Merge branch 'develop' into refactor/lint_black

bcgsc · Feb 29, 2024 · df3ca4b · df3ca4b
2 parents 5fe32cf + 15180c6
commit df3ca4b
Showing 1 changed file with 8 additions and 4 deletions.
diff --git a/graphkb/genes.py b/graphkb/genes.py
@@ -222,7 +222,9 @@ def get_preferred_gene_name(
     return gene_names[0]
 
 
-def get_cancer_predisposition_info(conn: GraphKBConnection) -> Tuple[List[str], Dict[str, str]]:
+def get_cancer_predisposition_info(
+    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
+) -> Tuple[List[str], Dict[str, str]]:
     """
     Return two lists from GraphKB, one of cancer predisposition genes and one of associated variants.
 
@@ -282,7 +284,7 @@ def get_cancer_predisposition_info(conn: GraphKBConnection) -> Tuple[List[str],
                     if name and biotype == "gene":
                         genes.add(name)
                     elif name:
-                        gene = get_preferred_gene_name(conn, name)
+                        gene = get_preferred_gene_name(conn, name, source)
                         if gene:
                             infer_genes.add((gene, name, biotype))
                         else:
@@ -301,7 +303,9 @@ def get_cancer_predisposition_info(conn: GraphKBConnection) -> Tuple[List[str],
     return sorted(genes), variants
 
 
-def get_pharmacogenomic_info(conn: GraphKBConnection) -> Tuple[List[str], Dict[str, str]]:
+def get_pharmacogenomic_info(
+    conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
+) -> Tuple[List[str], Dict[str, str]]:
     """
     Return two lists from GraphKB, one of pharmacogenomic genes and one of associated variants.
 
@@ -357,7 +361,7 @@ def get_pharmacogenomic_info(conn: GraphKBConnection) -> Tuple[List[str], Dict[s
                     if name and biotype == "gene":
                         genes.add(name)
                     elif name:
-                        gene = get_preferred_gene_name(conn, name)
+                        gene = get_preferred_gene_name(conn, name, source)
                         if gene:
                             infer_genes.add((gene, name, biotype))
                         else: