code: def readCovarianceMatrixFile(cfile,readCov=True,readEig=True):
      
      reading in similarity matrix
  
      cfile   File containing the covariance matrix. The corresponding ID file must be specified in cfile.id)
      """
      covFile = cfile+'.cov'
      evalFile = cfile+'.cov.eval'
      evecFile = cfile+'.cov.evec'
  
      RV = {}
      if readCov:
          assert os.path.exists(covFile), '%s is missing.'%covFile
          RV['K'] = SP.loadtxt(covFile)
      if readEig:
          assert os.path.exists(evalFile), '%s is missing.'%evalFile
          assert os.path.exists(evecFile), '%s is missing.'%evecFile
          RV['eval'] = SP.loadtxt(evalFile)
          RV['evec'] = SP.loadtxt(evecFile)
  
      return RV
docs: reading in similarity matrix
  
      cfile   File containing the covariance matrix. The corresponding ID file must be specified in cfile.id)