--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_filter_to_description.py	Tue Jun 14 08:15:55 2022 +0000
@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+"""Return a filter fasta file containing key words on description"""
+
+import argparse
+import sys
+
+from Bio import SeqIO
+
+desc = "Filter a fasta file based on description."
+command = argparse.ArgumentParser(
+    prog="fasta_filter_to_description", description=desc, usage="%(prog)s [options] key"
+)
+command.add_argument(
+    "-i",
+    "--input",
+    default=sys.stdin,
+    type=argparse.FileType("r"),
+    nargs="?",
+    help="Input fasta file to, default:stdin",
+)
+command.add_argument(
+    "-o",
+    "--output",
+    default=sys.stdout,
+    type=argparse.FileType("w"),
+    nargs="?",
+    help="Output result to, default:stdout",
+)
+# command.add_argument('-e','--perl', action='store_true', \
+#     help='Key word is an perl expression')
+command.add_argument(
+    "-V",
+    "--reverse",
+    action="store_true",
+    help="Return sequence without key in description",
+)
+command.add_argument(
+    "key", type=str, help="Key words that must be present in description"
+)
+
+if __name__ == "__main__":
+    """Performed job on execution script"""
+    args = command.parse_args()
+    output = args.output
+    count = 0
+    for seq in SeqIO.parse(args.input, "fasta"):
+        valid = False
+        if args.reverse:
+            if args.key not in seq.description:
+                valid = True
+        else:
+            if args.key in seq.description:
+                valid = True
+        if valid:
+            SeqIO.write(seq, output, "fasta")
+            count += 1
+    sys.stderr.write("Number of filter sequences : " + str(count) + "\n")