diff remove_annotations.py @ 0:d5c3354c166d draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_annotations.py	Fri Apr 29 10:33:36 2022 +0000
@@ -0,0 +1,19 @@
+#!/usr/bin/env python
+import sys
+import argparse
+from CPT_GFFParser import gffParse, gffWrite
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("gff3", type=argparse.FileType("r"), help="GFF3 annotations")
+    parser.add_argument("--remark", action="store_true", help="Remove remark features")
+    parser.add_argument("--region", action="store_true", help="Remove region features")
+    args = parser.parse_args()
+
+    for rec in gffParse(args.gff3):
+        rec.annotations = {}
+        if args.remark:
+            rec.features = [x for x in rec.features if x.type != "remark"]
+        if args.region:
+            rec.features = [x for x in rec.features if x.type != "region"]
+        gffWrite([rec], sys.stdout)