import gzip
import math
import sys
import cPickle as pickle
import argparse
    
def main(args):
    #arguements
    outname = args.out[0]
    cg_index = args.cgindex[0]
    #open cg index 
    try: index = open(cg_index,'r+b')
    except (IOError),err: 
        print 'Unable to open',cg_index 
        return
    try: outfile = open(outname,'w+b')
    except (IOError),err:
        print 'Unable to open',outname
        return
    cg=pickle.load(index)
    index.close()
    for chr in sorted(cg.keys()):
	for cpg in sorted(cg[chr]):
		outfile.write(str(chr)+'\t'+str(cpg)+'\n')


    print "Printing cgindex to ",outname



if __name__ == '__main__':
    parser = argparse.ArgumentParser(description = 'CG index to pickle file')
    parser.add_argument('--out',dest='out',nargs=1,type=str,help='Name for output file.')
    parser.add_argument('--cgindex', dest='cgindex',nargs=1,type=str,help='Input pickle index to be output as text.')
    args = parser.parse_args()
    main(args)