adapt to new pangolin lineage output
@@ -23,9 +23,8 @@ if __name__ == '__main__':
clades = {}
with open(args.clades, 'r') as fh:
for line in fh:
- strain, clade, _1, _2, status = line.strip().split(",")[:5]
- if status=='success':
- clades[strain]=clade
+ strain, country, travel_history, sample_date, epiweek, lineage, representative = line.strip().split(",")
+ clades[strain] = lineage
with open(args.input, "r") as f:
input_json = json.load(f)
