add preferred source arg

bcgsc · Dec 28, 2023 · 642fcd3 · 642fcd3
1 parent f3a17ae
commit 642fcd3
Showing 1 changed file with 6 additions and 4 deletions.
diff --git a/graphkb/genes.py b/graphkb/genes.py
@@ -218,14 +218,16 @@ def get_preferred_gene_name(
             genes = source_filtered_genes
 
     gene_names = [g["displayName"] for g in genes if g]
+    if 'ENS' in gene_name:
+        import pdb; pdb.set_trace()
     if len(gene_names) > 1:
         logger.error(
             f"Multiple gene names found for: {gene_name} - using {gene_names[0]}, ignoring {gene_names[1:]}"
         )
     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.
 
@@ -287,7 +289,7 @@ 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:
@@ -306,7 +308,7 @@ 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.
 
@@ -362,7 +364,7 @@ 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: