Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_generator.py @ 260:70b2bff188dd draft

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Uploaded
author francesco_lapi
date Tue, 04 Mar 2025 15:16:33 +0000
parents 91ad9bf5a734
children 1df2d8de156f
comparison
equal deleted inserted replaced
259:91ad9bf5a734 260:70b2bff188dd
219 219
220 gene_dup = [item for item, count in 220 gene_dup = [item for item, count in
221 collections.Counter(gene[gene.columns[0]]).items() if count > 1] 221 collections.Counter(gene[gene.columns[0]]).items() if count > 1]
222 pat_dup = [item for item, count in 222 pat_dup = [item for item, count in
223 collections.Counter(list(gene.columns)).items() if count > 1] 223 collections.Counter(list(gene.columns)).items() if count > 1]
224
225 gene_in_rule = None
224 226
225 if gene_dup: 227 if gene_dup:
226 if gene_custom == None: 228 if gene_custom == None:
229
227 if args.rules_selector == 'HMRcore': 230 if args.rules_selector == 'HMRcore':
228 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb')) 231 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb'))
229 232
230 elif args.rules_selector == 'Recon': 233 elif args.rules_selector == 'Recon':
231 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb')) 234 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb'))
232 235
233 elif args.rules_selector == 'ENGRO2': 236 elif args.rules_selector == 'ENGRO2':
234 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) 237 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb'))
235 238
236 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb'))
237
238 print(gene_in_rule)
239 print(f"{args.tool_dir}/local/pickle files/ENGRO2_genes.p")
240 utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log) 239 utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log)
241 print(args.rules_selector) 240
242 gene_in_rule = gene_in_rule.get(type_gene) 241 gene_in_rule = gene_in_rule.get(type_gene)
243 242
244 else: 243 else:
245 gene_in_rule = gene_custom 244 gene_in_rule = gene_custom
245
246 tmp = [] 246 tmp = []
247 for i in gene_dup: 247 for i in gene_dup:
248 if gene_in_rule.get(i) == 'ok': 248 if gene_in_rule.get(i) == 'ok':
249 tmp.append(i) 249 tmp.append(i)
250 if tmp: 250 if tmp: