--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cherry_pick_fasta.py	Mon Jun 08 18:55:07 2015 -0400
@@ -0,0 +1,36 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Chery pick of fasta sequences satisfying a query string in their header/name
+"""
+
+import argparse
+
+def Parser():
+    the_parser = argparse.ArgumentParser(
+        description="Cherry pick fasta sequences")
+    the_parser.add_argument(
+        '--input', action="store", type=str, help="input fasta file")
+    the_parser.add_argument(
+        '--query-string', dest="query_string", action="store", type=str,
+                            help="header containing the string will be extracted as well as the corresponding sequence")
+    the_parser.add_argument(
+        '--output', action="store", type=str, help="output fasta file")
+    args = the_parser.parse_args()
+    return args
+
+def __main__():
+    """ main function """
+    args = Parser()
+    search_term = args.query_string
+    CrudeFasta = open (args.input, "r").read()
+    Output = open (args.output, "w")
+    FastaListe = CrudeFasta.split(">")
+    for sequence in FastaListe:
+        if search_term in sequence:
+            print >> Output,  ">%s" % sequence.rstrip()
+    Output.close()
+
+
+if __name__ == "__main__":
+    __main__()