Mercurial > repos > bimib > cobraxy

comparison COBRAxy/ras_generator.py @ 44:76924a2fd939 draft

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author bimib
date Tue, 08 Oct 2024 16:54:51 +0000
parents a15126d5cd60
children 95d67e76d647
comparison
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43:a15126d5cd60 44:76924a2fd939
229 elif args.rules_selector == 'Recon': 229 elif args.rules_selector == 'Recon':
230 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb')) 230 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb'))
231 231
232 elif args.rules_selector == 'ENGRO2': 232 elif args.rules_selector == 'ENGRO2':
233 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) 233 gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb'))
234 #print(gene_in_rule)
235 print(args.tool_dir + '/local/pickle files/ENGRO2_genes.p')
236 gene_in_rule = gene_in_rule.get(type_gene) 234 gene_in_rule = gene_in_rule.get(type_gene)
237 235
238 else: 236 else:
239 gene_in_rule = gene_custom 237 gene_in_rule = gene_custom
240 tmp = [] 238 tmp = []
654 None 652 None
655 """ 653 """
656 # get args from frontend (related xml) 654 # get args from frontend (related xml)
657 global ARGS 655 global ARGS
658 ARGS = process_args() 656 ARGS = process_args()
659 657 print(ARGS.rules_selector)
660 # read dataset 658 # read dataset
661 dataset = read_dataset(ARGS.input, "dataset") 659 dataset = read_dataset(ARGS.input, "dataset")
662 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) 660 dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str)
663 661
664 # remove versioning from gene names 662 # remove versioning from gene names