#!/usr/bin/env python
"""
Converts our .variants.gff to the format expected by Vikas's leftjustify-indels.py.  Stdin to stdout.
"""
import sys
import os
import re
import string
import subprocess
import tempfile
import getopt
import fastaExtract
from datetime import datetime

def flipSequence(s):
    parts = s.strip().split("/")
    return "".join([parts[1], ":", parts[0]])


def main(argv=None):
    if argv is None:
        argv = sys.argv

    for line in sys.stdin:
        line.strip()
        if (len(line) == 0 or line[0] == '#'):
            continue
        fields = line.split("\t")
        if fields[2].startswith("INS"):
            position = long(fields[4])
        else:
            position = long(fields[3])
        print "ATAC\t%s\t%d\t%s\t%s\t" % (
            fields[0],
            position, 
            flipSequence(fields[8]),
            fields[6])
            


            
if __name__ == "__main__":
    sys.exit(main())