computing the covariance matrix via plink

def computeCovarianceMatrixPlink(plink_path,out_dir,bfile,cfile,sim_type='RRM'):
    """
    computing the covariance matrix via plink
    """

    print("Using plink to create covariance matrix")
    cmd = '%s --bfile %s '%(plink_path,bfile)

    if sim_type=='RRM':
        # using variance standardization
        cmd += '--make-rel square '
    else:
        raise Exception('sim_type %s is not known'%sim_type)

    cmd+= '--out %s'%(os.path.join(out_dir,'plink'))

    subprocess.call(cmd,shell=True)

    # move file to specified file
    if sim_type=='RRM':
        old_fn = os.path.join(out_dir, 'plink.rel')
        os.rename(old_fn,cfile+'.cov')

        old_fn = os.path.join(out_dir, 'plink.rel.id')
        os.rename(old_fn,cfile+'.cov.id')

    if sim_type=='IBS':
        old_fn = os.path.join(out_dir, 'plink.mibs')
        os.rename(old_fn,cfile+'.cov')

        old_fn = os.path.join(out_dir, 'plink.mibs.id')
        os.rename(old_fn,cfile+'.cov.id')