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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Perform Simple mutations on an organism's genome.
"""
# standard modules
import random
from Bio._py3k import range
class SinglePositionMutation(object):
"""Perform a conversion mutation, but only at a single point in the genome.
This does not randomize the genome as much as ConversionMutation, since
only one change is allowed per genome at the specified mutation rate.
"""
def __init__(self, mutation_rate=0.001):
"""Initialize a mutator.
Arguments:
o mutation_rate - The chance of a mutation happening once in the
genome.
"""
self._mutation_rate = mutation_rate
# a random number generator to test if we have a mutation
self._mutation_rand = random.Random()
# a random number generator to switch to a new alphabet letter
self._switch_rand = random.Random()
# a random number generator to find the mutation position
self._pos_rand = random.Random()
def mutate(self, organism):
"""Mutate the organisms genome.
"""
mutated_org = organism.copy()
gene_choices = mutated_org.genome.alphabet.letters
mutation_chance = self._mutation_rand.random()
if mutation_chance <= self._mutation_rate:
# pick a gene position to mutate at
mutation_pos = \
self._pos_rand.choice(list(range(len(mutated_org.genome))))
# get a new letter to replace the position at
new_letter = self._switch_rand.choice(gene_choices)
mutated_org.genome[mutation_pos] = new_letter
return mutated_org
class ConversionMutation(object):
"""Potentially mutate any item to another in the alphabet.
This just performs switching mutation -- changing one gene of a genome
to any other potential gene, at some defined frequency. If the organism
is determined to mutate, then the alphabet item it is equally likely
to switch to any other letter in the alphabet.
"""
def __init__(self, mutation_rate=0.001):
"""Inititialize a mutator.
Arguments:
o mutation_rate -- The chance of a mutation happening at any
position in the genome.
"""
self._mutation_rate = mutation_rate
# a random number generator to test if we have a mutation
self._mutation_rand = random.Random()
# a random number generator to switch to a new alphabet letter
self._switch_rand = random.Random()
def mutate(self, organism):
"""Mutate the organisms genome.
"""
mutated_org = organism.copy()
gene_choices = mutated_org.genome.alphabet.letters
# potentially mutate any gene in the genome
for gene_index in range(len(mutated_org.genome)):
mutation_chance = self._mutation_rand.random()
# if we have a mutation
if mutation_chance <= self._mutation_rate:
# get a new letter
new_letter = self._switch_rand.choice(gene_choices)
mutated_org.genome[gene_index] = new_letter
return mutated_org
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