--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_fix_sixpack/gff3_fix_sixpack.py	Fri May 13 18:01:18 2022 +0000
@@ -0,0 +1,46 @@
+#!/usr/bin/env python
+import sys
+import logging
+import argparse
+from CPT_GFFParser import gffParse, gffWrite
+from Bio.SeqFeature import SeqFeature
+from gff3 import feature_lambda, feature_test_type
+
+logging.basicConfig(level=logging.INFO)
+log = logging.getLogger(__name__)
+
+
+def fixed_feature(rec):
+    # Get all gene features to remove the mRNAs from
+    for feature in feature_lambda(
+        rec.features, feature_test_type, {"type": "gene"}, subfeatures=True
+    ):
+        gene = feature
+        sub_features = []
+        # Filter out mRNA subfeatures, save other ones to new gene object.
+        for sf in feature_lambda(
+            feature.sub_features,
+            feature_test_type,
+            {"type": "mRNA"},
+            subfeatures=True,
+            invert=True,
+        ):
+            sf.qualifiers["Parent"] = gene.qualifiers["ID"]
+            sub_features.append(sf)
+        # override original subfeatures with our filtered list
+        gene.sub_features = sub_features
+        yield gene
+
+
+def gff_filter(gff3):
+    for rec in gffParse(gff3):
+        rec.features = sorted(list(fixed_feature(rec)), key=lambda x: x.location.start)
+        rec.annotations = {}
+        gffWrite([rec], sys.stdout)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Fix gene model from naive ORF caller")
+    parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
+    args = parser.parse_args()
+    gff_filter(**vars(args))