Mercurial > repos > bimib > cobraxy

comparison COBRAxy/custom_data_generator_beta.py @ 444:06564187fba3 draft

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author francesco_lapi
date Thu, 11 Sep 2025 09:03:10 +0000
parents 00a78da611ba
children c3bb75ce07e6
comparison
equal deleted inserted replaced
443:3d4e10546917 444:06564187fba3
171 # Set medium conditions 171 # Set medium conditions
172 for reaction, value in medium.items(): 172 for reaction, value in medium.items():
173 if value is not None: 173 if value is not None:
174 model.reactions.get_by_id(reaction).lower_bound = -float(value) 174 model.reactions.get_by_id(reaction).lower_bound = -float(value)
175 175
176 if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default": 176 #if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default":
177 # logging.basicConfig(level=logging.INFO)
178 # logger = logging.getLogger(__name__)
179
180 #model = modelUtils.translate_model_genes(
181 # model=model,
182 # mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"), dtype={'entrez_id': str},
183 # target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
184 # source_nomenclature='HGNC_ID',
185 # logger=logger
186 #)
187 #model = modelUtils.convert_genes(model, ARGS.gene_format.replace("HGNC_", "HGNC "))
188
189 if (ARGS.name == "Recon" or ARGS.name == "ENGRO2") and ARGS.gene_format != "Default":
177 logging.basicConfig(level=logging.INFO) 190 logging.basicConfig(level=logging.INFO)
178 logger = logging.getLogger(__name__) 191 logger = logging.getLogger(__name__)
179 192
180 model = modelUtils.translate_model_genes( 193 model = modelUtils.translate_model_genes(
181 model=model, 194 model=model,
182 mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"), 195 mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv", dtype={'entrez_id': str}),
183 target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
184 source_nomenclature='HGNC_ID',
185 logger=logger
186 )
187 #model = modelUtils.convert_genes(model, ARGS.gene_format.replace("HGNC_", "HGNC "))
188
189 if ARGS.name == "Recon" and ARGS.gene_format != "Default":
190 logging.basicConfig(level=logging.INFO)
191 logger = logging.getLogger(__name__)
192
193 model = modelUtils.translate_model_genes(
194 model=model,
195 mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv"),
196 target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "), 196 target_nomenclature=ARGS.gene_format.replace("HGNC_", "HGNC "),
197 source_nomenclature='HGNC_symbol', 197 source_nomenclature='HGNC_symbol',
198 logger=logger 198 logger=logger
199 ) 199 )
200 200