INNER CODE UNIT · Python

check_model_validity

nickjcroucher/gubbins · python/gubbins/common.py:778

def check_model_validity(current_model,current_tree_builder,mar,recon_model,model_fitter,custom_model,custom_recon_model):
    # Check substitution model consistent with tree building algorithm
    invalid_model = False
    # Determine model to be used for subsequent iterations
    if not custom_model and current_model not in tree_models[current_tree_builder]:
        sys.stderr.write('Evolutionary model ' + current_model +
                        ' and algorithm ' + current_tree_builder +
                         ' are incompatible\n')
        invalid_model = True
    # Determine model to be used for ancestral state reconstruction
    if not mar:
        if not custom_recon_model and recon_model not in tree_models[model_fitter]:
            sys.stderr.write('Evolutionary model ' + recon_model +
                            ' and algorithm ' + model_fitter +
                             ' are incompatible\n')
            invalid_model = True
    # Information for rectifying incompatible combinations
    if invalid_model:

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