update threshold for Africa seqs
@@ -549,7 +549,7 @@ def missing_coordinates(data, path, geo_location_occurences):
missing_latlongs["country"][region] = []
missing_latlongs["country"][region].append(country)
- division_threshold_function = lambda division: division not in latlongs["division"] and geo_location_occurences["division"][division] >= 20
+ division_threshold_function = lambda division: division not in latlongs["division"] and (geo_location_occurences["division"][division] >= 20 or region == "Africa")
for division in filter(division_threshold_function, data[region][country]):
if region not in missing_latlongs["division"]:
missing_latlongs["division"][region] = {}
@@ -1074,6 +1074,7 @@ def find_conflicting_annotations(annotations, geoLocationAnnotations, manualAnno
(region2, country2, division2, location2) = manualAnnotations[id][1]
annotations_correct = {"region": (region, region2), "country": (country, country2), "division": (division, division2), "location": (location, location2)}
for type in annotations_correct:
+ if annotations_correct[type][0] != annotations_correct[type][1]:
if id not in annotations["geography"]:
annotations["geography"][id] = {}
if type not in annotations["geography"][id]:
