workaround

scripts/set_final_strain_name.py

@@ -2,13 +2,19 @@
 import json, argparse
 from augur.io import read_metadata
 
-def replace_name_recursive(node, lookup):
+def replace_name_recursive(node, lookup, saveoldcolumn):
     if node["name"] in lookup:
+        if saveoldcolumn == "accession" or saveoldcolumn == "genbank_accession":
+            node["accession"] = node["name"]
+            node["node_attrs"]["url"] = "https://www.ncbi.nlm.nih.gov/nuccore/" + node["name"]
+        else:
+            node["node_attrs"][saveoldcolumn] = node["name"]
+
         node["name"] = lookup[node["name"]]
 
     if "children" in node:
         for child in node["children"]:
-            replace_name_recursive(child, lookup)
+            replace_name_recursive(child, lookup, saveoldcolumn)
 
 if __name__=="__main__":
     parser = argparse.ArgumentParser(
@@ -24,15 +30,20 @@ def replace_name_recursive(node, lookup):
     args = parser.parse_args()
 
     metadata = read_metadata(args.metadata, id_columns=args.metadata_id_columns)
-    name_lookup = {}
-    for ri, row in metadata.iterrows():
-        strain_id = row.name
-        name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name]
 
-    with open(args.input_auspice_json, 'r') as fh:
-        data = json.load(fh)
+    if args.display_strain_name in metadata.columns:
+        name_lookup = {}
+        for ri, row in metadata.iterrows():
+            strain_id = row.name
+            name_lookup[strain_id] = args.display_strain_name if pd.isna(row[args.display_strain_name]) else row[args.display_strain_name]
+
+        with open(args.input_auspice_json, 'r') as fh:
+            data = json.load(fh)
 
-    replace_name_recursive(data['tree'], name_lookup)
+        replace_name_recursive(data['tree'], name_lookup, args.metadata_id_columns[0])
+    else:
+        with open(args.input_auspice_json, 'r') as fh:
+            data = json.load(fh)
 
     with open(args.output, 'w') as fh:
-        json.dump(data, fh)
+        json.dump(data, fh, allow_nan=False, indent=None, separators=",:")