start geocoding ancient samples

ktmeaton · Nov 12, 2020 · a740d08 · a740d08
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diff --git a/docs/main.md b/docs/main.md
@@ -70,28 +70,26 @@ geocoding can be provided afterwards if desired "Country:Province:Foci".
 
 Place names should be compatible with Nominatim as implemented in GeoPy.
 
-```python
-from geopy.geocoders import Nominatim
-geolocator = Nominatim(user_agent="plague-phylogeography")
-place_name = "Armenia:Shirak Province"
-country_address = place_name.split(":")[0]
-province_address = ":".join(place_name.split(":")[0:2])
-
-# Geocode at country level
-location = geolocator.geocode(country_address, language="en",)
-print(location.address)
-> 'Armenia'
-print(location.latitude, location.longitude)
+Example: Country
+
+```bash
+python workflow/scripts/geocode.py "Armenia"
+```
+
+> Armenia
 > 40.7696272 44.6736646
 
-# Geocode at province level
-location = geolocator.geocode(province_address, language="en",)
-print(location.address)
-> 'Shirak Province, Armenia'
-print(location.latitude, location.longitude)
-> 40.918594 43.8403536
+Example: Province
+
+```bash
+python workflow/scripts/geocode.py "Armenia:Shirak Province"
 ```
 
+> Armenia
+> 40.7696272 44.6736646
+> Shirak Province, Armenia
+> 40.918594 43.8403536
+
 ## Genomic Alignment
 
 ### Modern Assembly Remote

diff --git a/results/sqlite_db/yersinia_pestis_db.sqlite b/results/sqlite_db/yersinia_pestis_db.sqlite
diff --git a/workflow/scripts/geocode.py b/workflow/scripts/geocode.py
@@ -0,0 +1,21 @@
+# Module Import
+import sys
+from geopy.geocoders import Nominatim
+
+args = sys.argv
+place_name = args[1]
+
+geolocator = Nominatim(user_agent="plague-phylogeography")
+country_address = place_name.split(":")[0]
+province_address = ":".join(place_name.split(":")[0:2])
+
+# Geocode at country level
+location = geolocator.geocode(country_address, language="en",)
+print(location.address)
+print(location.latitude, location.longitude)
+
+# Geocode at province level
+if len(place_name.split(":")) > 1:
+    location = geolocator.geocode(province_address, language="en",)
+    print(location.address)
+    print(location.latitude, location.longitude)