Example #1
0
def write_data(args):
    path, ext = os.path.splitext( args.out )
    tped_file = TPedFile( path + ".tped" )
    tfam_file = TFamFile( path + ".tfam" )
    pair_file = PairFile( path + ".pair" )
    
    write_genotypes( args, tped_file, tfam_file, pair_file )

    tped_file.close( )
    tfam_file.close( )
    pair_file.close( )
    
    status = os.system( "plink --tfile {0} --make-bed --out {1} > /dev/null".format( path, path ) )
    if status == -1:
        print( "Could not run plink, is it installed?" )
        exit( 1 )
def write_data(args):
    path, ext = os.path.splitext( args.out )
    ped_file = PedFile( path + ".ped" )
    map_file = MapFile( path + ".map" )
    pair_file = PairFile( path + ".pair" )

    cov_file = None
    if args.covariate:
        cov_file = CovFile( path + ".cov", [ c.name for c in args.covariate ] )
    
    write_genotypes( args, ped_file, map_file, pair_file, cov_file )

    ped_file.close( )
    map_file.close( )
    pair_file.close( )

    if args.covariate:
        cov_file.close( )
    
    status = os.system( "plink --file {0} --make-bed --out {1} > /dev/null".format( path, path ) )
    if status == -1:
        print( "Could not run plink, is it installed?" )
        exit( 1 )