htsohm.py 文件源码

def calculate_mutation_strength(run_id, generation, mutation_strength_bin):
    """Query mutation_strength for bin and adjust as necessary.

    Args:
        run_id (str): identification string for run.
        generation (int): iteration in bin-mutate-simulate routine.
        parent (sqlalchemy.orm.query.Query): parent-material corresponding to
            the bin being queried.

    Returns:
        mutation_strength.strength (float): mutation strength to be used for
        parents in the bin being queried. If the fraction of children from
        previous generation which populate the SAME bin as their parent is LESS
        THAN 10% then the mutation strength is REDUCED BY 5%. If the fraction
        of these children populating the SAME bin as their parent is GREATER
        THAN 50% then the mutation strength is INCREASED BY 5%.

    """
    mutation_strength_key = [run_id, generation] + mutation_strength_bin
    mutation_strength = session.query(MutationStrength).get(mutation_strength_key)

    if mutation_strength:
        print("Mutation strength already calculated for this bin and generation.")
    else:
        print("Calculating mutation strength...")
        mutation_strength = MutationStrength.get_prior(*mutation_strength_key).clone()
        if config['interactive_mode'] == 'on':
            print('Prior mutation strength :\t{}'.format(mutation_strength.strength))
        mutation_strength.generation = generation

        try:
            fraction_in_parent_bin = calculate_percent_children_in_bin(run_id, generation, mutation_strength_bin)

            if config['interactive_mode'] != 'on':
                if fraction_in_parent_bin < 0.1 and mutation_strength.strength - 0.05 > 0:
                    mutation_strength.strength -= 0.05
                elif fraction_in_parent_bin > 0.5 and mutation_strength.strength + 0.05 < 1:
                    mutation_strength.strength += 0.05

            elif config['interactive_mode'] == 'on':
                print('\tFor adaptive mutation strength(s), DECREASE strength \n' +
                        '\tby 5% if the fraction of children in parent-bin is \n' +
                        '\tLESS THAN 0.1; INCREASE strength by 5% if the \n' +
                        '\tfraction of children in parent-bin is GREATER THAN \n' +
                        '\t0.5.')
                mutation_strength.strength = set_variable(
                    'Please Enter new mutation strength :\t', 'mutation_strength.strength')
        except ZeroDivisionError:
            print("No prior generation materials in this bin with children.")

        try:
            session.add(mutation_strength)
            session.commit()
        except (FlushError, IntegrityError) as e:
            print("Somebody beat us to saving a row with this generation. That's ok!")
            session.rollback()
            # it's ok b/c this calculation should always yield the exact same result!
    sys.stdout.flush()
    return mutation_strength.strength