gatk-3.8/python/vcf_b36_to_hg18.py

from farm_commands2 import *
import os
import sys
from optparse import OptionParser
from datetime import date
import glob
import operator
import faiReader
import math
import shutil
import string

def main():
    global OPTIONS
    usage = "usage: %prog [options] b36VCF hg18VCF"
    parser = OptionParser(usage=usage)
    parser.add_option("", "--dry", dest="dry",
                        action='store_true', default=False,
                        help="If provided, nothing actually gets run, just a dry run")
    parser.add_option("-r","--reverse",dest="reverse",action="store_true",default=False,help="If set, will convert the hg18VCF to a b36VCF (thus reversing the functionality)")
                       
    (OPTIONS, args) = parser.parse_args()
    if len(args) != 2:
        parser.error("incorrect number of arguments")

    b36vcf, hg18vcf = args

    temp = open("tmp", 'w')
    mitotemp = open("mtmp",'w')
    if not OPTIONS.reverse:
        for line in open(b36vcf):
            length = len(line)
            if length > 2 :
                if line[0:2] == 'MT' or line[0] == "#":
                    if line[0] == "#":
                        mitotemp.write(line)
                    else:
                        spline = line.split("\t")
                        spline[0] = "chrM"
                        mitotemp.write("\t".join(spline))
                else:
                    line = 'chr' + line
                    temp.write(line)
        temp.close()
        mitotemp.close()
        os.system("cat mtmp tmp > "+hg18vcf+" ; rm mtmp ; rm tmp")
    else:
        for line in open(hg18vcf):
            if line.startswith("#") :
                temp.write(line)
            else:
                spline = line.split("\t")
                if ( spline[0] == "chrM" ):
                    spline[0] = "MT"
                    mitotemp.write("\t".join(spline))
                else:
                    spline[0] = spline[0].split("chr")[1]
                    temp.write("\t".join(spline))
        temp.close()
        mitotemp.close()
        os.system("cat tmp mtmp > "+b36vcf+" ; rm mtmp ; rm tmp")

if __name__ == "__main__":
    main()