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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 uniform crossovers between the genomes of two organisms.
| genome 1 -- A B C D E F G
| . . . .
| genome 2 -- a b c d e f g
|
| After crossover:
|
| new genome 1 -- a B c d E f G
| new genome 2 -- A b C D e F g
Uniform Crossover is a standard crossover technique for
rapid mutation-behavior.
"""
# standard modules
import random
class UniformCrossover(object):
"""Perform single point crossover between genomes at some defined rates.
This performs a single crossover between two genomes at some
defined frequency. The location of the crossover is chosen randomly
if the crossover meets the probability to occur.
"""
def __init__(self, crossover_prob=.1, uniform_prob=0.7):
"""Initialize to do uniform crossover at the specified probability and frequency.
"""
self._crossover_prob = crossover_prob
self._uniform_prob = uniform_prob
return
def do_crossover(self, org_1, org_2):
"""Potentially do a crossover between the two organisms.
"""
new_org_1 = org_1.copy()
new_org_2 = org_2.copy()
# determine if we have a crossover
crossover_chance = random.random()
if crossover_chance <= self._crossover_prob:
minlen = min(len(new_org_1.genome), len(new_org_2.genome))
for i in range(minlen):
uniform_chance = random.random()
if uniform_chance <= self._uniform_prob:
# cycle element
temp = new_org_1.genome[i]
new_org_1.genome[i] = new_org_2.genome[i]
new_org_2.genome[i] = temp
return new_org_1, new_org_2
|
