dry out import

scripts/variantstore/scripts/create_vt_bqloadjson_from_annotations.py

@@ -6,7 +6,7 @@
 import argparse
 import logging
 import sys
-import Bio.Seq
+from Bio.Seq import reverse_complement
 
 vat_nirvana_positions_dictionary = {
     "position": "position", # required
@@ -239,8 +239,9 @@ def make_annotated_json_row(row_position, row_ref, row_alt, variant_line, transc
         ## TODO add clinvar star rating!!!
         for clinvar_obj in clinvar_objs:
             # get only the clinvar objs with right variant and the id that starts with RCV
-            if (((clinvar_obj.get("refAllele") == var_ref) and (clinvar_obj.get("altAllele") == var_alt)) or
-            ((clinvar_obj.get("refAllele") == Bio.Seq.reverse_complement(variant_line["refAllele"])) and (clinvar_obj.get("altAllele") == Bio.Seq.reverse_complement(variant_line["altAllele"])))) and (clinvar_obj.get("id")[:3] == "RCV"):
+            if (((clinvar_obj.get("refAllele") == var_ref) and (clinvar_obj.get("altAllele") == var_alt)) \
+            or ((clinvar_obj.get("refAllele") == reverse_complement(variant_line["refAllele"])) and (clinvar_obj.get("altAllele") == reverse_complement(variant_line["altAllele"])))) \
+            and (clinvar_obj.get("id")[:3] == "RCV"):
                 clinvar_ids.append(clinvar_obj.get("id"))
                 significance_values.extend([x.lower() for x in clinvar_obj.get("significance")])
                 updated_dates.append(clinvar_obj.get("lastUpdatedDate"))