def optimize_model(self, treefile, seqfile, extra="-m GTRGAMMA -n test"): """Optimizes the RAxML model""" # initialize parameters based on input cmd = "raxmlHPC -t %s -s %s %s" %\ (treefile, seqfile, extra) raxml.init_program(self.adef, self.tr, cmd.split(' ')) # optimize raxml.optimize_model(self.adef, self.tr) # reset best LH if self.best_vector is not None: raxml.delete_best_vector(self.best_vector) self.best_vector, self.best_LH, self.weight_sum = raxml.compute_best_LH(self.tr) # set flags self.optimal = True
def __del__(self): raxml.delete_analdef(self.adef) raxml.delete_tree(self.tr) if self.best_vector is not None: raxml.delete_best_vector(self.best_vector)