--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_type_filter/filter_type.py	Fri May 13 18:05:32 2022 +0000
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+import sys
+import argparse
+from CPT_GFFParser import gffParse, gffWrite
+from gff3 import feature_lambda, feature_test_type
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
+    parser.add_argument("types", type=str, nargs="+", help="Feature type to filter on")
+    parser.add_argument("--invert", action="store_true")
+    args = parser.parse_args()
+
+    for rec in gffParse(args.gff3):
+        tempFeats = feature_lambda(
+            rec.features,
+            feature_test_type,
+            {"types": args.types},
+            invert=args.invert,
+            subfeatures=False,
+        )
+        rec.features = []
+        for x in tempFeats:
+          rec.features.append(x)
+        for x in rec.features:
+          if "Parent" in x.qualifiers.keys():
+            found = 0
+            for seek in x.qualifiers["Parent"]:
+              for y in rec.features:
+                if y.id == seek:
+                  found += 1
+                  break
+            if found < len(x.qualifiers["Parent"]):
+              del x.qualifiers["Parent"]
+        gffWrite([rec], sys.stdout)