MLR lineage fitness: Save missing values as null rather than NaN

Explicitly set these entries as Python None rather than the NaN that Pandas wants to do. Then the resulting JSON gets values of `null` rather than `NaN`.

Author: trvrb

scripts/fetch_mlr_lineage_fitness.py

@@ -2,7 +2,6 @@
 importjson
 importpandasaspd
 importrequests
-importmath
 importsys
 fromaugur.ioimportread_metadata
 fromaugur.utilsimportwrite_json
@@ -30,7 +29,7 @@ def fetch_growth_advantages(mlr_url):
 growth_advantages[entry["variant"]] =entry["value"]
 returngrowth_advantages
 exceptExceptionase:
-print(f"Error fetching the JSON file: {e}")
+print(f"Error fetching the JSON file: {e}", file=sys.stderr)
 returnNone
 
 defmain():
@@ -60,13 +59,13 @@ def main():
 ifgrowth_advantages:
 metadata[args.metadata_clade_attribute] =metadata[args.metadata_clade_attribute].map(growth_advantages)
 else:
-metadata[args.metadata_clade_attribute] =math.nan
+metadata[args.metadata_clade_attribute] =None
 
 # Create a node data object with growth advantages
 node_data= {}
 forindex, recordinmetadata.iterrows():
 node_data[index] = {
-"mlr_lineage_fitness": record[args.metadata_clade_attribute]
+"mlr_lineage_fitness": record[args.metadata_clade_attribute]ifpd.notna(record[args.metadata_clade_attribute]) elseNone
  }
 
 # Save node data