Mercurial > repos > jjohnson > spectrast

comparison spectrast_params.py @ 5:274fdc50169b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast commit e5b5b15b0a995c8588ff62f92fd0a2329fb7a6a5-dirty
author jjohnson
date Wed, 25 Jul 2018 15:05:34 -0400
parents c9bfe6adb7cd
children
comparison
equal deleted inserted replaced
4:c9bfe6adb7cd 5:274fdc50169b
201 ' to create an updated search.params') 201 ' to create an updated search.params')
202 parser.add_argument( 202 parser.add_argument(
203 'param_files', nargs='*', 203 'param_files', nargs='*',
204 help='A SpectraST search.params files') 204 help='A SpectraST search.params files')
205 parser.add_argument( 205 parser.add_argument(
206 '-m', '--mode', choices=['search','create','filter'], 206 '-m', '--mode', choices=['search', 'create', 'filter'],
207 help='') 207 help='')
208 parser.add_argument( 208 parser.add_argument(
209 '-o', '--output', 209 '-o', '--output',
210 help='Output file (-) for stdout') 210 help='Output file (-) for stdout')
211 args = parser.parse_args() 211 args = parser.parse_args()
213 output_wtr = open(args.output, 'w')\ 213 output_wtr = open(args.output, 'w')\
214 if args.output and args.output != '-' else sys.stdout 214 if args.output and args.output != '-' else sys.stdout
215 215
216 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$') 216 optpat = re.compile('^([a-z]\w+)\s*[=:]\s*([^=]+)$')
217 217
218 valid_opts = search_opts if args.mode == 'search' else create_opts if args.mode == 'create' else filter_opts 218 valid_opts = search_opts if args.mode == 'search'\
219 else create_opts if args.mode == 'create' else filter_opts
219 valid_params = dict() 220 valid_params = dict()
220 221
221 # Collect all valid_params 222 # Collect all valid_params
222 def parse_params(param_file, fh, valid_opts): 223 def parse_params(param_file, fh, valid_opts):
223 for i, line in enumerate(fh): 224 for i, line in enumerate(fh):
245 print('parse_params: %s' % e, file=sys.stderr) 246 print('parse_params: %s' % e, file=sys.stderr)
246 247
247 # Write valid_params 248 # Write valid_params
248 for valid_opt in valid_opts: 249 for valid_opt in valid_opts:
249 if valid_opt in valid_params: 250 if valid_opt in valid_params:
250 print('%s = %s' % (valid_opt, valid_params[valid_opt]), file=output_wtr) 251 print('%s = %s' % (valid_opt, valid_params[valid_opt]),
252 file=output_wtr)
251 253
252 254
253 if __name__ == "__main__": 255 if __name__ == "__main__":
254 __main__() 256 __main__()
255