##################################
#                                #
# Last modified 07/08/2014       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string

try:
	import psyco
	psyco.full()
except:
	pass

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s ERANGEhtsfilename outfilename [-radiusAroundPeak bp]' % sys.argv[0]
        sys.exit(1)

    inputfilename = sys.argv[1]
    outputfilename = sys.argv[2]

    doRAP = False
    if '-radiusAroundPeak' in sys.argv:
        doRAP = True
        RAP = int(sys.argv[sys.argv.index('-radiusAroundPeak') + 1])

    outfile = open(outputfilename, 'w')

    lineslist = open(inputfilename)
    i=1
    for line in lineslist:
        if line[0]=='#':
            continue
        fields=line.split('\n')[0].split('\t')
        if doRAP:
            line = fields[1] + '\t' + str(int(fields[9]) - RAP) + '\t' + str(int(fields[9]) + RAP) + '\t'+str(i)+'\n'
        else:
            line=fields[1]+'\t'+fields[2]+'\t'+fields[3]+'\t'+str(i)+'\n'
        i+=1
        outfile.write(line)
                
    outfile.close()

run()