pgx-main from prod added

pgx-main/scripts/novel/core_var.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env/ python3
+
+import os
+import sys
+
+annot_file = sys.argv[1]
+gene_symbol = sys.argv[2]
+transcript = sys.argv[3]
+
+var_conseq = ["missense", "frameshift", "stop_gained", "splice_donor", "splice_acceptor", "inframe_insertion", "inframe_deletion", "start_lost", "stop_lost"] 
+
+for line in open(annot_file, "r"):
+    line = line.strip()
+
+    if line.startswith("#"):
+        pass
+    
+    else:
+        for i in var_conseq:
+            pattern = i + "|" + gene_symbol + "|" + transcript
+            
+            if pattern in line:
+                print(line)
+
+            else:
+                pass