Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Fetching contributors…
Cannot retrieve contributors at this time
177 lines (138 sloc) 5.04 KB
#!/usr/bin/env python
"""Tests for Genetic Algorithm classes that provide selection capabilities.
# standard library
import sys
import random
# biopython
from Bio.Seq import MutableSeq
# local stuff
from Bio.GA.Organism import Organism
from Bio.GA.Selection.Diversity import DiversitySelection
from Bio.GA.Selection.Tournament import TournamentSelection
from Bio.GA.Selection.RouletteWheel import RouletteWheelSelection
# PyUnit
import unittest
def run_tests(argv):
ALL_TESTS = [DiversitySelectionTest, TournamentSelectionTest,
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
for test in ALL_TESTS:
cur_suite = test_loader.loadTestsFromTestCase(test)
# --- helper classes and functions
class TestAlphabet:
"""Simple test alphabet.
letters = ["0", "1", "2", "3"]
def test_fitness(genome):
"""Simple class for calculating fitnesses.
genome_seq = genome.toseq()
return int(
class NoSelection:
"""A simple 'selection' class that just returns the generated population.
def select(self, population):
return population
class NoMutation:
"""Simple 'mutation' class that doesn't do anything.
def mutate(self, org):
return org.copy()
class NoCrossover:
"""Simple 'crossover' class that doesn't do anything.
def do_crossover(self, org_1, org_2):
return org_1.copy(), org_2.copy()
class NoRepair:
"""Simple 'repair' class that doesn't do anything.
def repair(self, org):
return org.copy()
def random_genome():
"""Return a random genome string.
alphabet = TestAlphabet()
new_genome = ""
for letter in range(3):
new_genome += random.choice(alphabet.letters)
return MutableSeq(new_genome, alphabet)
def random_organism():
"""Generate a random organism.
genome = random_genome()
return Organism(genome, test_fitness)
# --- the actual test classes
class AbstractSelectionTest(unittest.TestCase):
"""Some base tests that all selection classes should pass.
def setUp(self):
raise NotImplementError("Need to subclass and define a selector.")
def t_selection(self):
"""Test basic selection on a small population.
pop = []
for org_num in range(50):
new_pop =
assert len(new_pop) == len(pop), "Did not maintain population size."
class DiversitySelectionTest(AbstractSelectionTest):
"""Test selection trying to maximize diversity.
def setUp(self):
self.selector = DiversitySelection(NoSelection(), random_genome)
def t_get_new_organism(self):
"""Getting a new organism not in the new population.
org = random_organism()
old_pop = [org]
new_pop = []
new_org = self.selector._get_new_organism(new_pop, old_pop)
assert new_org == org, "Got an unexpected organism %s" % new_org
def t_no_retrive_organism(self):
"""Test not getting an organism already in the new population.
org = random_organism()
old_pop = [org]
new_pop = [org]
new_org = self.selector._get_new_organism(new_pop, old_pop)
assert new_org != org, "Got organism already in the new population."
class TournamentSelectionTest(AbstractSelectionTest):
"""Test selection based on a tournament style scheme.
def setUp(self):
self.selector = TournamentSelection(NoMutation(), NoCrossover(),
NoRepair(), 2)
def t_select_best(self):
"""Ensure selection of the best organism in a population of 2.
org_1 = random_organism()
while 1:
org_2 = random_organism()
if <
pop = [org_1, org_2]
new_pop =
for org in new_pop:
assert org == org_1, "Got a worse organism selected."
class RouletteWheelSelectionTest(AbstractSelectionTest):
"""Test selection using a roulette wheel selection scheme.
def setUp(self):
self.selector = RouletteWheelSelection(NoMutation(), NoCrossover(),
def t_select_best(self):
"""Ensure selection of a best organism in a population of 2.
worst_genome = MutableSeq("0", TestAlphabet())
worst_org = Organism(worst_genome, test_fitness)
better_genome = MutableSeq("1", TestAlphabet())
better_org = Organism(better_genome, test_fitness)
new_pop =[worst_org, better_org])
for org in new_pop:
assert org == better_org, "Worse organism unexpectly selected."
if __name__ == "__main__":
Jump to Line
Something went wrong with that request. Please try again.