Mercurial > repos > bgruening > openbabel_obgrep

comparison ob_filter.py @ 9:8b23033ff72c draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openbabel commit 6c84abdd07f292048bf2194073e2e938e94158c4"
author bgruening
date Wed, 25 Mar 2020 16:44:07 -0400
parents f7e1b289b811
children f27e2eaffb5f
comparison
equal deleted inserted replaced
8:14712e15f196 9:8b23033ff72c
26 help='Output file name', 26 help='Output file name',
27 required=True) 27 required=True)
28 parser.add_argument('--filters', 28 parser.add_argument('--filters',
29 help="Specify the filters to apply", 29 help="Specify the filters to apply",
30 required=True, 30 required=True,
31 )
32 parser.add_argument('--list_of_names',
33 help="A file with list of molecule names to extract. Every name is in one line.",
34 required=False,
31 ) 35 )
32 return parser.parse_args() 36 return parser.parse_args()
33 37
34 def filter_precalculated_compounds(args, filters): 38 def filter_precalculated_compounds(args, filters):
35 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True) 39 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
81 sys.stderr.write("%s\n" % cmd) 85 sys.stderr.write("%s\n" % cmd)
82 else: 86 else:
83 sys.stdout.write(stdout.decode('utf-8')) 87 sys.stdout.write(stdout.decode('utf-8'))
84 sys.stdout.write(stderr.decode('utf-8')) 88 sys.stdout.write(stderr.decode('utf-8'))
85 89
90 def filter_by_name(args):
91 outfile = pybel.Outputfile(args.oformat, args.output, overwrite=True)
92 for mol in pybel.readfile('sdf', args.input):
93 for name in open(args.list_of_names):
94 if mol.title.strip() == name.strip():
95 outfile.write(mol)
96 outfile.close()
86 97
87 def __main__(): 98 def __main__():
88 """ 99 """
89 Select compounds with certain properties from a small library 100 Select compounds with certain properties from a small library
90 """ 101 """
91 args = parse_command_line() 102 args = parse_command_line()
103
104 if args.filters == '__filter_by_name__':
105 filter_by_name(args)
106 return
107
92 # Its a small trick to get the parameters in an easy way from the xml file. 108 # Its a small trick to get the parameters in an easy way from the xml file.
93 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed. 109 # To keep it readable in the xml file, many white-spaces are included in that string it needs to be removed.
94 # Also the last loop creates a ',{' that is not an valid jason expression. 110 # Also the last loop creates a ',{' that is not an valid jason expression.
95 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}')) 111 filters = json.loads((args.filters).replace(' ', '').replace(',}', '}'))
96 if args.iformat == 'sdf': 112 if args.iformat == 'sdf':