def computeCovarianceMatrix(plink_path,bfile,cfile,sim_type='RRM'):
    """
    compute similarity matrix using plink

    Input:
    plink_path   :   plink path
    bfile        :   binary bed file (bfile.bed, bfile.bim and bfile.fam are required)
    cfile        :   the covariance matrix will be written to cfile.cov and the corresponding identifiers
                         to cfile.cov.id. If not specified, the covariance matrix will be written to cfile.cov and
                         the individuals to cfile.cov.id in the current folder.
    sim_type     :   {IBS/RRM} are supported
    """
    try:
        output    = subprocess.check_output('%s --version --noweb'%plink_path,shell=True)
        m = re.match(b"^PLINK v(\d+\.\d+).*$", output)
        if m:
            use_plink = float(m.group(1)) >= 1.9
        else:
            use_plink = False
    except:
        use_plink = False

    assert bfile!=None, 'Path to bed-file is missing.'
    assert os.path.exists(bfile+'.bed'), '%s.bed is missing.'%bfile
    assert os.path.exists(bfile+'.bim'), '%s.bim is missing.'%bfile
    assert os.path.exists(bfile+'.fam'), '%s.fam is missing.'%bfile

    # create dir if it does not exist
    out_dir = os.path.split(cfile)[0]
    if out_dir!='' and (not os.path.exists(out_dir)):
        os.makedirs(out_dir)


    if use_plink:
        computeCovarianceMatrixPlink(plink_path,out_dir,bfile,cfile,sim_type=sim_type)
    else:
        computeCovarianceMatrixPython(out_dir,bfile,cfile,sim_type=sim_type)
def computeCovarianceMatrix ( plink_path , bfile , cfile , sim_type = 'RRM' ) : try : output = subprocess . check_output ( '%s --version --noweb' % plink_path , shell = True ) m = re . match ( b"^PLINK v(\d+\.\d+).*$" , output ) if m : use_plink = float ( m . group ( 1 ) ) >= 1.9 else : use_plink = False except : use_plink = False assert bfile != None , 'Path to bed-file is missing.' assert os . path . exists ( bfile + '.bed' ) , '%s.bed is missing.' % bfile assert os . path . exists ( bfile + '.bim' ) , '%s.bim is missing.' % bfile assert os . path . exists ( bfile + '.fam' ) , '%s.fam is missing.' % bfile out_dir = os . path . split ( cfile ) [ 0 ] if out_dir != '' and ( not os . path . exists ( out_dir ) ) : os . makedirs ( out_dir ) if use_plink : computeCovarianceMatrixPlink ( plink_path , out_dir , bfile , cfile , sim_type = sim_type ) else : computeCovarianceMatrixPython ( out_dir , bfile , cfile , sim_type = sim_type )
compute similarity matrix using plink

    Input:
    plink_path   :   plink path
    bfile        :   binary bed file (bfile.bed, bfile.bim and bfile.fam are required)
    cfile        :   the covariance matrix will be written to cfile.cov and the corresponding identifiers
                         to cfile.cov.id. If not specified, the covariance matrix will be written to cfile.cov and
                         the individuals to cfile.cov.id in the current folder.
    sim_type     :   {IBS/RRM} are supported