diff gff3_splitgff.py @ 3:8bd03ba8510a draft

planemo upload commit edc74553919d09dcbe27fcadf144612c1ad3a2a2

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gff3_splitgff.py	Fri Apr 28 01:35:25 2023 +0000
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+import sys
+import argparse
+from Bio import SeqIO
+from Bio.Seq import Seq
+from CPT_GFFParser import gffParse, gffWrite
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Sample script to add an attribute to a feature via web services"
+    )
+    parser.add_argument("data", type=argparse.FileType("r"), help="GFF3 File")
+    parser.add_argument(
+        "--gff",
+        type=argparse.FileType("w"),
+        help="Output Annotations",
+        default="data.gff3",
+    )
+    parser.add_argument(
+        "--fasta",
+        type=argparse.FileType("w"),
+        help="Output Sequence",
+        default="data.fa",
+    )
+    args = parser.parse_args()
+
+    for record in gffParse(args.data):
+        gffWrite([record], args.gff)
+        record.description = ""
+
+        if isinstance(record.seq, str):
+            record.seq = Seq(record.seq)
+
+        SeqIO.write([record], args.fasta, "fasta")
+        sys.exit()