Mercurial > repos > bimib > cobraxy
changeset 393:52658ddcaa5d draft
Uploaded
| author | francesco_lapi |
|---|---|
| date | Fri, 05 Sep 2025 13:02:22 +0000 |
| parents | f73d57641124 |
| children | a0b53ccc73a8 |
| files | COBRAxy/custom_data_generator.py COBRAxy/custom_data_generator.xml COBRAxy/marea_macros.xml |
| diffstat | 3 files changed, 28 insertions(+), 22 deletions(-) [+] |
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--- a/COBRAxy/custom_data_generator.py Fri Sep 05 10:53:36 2025 +0000 +++ b/COBRAxy/custom_data_generator.py Fri Sep 05 13:02:22 2025 +0000 @@ -31,9 +31,10 @@ help="Model name (default or custom)") parser.add_argument("--medium_selector", type=str, required=True, - help="Medium selection option (default/custom)") - parser.add_argument("--medium", type=str, - help="Custom medium file if medium_selector=Custom") + help="Medium selection option") + + parser.add_argument("--gene_format", type=str, default="Default", + help="Gene nomenclature format: Default (original), ENSNG, HGNC_SYMBOL, HGNC_ID, ENTREZ") parser.add_argument("--out_tabular", type=str, help="Output file for the merged dataset (CSV or XLSX)") @@ -226,7 +227,27 @@ raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}") # Determine final model name: explicit --name overrides, otherwise use the model id + model_name = ARGS.name if ARGS.name else ARGS.model + + + if ARGS.name == "ENGRO2" and ARGS.medium_selector != "Default": + df_mediums = pd.read_csv(ARGS.tool_dir + "/local/medium/medium.csv", index_col = 0) + ARGS.medium_selector = ARGS.medium_selector.replace("_", " ") + medium = df_mediums[[ARGS.medium_selector]] + medium = medium[ARGS.medium_selector].to_dict() + + # Set all reactions to zero in the medium + for rxn_id, _ in model.medium.items(): + model.reactions.get_by_id(rxn_id).lower_bound = float(0.0) + + # Set medium conditions + for reaction, value in medium.items(): + if value is not None: + model.reactions.get_by_id(reaction).lower_bound = -float(value) + + if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default": + utils.convert_genes(model, ARGS.gene_format) # generate data rules = generate_rules(model, asParsed = False)
--- a/COBRAxy/custom_data_generator.xml Fri Sep 05 10:53:36 2025 +0000 +++ b/COBRAxy/custom_data_generator.xml Fri Sep 05 13:02:22 2025 +0000 @@ -23,9 +23,6 @@ --model $cond_model.model_selector --name $cond_model.model_selector #end if - #if $cond_model.medium_selector == 'Custom' - --medium $cond_model.medium - #end if --gene_format $gene_format @@ -42,9 +39,6 @@ <param name="name" argument="--name" type="text" value="ENGRO2" hidden="true" /> <conditional name="medium_selector"> <expand macro="options_ras_to_bounds_medium"/> - <when value="Custom"> - <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> - </when> </conditional> </when> @@ -54,14 +48,10 @@ <conditional name="medium_selector"> <param name="medium_selector" argument="--medium_selector" type="select" label="Medium"> <option value="Default" selected="true">Default (Recon built-in medium)</option> - <option value="Custom">Custom medium file</option> </param> <when value="Default"> <!-- Nessun parametro aggiuntivo necessario --> </when> - <when value="Custom"> - <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> - </when> </conditional> </when> @@ -72,24 +62,20 @@ <conditional name="medium_selector"> <param name="medium_selector" argument="--medium_selector" type="select" label="Medium"> <option value="Default" selected="true">Don't use a separate medium file (use model defaults)</option> - <option value="Custom">Custom medium file (required)</option> </param> <when value="Default"> <!-- Nessun parametro aggiuntivo necessario --> </when> - <when value="Custom"> - <param name="medium" argument="--medium" type="data" format="tabular,csv,tsv" label="Custom medium file:" /> - </when> </conditional> </when> </conditional> <param name="gene_format" argument="--gene_format" type="select" label="Gene nomenclature format:"> <option value="Default" selected="true">Keep original gene nomenclature</option> - <option value="ENSNG">ENSNG (Ensembl Gene ID)</option> - <option value="HGNC_SYMBOL">HGNC Symbol</option> - <option value="HGNC_ID">HGNC ID</option> - <option value="ENTREZ">Entrez Gene ID</option> + <option value="ENSG">ENSNG (Ensembl Gene ID)</option> + <option value="HGNC symbol">HGNC Symbol</option> + <option value="HGNC ID">HGNC ID</option> + <option value="entrez_id">Entrez Gene ID</option> </param> </inputs>
--- a/COBRAxy/marea_macros.xml Fri Sep 05 10:53:36 2025 +0000 +++ b/COBRAxy/marea_macros.xml Fri Sep 05 13:02:22 2025 +0000 @@ -28,7 +28,6 @@ <param name="medium_selector" argument="--medium_selector" type="select" label="Medium:"> <option value="Default" selected="true">Default (ENGRO2 built-in medium)</option> <option value="allOpen">Open</option> - <option value="Custom">Custom medium</option> <option value="RPMI_1640">RPMI 1640</option> <option value="DMEM">DMEM</option> <option value="EMEM">EMEM</option>