def create_genius(self):
genius = DNA()
genius.dna = [ 3,0.06,0.0001,10,5, # PID Ramp Up
7,0.05,0,2,5, # PID Overshoot Over
1,0.04,0.01,5,10, # PID Hold Over
10,0.03,0,2,5, # PID Land Over
0.9,0.04,0.01,5,10, # PID Hold
3,0.06,0.0001,10,5, # PID Ramp Down
7,0.05,0,2,5, # PID Overshoot Under
1,0.04,0.01,5,10, # PID Hold Under
10,0.03,0,2,5, # PID Land Under
2.8, # Max Heat Overshoot
3.4, # Max Cool Overshoot
2, # Heat Sample Window
2, # Cool Sample Window
40, # Max Hold Power
150, # Max Ramp Power
4, # Heat Block Window
3, # Cool Block Window
1.2, # Heat Overshoot Attenuation
0.2, # Heat Overshoot Activation RR
0.1, # Heat Overshoot Activation SP
1.5, # Cool Overshoot Attenuation
0.3, # Cool Overshoot Activation RR
-0.1, # Cool Overshoot Activation SP
1.6, # Temp Ctrl Over RR Limit
1.5, # Temp Ctrl Under RR Limit
1.5, # Temp Ctrl Over Block Window
1.75, # Temp Ctrl Under Block Window
]
return genius
class TestGetPair(unittest.TestCase):
def setUp(self):
self.dna = DNA()
def test_lowercase(self):
self.dna.to_pair = "a"
self.dna.get_pair()
self.assertEqual(self.dna.to_pair, "A")
def test_a_t(self):
self.dna.to_pair = "A"
self.dna.get_pair()
self.assertEqual(self.dna.pair, "T")
def test_t_a(self):
self.dna.to_pair = "T"
self.dna.get_pair()
self.assertEqual(self.dna.pair, "A")
def test_g_c(self):
self.dna.to_pair = "G"
self.dna.get_pair()
self.assertEqual(self.dna.pair, "C")
def test_c_g(self):
self.dna.to_pair = "C"
self.dna.get_pair()xb
self.assertEqual(self.dna.pair, "G")
def main():
# Open master image in RGB mode
master_image = Image.open("obama.png").convert(mode="RGB")
width, height = master_image.size
# Create initial polygons
polygons = []
for i in range(200):
x_points = np.random.random_integers(low=0,high=width,size=3).tolist()
y_points = np.random.random_integers(low=0,high=height,size=3).tolist()
points = zip(x_points, y_points)
color = tuple(np.random.random_integers(low=0, high=255, size=4).tolist())
polygon = Polygon(points, color)
polygons.append(polygon)
# Create initial DNA
parent = DNA(polygons, master_image)
# Evolve DNA and breed fittest
for i in range(1000):
child = parent.breed()
if child.fitness < parent.fitness:
parent = child
# Save image and polygon information
parent.save()
def __init__(self,
gameDisplay,
w=40,
h=40,
snake_len=3,
life=10000,
food_energy=10,
dna=None,
color=None):
self.w = w
self.h = h
self.body = []
self.xdir = 1
self.ydir = 0
self.dir = 1
self.grow = False
self.snake_len = snake_len
self.gameDisplay = gameDisplay
self.create_snake()
self.died = False
if color is None:
self.color = (randint(0, 255), randint(0, 255), randint(0, 200))
else:
self.color = (randint(0, 255), randint(0, 255), randint(0, 200))
self.score = 0
self.life = life
self.life_orig = life
self.food_energy = food_energy
if dna is None:
self.dna = DNA(6, 4, [0, 10])
else:
self.dna = dna
self.food = []
self.cur_state = None
self.reward = 0
def test_container_inequality(self):
dna1 = DNA([ScoreCard(1, 10), ScoreCard(2, 20)])
dna2 = DNA([ScoreCard(3, 30), ScoreCard(4, 40)])
self.assertNotEqual(dna1, dna2)
container1 = Container(dna1, 1)
container2 = Container(dna2, 1)
self.assertNotEqual(container1, container2)
self.assertNotEqual(container1.__hash__(), container2.__hash__())
def test():
test_input = "A A T G C C T A T G G C"
expected_output = "A A T G C C T A T G G C\nT T A C G G A T A C C G"
dna = DNA()
strand = dna.get_strand(test_input)
print "Output:\n%s" % (strand)
print "Expected:\n%s" % (expected_output)
if strand == expected_output: print "PASS"
else: print "FAIL"
def random_dna(self):
population_dna = []
for _ in range(self.population):
dna = DNA(self.goal_len)
dna.random_dna()
population_dna.append(dna)
