code: def computePCsPlink(plink_path,k,out_dir,bfile,ffile):
      
      print("Using plink to compute principal components")
      cmd = '%s --bfile %s --pca %d '%(plink_path,bfile,k)
      cmd+= '--out %s'%(os.path.join(out_dir,'plink'))
      subprocess.call(cmd,shell=True)
      plink_fn = os.path.join(out_dir, 'plink.eigenvec')
      M = sp.loadtxt(plink_fn,dtype=str)
      U = sp.array(M[:,2:],dtype=float)
      U-= U.mean(0)
      U/= U.std(0)
      sp.savetxt(ffile,U)
docs: computing the covariance matrix via plink