Mercurial > repos > bimib > cobraxy
diff COBRAxy/ras_generator.py @ 309:38c9a958ea78 draft
Uploaded
author | francesco_lapi |
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date | Thu, 22 May 2025 16:03:37 +0000 |
parents | 0025449eadba |
children |
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--- a/COBRAxy/ras_generator.py Tue May 20 16:01:21 2025 +0000 +++ b/COBRAxy/ras_generator.py Thu May 22 16:03:37 2025 +0000 @@ -8,6 +8,7 @@ import utils.general_utils as utils import utils.rule_parsing as ruleUtils from typing import Union, Optional, List, Dict, Tuple, TypeVar +import os ERRORS = [] ########################## argparse ########################################## @@ -212,7 +213,7 @@ Returns: dict: A dictionary containing gene data with gene IDs as keys and corresponding values. """ - args = process_args() + for i in range(len(gene)): tmp = gene.iloc[i, 0] gene.iloc[i, 0] = tmp.strip().split('.')[0] @@ -227,16 +228,16 @@ if gene_dup: if gene_custom == None: - if str(args.rules_selector) == 'HMRcore': - gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb')) + if str(ARGS.rules_selector) == 'HMRcore': + gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/HMRcore_genes.p', 'rb')) - elif str(args.rules_selector) == 'Recon': - gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/Recon_genes.p', 'rb')) + elif str(ARGS.rules_selector) == 'Recon': + gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/Recon_genes.p', 'rb')) - elif str(args.rules_selector) == 'ENGRO2': - gene_in_rule = pk.load(open(args.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) + elif str(ARGS.rules_selector) == 'ENGRO2': + gene_in_rule = pk.load(open(ARGS.tool_dir + '/local/pickle files/ENGRO2_genes.p', 'rb')) - utils.logWarning(f"{args.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log) + utils.logWarning(f"{ARGS.tool_dir}'/local/pickle files/ENGRO2_genes.p'", ARGS.out_log) gene_in_rule = gene_in_rule.get(type_gene) @@ -662,7 +663,7 @@ # get args from frontend (related xml) global ARGS ARGS = process_args(args) - print(ARGS.rules_selector) + # read dataset dataset = read_dataset(ARGS.input, "dataset") dataset.iloc[:, 0] = (dataset.iloc[:, 0]).astype(str) @@ -672,6 +673,7 @@ # handle custom models model :utils.Model = ARGS.rules_selector + if model is utils.Model.Custom: rules = load_custom_rules() reactions = list(rules.keys()) @@ -703,4 +705,4 @@ ############################################################################### if __name__ == "__main__": - main() \ No newline at end of file + main()