return population_dna
def crossover(self, first, second):
point = random.randint(0, len(self.aim) - 1)
new_dna = DNA(self.aim, self.mutation_rate)
for i in range(len(self.aim)):
if i <= point:
new_dna.dna.append(first.dna[i])
else:
new_dna.dna.append(second.dna[i])
new_dna.calc_fitness()
return new_dna
class TestGetOutput(unittest.TestCase):
def setUp(self):
self.dna = DNA()
def test_output(self):
self.dna.in_sequence = "1234"
self.dna.out_sequence = "5678"
self.dna.get_output()
expected = "1234\n5678"
self.assertEqual(self.dna.strand, expected)
class DNAVis(Widget):
def __init__(self, **kw):
super(DNAVis, self).__init__(**kw)
self.dna = DNA()
self.crawler = self.dna.spawn_crawler()
self.bind(size=self.redraw, pos=self.redraw)
def redraw(self, *ar):
for w in self.children[:]:
if isinstance(w, NodeVis):
self.remove_widget(w)
node_lookup = {}
y = self.top - 100
crawler = self.dna.spawn_crawler()
crawler.reset()
indent = 100
for n, indent_no in crawler.crawl_indents():
indent += 100 * indent_no
nv = NodeVis(size=(100, 100), text=n.name)
node_lookup[n] = nv
nv.x = self.x + indent
nv.y = y
self.add_widget(nv)
y -= 100
crawler = self.crawler
cv = NodeVis(size=(100, 100), text="CRAWLER", color=[0.7, 0.05, 0])
if crawler.current_node is not None:
cv.x = node_lookup[crawler.current_node].x - 100
cv.y = node_lookup[crawler.current_node].y
else:
cv.y = self.top - 100
cv.x = self.width - cv.width
self.add_widget(cv)
def eval_input(self, text):
dna = self.dna
crawler = self.crawler
if not hasattr(self, "exec_locals"):
self.exec_locals = locals()
try:
to_run = compile(text, "", "exec")
exec(to_run, globals(), self.exec_locals)
except (NameError, SyntaxError, AttributeError, TypeError) as err:
print(err)
self.redraw()
def test_does_not_actually_shorten_original_strand(self):
self.assertEqual(
1,
DNA('AGACAACAGCCAGCCGCCGGATT').hamming_distance('AGGCAA'))
self.assertEqual(
4,
DNA('AGACAACAGCCAGCCGCCGGATT').hamming_distance(
'AGACATCTTTCAGCCGCCGGATTAGGCAA'))
self.assertEqual(
1,
DNA('AGACAACAGCCAGCCGCCGGATT').hamming_distance('AGG'))
def create_population(self, pop_size, genius=None):
population = []
for i in range(0, pop_size):
creature = DNA()
creature.generate_DNA()
population.append(creature)
if genius != None:
population = population[:-1] + [genius]
return population
def _get_query_seqs(count_start, ref, ref_complement, sRNA_length):
"""
:param count_start:
:param ref:
:param ref_complement:
:param sRNA_length:
:return:
"""
query_seq_fwd = DNA(ref[count_start:(count_start + sRNA_length)])
query_seq_rvs = DNA(ref_complement[count_start:(count_start +
sRNA_length)])
return query_seq_fwd, query_seq_rvs
def run(self, pcr_model_path="hybrid_pcr_model.ml", record_path=None, warm_up=True, stagnant_period=None):
population = []
if warm_up:
best_creature = self.create_genius()
else:
best_creature = DNA()
best_creature.generate_DNA()
best_creature.score = -1000000
cgeneration = 0
if stagnant_period == None:
stagnant_period = self.max_generation
# Increase mutation chance if the fitness score not improved over generations
# Reach the mutation limit in half of the stagnant period
mutation_initial_value = self.mutation_chance
mutation_step = (self.mutation_limit - mutation_initial_value) / stagnant_period * 2
for noGeneration in range(0, self.max_generation):
population = self.breed_population(population=population, genius=best_creature)
print(f"-------- Generation={noGeneration} / {self.max_generation} Population={len(population)} --------")
for loc, creature in enumerate(population):
self.eval_fitness_score(creature=creature, pcr_model=self.load_model(pcr_model_path))
print(f"Creature {loc} scores {creature.score:.2f} fitness points")
