# Custom script for handling peak data from P. Farnham's lab
# 
# Find the center of each peak, and generate coordinates +/- 3kb from center
# Also add 'name' attribute

import sys

in_fn = None
out_fn = None

if len(sys.argv) != 3:
    print "\nSpecify:\n"
    print "(1) input peaks file in GFF format,"
    print "(2) output GFF file name\n"
    sys.exit()
else:
    in_fn = sys.argv[1]
    out_fn = sys.argv[2]

in_fh = open(in_fn, 'r')
out_fh = open(out_fn, 'w')

while 1:
    line = in_fh.readline()
    if not line: break
    line = line.strip()
    pieces = line.split("\t")
    start = int(pieces[3])
    end = int(pieces[4])
    middle = start + (end-start)/2;
    nStart = middle - 3000;
    nEnd = middle + 3000;
    name = pieces[0] + "_" + str(start) + "_" + str(end)
    out_fh.write(pieces[0] + "\t" + pieces[1] + "\t" + pieces[2] + "\t" + 
                 str(nStart) + "\t" + str(nEnd) + "\t" + pieces[5] + "\t" + 
                 pieces[6] + "\t" + pieces[7] + 
                 # '\tname \"' + name +'\"\n')
                 "\t" + name + "\n")

in_fh.close()
out_fh.close()