Renaming cancerGene flag

bcgsc · Nov 16, 2023 · 31b886b · 31b886b
1 parent 0f0f1cd
commit 31b886b
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/graphkb/genes.py b/graphkb/genes.py
@@ -392,7 +392,7 @@ def get_gene_information(
 
     Function is originally from pori_ipr_python::annotate.py
 
-    Gene flags (categories) are: ['cancerRelated', 'knownFusionPartner', 'knownSmallMutation',
+    Gene flags (categories) are: ['cancerGene', 'cancerRelated', 'knownFusionPartner', 'knownSmallMutation',
                                   'oncogene', 'therapeuticAssociated', 'tumourSuppressor']
 
     Args:
@@ -444,8 +444,8 @@ def get_gene_information(
     gene_flags["oncogene"] = convert_to_rid_set(get_oncokb_oncogenes(graphkb_conn))
     logger.info("fetching tumour supressors list")
     gene_flags["tumourSuppressor"] = convert_to_rid_set(get_oncokb_tumour_supressors(graphkb_conn))
-    logger.info("fetching cancer_gene list")
-    gene_flags["cancer_gene"] = convert_to_rid_set(get_cancer_genes(graphkb_conn))
+    logger.info("fetching cancerGene list")
+    gene_flags["cancerGene"] = convert_to_rid_set(get_cancer_genes(graphkb_conn))
 
     logger.info("fetching therapeutic associated genes lists")
     gene_flags["therapeuticAssociated"] = convert_to_rid_set(

diff --git a/tests/test_genes.py b/tests/test_genes.py
@@ -251,5 +251,5 @@ def test_get_gene_information(conn):
 
     for gene in CANONICAL_CG:
         assert gene in [
-            g["name"] for g in gene_info if g.get("cancer_gene")
-        ], f"Missed cancer_gene {gene}"
+            g["name"] for g in gene_info if g.get("cancerGene")
+        ], f"Missed cancerGene {gene}"