add adjustment for Hunan sequences
@@ -142,6 +142,18 @@ def read_metadata(metadata):
division = location
location = ""
+ if country == "Hunan":
+ additions_to_annotation.append(strain + "\t" + id + "\tcountry\tChina #previously Hunan")
+ additions_to_annotation.append(strain + "\t" + id + "\tdivision\tHunan")
+ additions_to_annotation.append(strain + "\t" + id + "\tlocation\t" + division)
+ print("Warning: Changed Hunan from country to Chinese division for " + id)
+ if location != "":
+ print("Lost location " + location)
+ country = "China"
+ location = division
+ division = "Hunan"
+
+
if region not in data:
data[region] = {}
if country not in data[region]:
