##################################
#                                #
# Last modified 2018/01/18       # 
#                                #
# Georgi Marinov                 #
#                                # 
##################################

import sys
import string

try:
    import psyco
    psyco.full()
except:
    print 'psyco not running'

def run():

    if len(sys.argv) < 2:
        print 'usage: python %s input outfile' % sys.argv[0]
        sys.exit(1)

    input = sys.argv[1]
    outfile = open(sys.argv[2],'w')

    listoflines = open(input)
    for line in listoflines:
        fields = line.strip().split('\t')
        if line.startswith('chromosome'):
            outline = '#' + fields[0] + '\t' + fields[1] + '\t' + fields[2] + '\t' + fields[3] + '\t' + '.\t' + fields[4] + '\t' + fields[5] + '\t' + fields[6] + '\t' + fields[7]
        elif line.startswith('#'):
            outline = fields[0] + '\t' + fields[1] + '\t' + fields[2] + '\t' + fields[3] + '\t' + '.\t' + fields[4] + '\t' + fields[5] + '\t' + fields[6] + '\t' + fields[7]
        else:
            outline = fields[0] + '\t' + fields[1].split('.')[0] + '\t' + fields[2].split('.')[0] + '\t' + fields[3] + '\t' + '.\t' + fields[4] + '\t' + fields[5] + '\t' + fields[6] + '\t' + fields[7]
        outfile.write(outline + '\n')
        
    outfile.close()

run()