# Rank the creature fitness scores
population.sort(key=self.getScore, reverse=True)
# Kill the bottom half of the population
population = population[:self.pop_size // 2]
if population[0].score > best_creature.score:
best_creature = population[0].copy()
self.mutation_chance = mutation_initial_value
cgeneration = 0
print(f"*** Generation {noGeneration} new genius scores {best_creature.score} fitness points\n\n")
else:
cgeneration += 1
if self.mutation_chance < self.mutation_limit:
self.mutation_chance += mutation_step
print(f"-------- Stagnant Period = {cgeneration} / {stagnant_period}")
if cgeneration >= stagnant_period:
print(f"WARNING: Population quality has reach its peak. Algorithm ends.\n")
break
print("==============================================================")
print(f"The best creature score is {best_creature.score:.2f} fitness points")
self.export_creature(creature=best_creature,
filepath=record_path[:-4] + f"score{int(best_creature.score)}" + record_path[-4:],
pcr_model_path=pcr_model_path,)
def __init__(self, dna = -1):
# Genetic
if dna == -1:
self.dna = DNA()
else:
self.dna = deepcopy(dna)
self.dna.mutate()
# Copying evaluation function
m, b = self.dna.eval_data
self.evaluate = lambda x: m * x + b > 0
# Cultural
self.meme = np.random.choice([0, 1], size = str_len)
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem6')
solution_dir = os.path.join("Problems", "Problem6Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
genome = case[0]
k = case[1][0]
l = case[1][1][0]
t = case[1][1][1]
dna = DNA(genome)
clumps_patterns = dna.get_clumps_patterns(int(k), int(t), int(l))
if clumps_patterns.sort() != case_output.sort():
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + clumps_patterns)
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output), len(test_cases)):
usage.start()
case = test_cases[test_i]
genome = case[0]
k = case[1][0]
l = case[1][1][0]
t = case[1][1][1]
dna = DNA(genome)
clumps_patterns = dna.get_clumps_patterns(int(k), int(t), int(l))
usage.end()
writer.write_data(test_i, clumps_patterns, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + genome + "\n" + str(k) + " " + str(l) + " " + str(t))
print("\n\nOutput")
print("=====")
for clump in clumps_patterns:
print(clump)
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def generate_dna_from(alpha, beta):
# handler = JSONHandler()
# handler.load_file("./data/pudgies/" + alpha + ".json")
# alpha_json = handler.get_data()
# handler.load_file("./data/pudgies/" + beta + ".json")
# beta_json = handler.get_data()
#
# alpha_dna = DNA(alpha_json["dna"])
# beta_dna = DNA(beta_json["dna"])
alpha_dna = DNA(alpha["dna"])
beta_dna = DNA(beta["dna"])
strand = DNA.combine_dna(alpha_dna, beta_dna)
return DNA(strand)
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem2')
solution_dir = os.path.join("Problems", "Problem2Solution")
data_reader = DataReader(problem_dataset_dir)
training_data, testing_data = data_reader.get_data()
codons_table = data_reader.get_rna_codon_table()
for sample in training_data:
dna_string = sample[0][0]
amino_acid = sample[0][1]
output = sample[1]
dna = DNA(dna_string)
dna.set_codon_table(codons_table)
candidates = dna.get_dna_to_amino_acid_candidates(amino_acid)
if set(candidates) != set(output):
raise Exception("Output not matched!\nExpecting: " + str(output) +
"\nFound: " + str(candidates))
print("Passed training data..\n\n")
writer = DataWriter(solution_dir)
usage = Usage()
for sample in testing_data:
usage.start()
dna_string = sample[0][0]
amino_acid = sample[0][1]
dna = DNA(dna_string)
dna.set_codon_table(codons_table)
candidates = dna.get_dna_to_amino_acid_candidates(amino_acid)
