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 )