
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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29 required=True, help="the metadata key from the sdf file which should inlcude the new title")
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30 parser.add_argument('--random', '-r',
da03b00048b1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit c4274133a07c323627e3ac5374502da9ecf669fe-dirty"
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31 action="store_true", help="Add random suffix to the title.")
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0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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33 args = parser.parse_args()
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35 output = pybel.Outputfile("sdf", args.outfile, overwrite=True)
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36 for mol in pybel.readfile("sdf", args.infile):
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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37 if args.key in mol.data:
0d6e836460be planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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38 mol.title = mol.data[args.key]
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39 if args.random:
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40 suffix = ''.join(random.choice(string.ascii_lowercase + string.digits) for _ in range(13))
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41 mol.title += '__%s' % suffix
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42 output.write( mol )
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44 output.close()
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47 if __name__ == "__main__":
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48 main()
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