@@ -0,0 +1,959 @@
+#!/usr/bin/env python%0A# -*- coding: utf-8 -*-%0A%22%22%22%0A%0A%22%22%22%0Afrom __future__ import print_function%0A%0Aimport argparse%0A%0Adef get_parser():%0A    parser = argparse.ArgumentParser(%0A        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)%0A%0A    #parser.add_argument('-', %22--%22, help=%22%22, default=%22%22)%0A%0A    parser.add_argument(%22-v%22, %22--verbose%22,%0A                        action=%22store_true%22, help=%22be verbose%22)%0A    parser.add_argument(%22file%22, help=%22%22, default=%22%22)%0A    return parser%0A%0A%0Aif __name__ == '__main__':%0A    parser = get_parser()%0A    args = parser.parse_args()%0A%0A    for l in open(args.file):%0A        if l.startswith('# ') or l.strip() == '//':%0A            print(l)%0A        if l.startswith('#=GF'):%0A            print(l)%0A        elif '%7C' in l and '#' not in l:%0A            #0000%7CChr4_88684848__88684954             GUGCUCg........%0A            # print(l)%0A            # print(l.split('%7C'))%0A            x = l.split('%7C')%5B1%5D%0A            print(x.strip())%0A

add simple script to remove uniq ids after cmalign