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scripts_CNV/get_genes_list.py

+#! /usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+import sys
+
+
+genes_list = set()
+with open(sys.argv[1]) as bed_file:
+    for line in bed_file:
+        name = line.strip().split(";")
+        if len(name) < 6:
+			pass
+        else:
+			name = line.strip().split(";")[5].split()[1]
+			if "havana" not in name and "ensembl" not in name and "protein_coding" not in name:
+					genes_list.add(name)
+
+
+with open(sys.argv[2], "w") as out_file:
+        for i in genes_list:
+                out_file.write(i)
+                out_file.write("\n")
+