code: def compute_eigenvalues(in_prefix, out_prefix):
      
      # First, we create the parameter file
      with open(out_prefix + ".parameters", "w") as o_file:
          print >>o_file, "genotypename:    " + in_prefix + ".bed"
          print >>o_file, "snpname:         " + in_prefix + ".bim"
          print >>o_file, "indivname:       " + in_prefix + ".fam"
          print >>o_file, "evecoutname:     " + out_prefix + ".evec.txt"
          print >>o_file, "evaloutname:     " + out_prefix + ".eval.txt"
          print >>o_file, "numoutlieriter:  0"
          print >>o_file, "altnormstyle:    NO"
  
      # Executing smartpca
      command = ["smartpca", "-p", out_prefix + ".parameters"]
      runCommand(command)
docs: Computes the Eigenvalues using smartpca from Eigensoft.
  
      :param in_prefix: the prefix of the input files.
      :param out_prefix: the prefix of the output files.
  
      :type in_prefix: str
      :type out_prefix: str
  
      Creates a "parameter file" used by smartpca and runs it.