compute similarity matrix using plink

    Input:
    cfile        :   the covariance matrix will be read from cfile.cov while the eigenvalues and the eigenverctors will
                        be written to cfile.cov.eval and cfile.cov.evec respectively

def eighCovarianceMatrix(cfile):
    """
    compute similarity matrix using plink

    Input:
    cfile        :   the covariance matrix will be read from cfile.cov while the eigenvalues and the eigenverctors will
                        be written to cfile.cov.eval and cfile.cov.evec respectively
    """
    # precompute eigenvalue decomposition
    K = np.loadtxt(cfile+'.cov')
    K+= 1e-4*sp.eye(K.shape[0])
    S,U = la.eigh(K); S=S[::-1]; U=U[:,::-1]
    np.savetxt(cfile+'.cov.eval',S,fmt='%.6f')
    np.savetxt(cfile+'.cov.evec',U,fmt='%.6f')