INNER CODE UNIT · Python

process_input_arguments

nickjcroucher/gubbins · python/gubbins/common.py:721

def process_input_arguments(input_args):
    # Alter settings if pairwise comparison of sequences
    if input_args.pairwise:
        input_args.iterations = 1
        input_args.model_fitter = 'fasttree'
        input_args.tree_builder = 'star'
        input_args.model = 'GTRGAMMA'
        if input_args.mar:
            sys.stderr.write('Cannot use marginal reconstruction for a pairwise comparison; switching to joint reconstruction')
            input_args.mar = False
    else:
        if input_args.tree_builder == 'hybrid':
            input_args.first_tree_builder = "fasttree"
            input_args.tree_builder = "raxml"
        # Parse IQtree in fast mode
        elif input_args.tree_builder == "iqtree-fast":
            input_args.tree_builder = "iqtree"
            input_args.tree_args = utils.extend_args(input_args.tree_args,"--fast")

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