Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_generator.py @ 265:bae18f67004c draft

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Uploaded
author francesco_lapi
date Tue, 04 Mar 2025 15:30:59 +0000
parents a4f02ba0f64c
children 0025449eadba
comparison
equal deleted inserted replaced
264:a4f02ba0f64c 265:bae18f67004c
26 usage = '%(prog)s [options]', 26 usage = '%(prog)s [options]',
27 description = "process some value's genes to create a comparison's map.") 27 description = "process some value's genes to create a comparison's map.")
28 28
29 parser.add_argument( 29 parser.add_argument(
30 '-rs', '--rules_selector', 30 '-rs', '--rules_selector',
31 type = utils.Model, default = utils.Model.HMRcore, choices = list(utils.Model), 31 type = utils.Model, default = utils.Model.ENGRO2, choices = list(utils.Model),
32 help = 'chose which type of dataset you want use') 32 help = 'chose which type of dataset you want use')
33 33
34 parser.add_argument("-rl", "--rule_list", type = str, 34 parser.add_argument("-rl", "--rule_list", type = str,
35 help = "path to input file with custom rules, if provided") 35 help = "path to input file with custom rules, if provided")
36 36
224 224
225 gene_in_rule = None 225 gene_in_rule = None
226 226
227 if gene_dup: 227 if gene_dup:
228 if gene_custom == None: 228 if gene_custom == None:
229 print(args.rules_selector) 229
230 print(str(args.rules_selector) == 'ENGRO2') 230 if str(args.rules_selector) == 'HMRcore':
231
232 if args.rules_selector == 'HMRcore':
233 print(1) 231 print(1)
234 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb')) 232 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb'))
235 233
236 elif args.rules_selector == 'Recon': 234 elif str(args.rules_selector) == 'Recon':
237 print(2) 235 print(2)
238 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb')) 236 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb'))
239 237
240 elif args.rules_selector == 'ENGRO2': 238 elif str(args.rules_selector) == 'ENGRO2':
241 print(3) 239 print(3)
242 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) 240 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb'))
243 241
244 utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log) 242 utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log)
245 243