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changeset 396:dab29c3a5281 draft

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Uploaded
author francesco_lapi
date Fri, 05 Sep 2025 13:28:09 +0000
parents 64563ca68ace
children de4a373e338b
files COBRAxy/custom_data_generator.py COBRAxy/custom_data_generator.xml
diffstat 2 files changed, 4 insertions(+), 3 deletions(-) [+]
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line diff
--- a/COBRAxy/custom_data_generator.py	Fri Sep 05 13:22:34 2025 +0000
+++ b/COBRAxy/custom_data_generator.py	Fri Sep 05 13:28:09 2025 +0000
@@ -249,7 +249,8 @@
                 model.reactions.get_by_id(reaction).lower_bound = -float(value)
 
     if ARGS.name == "ENGRO2" and ARGS.gene_format != "Default":
-        model = utils.convert_genes(model, ARGS.gene_format)
+
+        model = utils.convert_genes(model, ARGS.gene_format.replace(" ", "_"))
 
     # generate data
     rules = generate_rules(model, asParsed = False)
--- a/COBRAxy/custom_data_generator.xml	Fri Sep 05 13:22:34 2025 +0000
+++ b/COBRAxy/custom_data_generator.xml	Fri Sep 05 13:28:09 2025 +0000
@@ -73,8 +73,8 @@
         <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="ENSG">ENSNG (Ensembl Gene ID)</option>
-            <option value="HGNC symbol">HGNC Symbol</option>
-            <option value="HGNC ID">HGNC 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>