def beagle(args):
    """
    %prog beagle input.vcf 1

    Use BEAGLE4.1 to impute vcf on chromosome 1.
    """
    p = OptionParser(beagle.__doc__)
    p.set_home("beagle")
    p.set_ref()
    p.set_cpus()
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    vcffile, chr = args
    pf = vcffile.rsplit(".", 1)[0]
    outpf = pf + ".beagle"
    outfile = outpf + ".vcf.gz"

    mm = MakeManager()
    beagle_cmd = opts.beagle_home
    kg = op.join(opts.ref, "1000GP_Phase3")
    cmd = beagle_cmd + " gt={0}".format(vcffile)
    cmd += " ref={0}/chr{1}.1kg.phase3.v5a.bref".format(kg, chr)
    cmd += " map={0}/plink.chr{1}.GRCh37.map".format(kg, chr)
    cmd += " out={0}".format(outpf)
    cmd += " nthreads=16 gprobs=true"
    mm.add(vcffile, outfile, cmd)

    mm.write()
def beagle ( args ) : p = OptionParser ( beagle . __doc__ ) p . set_home ( "beagle" ) p . set_ref ( ) p . set_cpus ( ) opts , args = p . parse_args ( args ) if len ( args ) != 2 : sys . exit ( not p . print_help ( ) ) vcffile , chr = args pf = vcffile . rsplit ( "." , 1 ) [ 0 ] outpf = pf + ".beagle" outfile = outpf + ".vcf.gz" mm = MakeManager ( ) beagle_cmd = opts . beagle_home kg = op . join ( opts . ref , "1000GP_Phase3" ) cmd = beagle_cmd + " gt={0}" . format ( vcffile ) cmd += " ref={0}/chr{1}.1kg.phase3.v5a.bref" . format ( kg , chr ) cmd += " map={0}/plink.chr{1}.GRCh37.map" . format ( kg , chr ) cmd += " out={0}" . format ( outpf ) cmd += " nthreads=16 gprobs=true" mm . add ( vcffile , outfile , cmd ) mm . write ( )
%prog beagle input.vcf 1

    Use BEAGLE4.1 to impute vcf on chromosome 1.