Prepend PHARMGKB to gene IDs for which we can't find Uniprot IDs

Knowledge-Graph-Hub · May 11, 2020 · 5577772 · 5577772
1 parent 6e120aa
commit 5577772
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/kg_covid_19/transform_utils/pharmgkb/pharmgkb.py b/kg_covid_19/transform_utils/pharmgkb/pharmgkb.py
@@ -231,12 +231,13 @@ def make_pharmgkb_gene_node(self,
         write_node_edge_item(fh=fh, header=self.node_header, data=data)
 
     def get_uniprot_id(self,
-                       this_id: str):
+                       this_id: str,
+                       pharmgkb_prefix: str='PHARMGKB'):
         try:
             gene_id = self.uniprot_curie_prefix + \
                       self.gene_id_map[this_id][self.key_parsed_ids][self.uniprot_id_key]
         except KeyError:
-            gene_id = this_id
+            gene_id = pharmgkb_prefix + ":" + this_id
         return gene_id
 
     def make_pharmgkb_chemical_node(self,