parse the subpop ac/an/af in python

scripts/variantstore/wdl/extract/create_variant_annotation_table.py

@@ -91,6 +91,16 @@
   "'-'"
  ]
 
+gvsSubpopulations = [
+  "afr",
+  "amr",
+  "eas",
+  "eur",
+  "mid",
+  "oth",
+  "sas"
+]
+
 def check_filtering(variant):
     # skip any row (with a warning) if no gvsAnnotations exist
     if variant.get("gvsAnnotations") == None: # <-- enum since we need this to be in tandem with the custom annotations header / template
@@ -113,6 +123,35 @@ def check_filtering(variant):
     else:
       return True
 
+def getSubpopulationCalculations(variant):
+    row = {}
+    max_af = None
+    max_ac = None
+    max_an = None
+    for gvs_subpop in gvsSubpopulations: # TODO check with Lee on order
+      subpop_annotations = variant.get("".join([gvs_subpop, "SubpopulationAnnotations"]))
+      if variant.get(subpop_annotations) != None:
+        subpop_ac_val = subpop_annotations.get("AC") # note that these can be null if there is no value in the annotations. They will be null in the VAT
+        subpop_an_val = subpop_annotations.get("AN")
+        subpop_af_val = subpop_annotations.get("AF")
+        # here we set the subpopulation ac/an/af values
+        row["_".join(["gvs", gvs_subpop, "ac"])] = subpop_ac_val
+        row["_".join(["gvs", gvs_subpop, "an"])] = subpop_an_val
+        row["_".join(["gvs", gvs_subpop, "af"])] = subpop_af_val
+        if subpop_af_val != None and max_af == None: # this will set the first max_af value
+          max_af = subpop_af_val
+        if subpop_af_val != None and subpop_af_val > max_af:
+          max_subpop = gvs_subpop
+          max_ac = subpop_ac_val
+          max_an = subpop_an_val
+          max_af = subpop_af_val
+    # here we set the MAX subpopulation ac/an/af values
+    row["gvs_max_subpop"] = max_subpop
+    row["gvs_max_ac"] = max_ac
+    row["gvs_max_an"] = max_an
+    row["gvs_max_af"] = max_af
+    return row
+
 def make_annotated_json_row(row_position, variant_line, transcript_line):
     row = {}
     row["position"] = row_position # this is a required field