fix wrong number of reported removed snps

associations/minerva_variants.py

@@ -25,7 +25,15 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
     logging.info("Retrieved data from myvariant API")
     if res.status_code == requests.codes.ok:
         content = json.loads(res.text)
+        cnt = 0
         for res in content:
+
+            genes = res["dbsnp"]["gene"]
+            if not isinstance(genes, list):
+                genes = [genes]
+
+            cnt += len(genes)
+
             if "dbnsfp" not in res \
                     or "uniprot" not in res["dbnsfp"] \
                     or "aa" not in res["dbnsfp"] :
@@ -48,7 +56,6 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
             #     uniprot_acc = uniprot_ids.pop()
             uniprot_acc = uniprot_ids.pop()
 
-
             aa = res["dbnsfp"]["aa"]
             aas = aa if isinstance(aa, list) else [aa] #we can hav multiple aa mappings if there is a splice site
 
@@ -57,11 +64,6 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
                 if "ref" not in aa:
                     continue
 
-                genes = res["dbsnp"]["gene"]
-
-                if not isinstance(genes, list):
-                    genes = [genes]
-
                 for gene in genes:
 
                     position = str(res["hg19"]["start"])
@@ -118,7 +120,7 @@ def get_dbsnp(ids: List[str]) -> List[Dict]:
                         "uniprot_acc": uniprot_acc
                     })
 
-        logging.info("Skipped {} variants out of {}".format(len(content) - len(snps), len(content)))
+        logging.info("Skipped {} variants out of {}".format(cnt - len(snps), cnt))
 
     return snps