usage.end()
writer.write_data((dna_string, amino_acid), candidates,
usage.get_execution_time(), usage.get_memory_usage())
print("DNA:\n" + dna_string)
print("Protein\n" + amino_acid)
print("\n\nOutput")
print("=====")
print(str(len(candidates)))
for substring in candidates:
print(substring)
print("\n\nExecution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Usage: " + str(usage.get_memory_usage()) + " MB")
def selection1(self):
m = DNA.get_total_fitness()
num1 = random.randint(1, m + 10)
num2 = random.randint(1, m + 10)
num_1 = num1
num_2 = num2
first_population = None
second_population = None
i = 0
while first_population == None or second_population == None:
if first_population == None:
num1 -= self.population[4].fitness
if num1 <= 0:
first_population = self.population[i]
if second_population == None:
num2 -= self.population[2].fitness
if num2 <= 0:
second_population = self.population[i]
i += 1
if i >= self.strength:
if num2 == num_2 or num1 == num_1:
first_population = self.population[random.randint(
0, self.strength - 1)]
second_population = self.population[random.randint(
0, self.strength - 1)]
else:
i = 0
return {'first': first_population, 'second': second_population}
def generate_random_creature(self):
return BrainCreature(x=random.uniform(0, self.width),
y=random.uniform(0, self.height),
dna=DNA(),
brain_dna=BrainDNA(),
name='Creature ' +
str(creature_id_generator.get_next_id()))
def _CreatesPop(self):
self.members = [
DNA(func=self.func,
upper_bound_vector=self.upper_bound,
lower_bound_vector=self.lower_bound,
size=len(self.upper_bound)) for _ in range(self.pop_size)
]
def snakes_init(self):
self.snakes = []
for i in range(0, self.population):
if self.dna is None:
snake_dna = DNA()
snake_dna.Q_table = self.load_dna()
self.dna = snake_dna
else:
snake_dna = self.dna
snake = Snake(self.gameDisplay,
self.w,
self.h,
snake_len=SNAKE_LEN,
life=LIFE,
food_energy=FOOD_ENERGY,
dna=snake_dna)
self.snakes.append(snake)
def __init__(self):
self.gene_pool = []
for index in range(self.POPULATION_SIZE):
new_dna = DNA()
self.gene_pool.append(new_dna)
heapq.heapify(self.gene_pool)
def __init__(self, num):
self.num = num
self.food = Food(num)
self.bloops = []
for i in range(num):
loc = PVector(random(width), random(height))
dna = DNA()
self.bloops.append(Bloop(dna, loc))
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem9')
solution_dir = os.path.join("Problems", "Problem9Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
genome = case[0]
k = case[1][0]
d = case[1][1]
dna = DNA(genome)
k_mers = dna.most_frequent_missmatched_k_mer(int(k), int(d))
if set(case_output) != set(k_mers):
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + str(k_mers))
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output) + 1, len(test_cases)):
usage.start()
case = test_cases[test_i]
genome = case[0]
k = case[1][0]
d = case[1][1]
dna = DNA(genome)
k_mers = dna.most_frequent_missmatched_k_mer(int(k), int(d))
usage.end()
writer.write_data(test_i, k_mers, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + genome + "\n" + str(k) + "\n" + str(d))
print("\n\nOutput")
print("=====")
print('\n'.join(map(lambda v: str(v), k_mers)))
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem5')
solution_dir = os.path.join("Problems", "Problem5Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
pattern = case[0]
genome = case[1]
dna = DNA(genome)
pattern_indices = dna.get_pattern_indices(pattern)
if pattern_indices != case_output:
raise Exception("Output not matched!\nExpecting: " +
str(case_output) + "\nFound: " + pattern_indices)
def __init__(self):
self.win = tk.Tk()
self.configWin()
self.spawnTarget()
self.spawnObst()
self.pop = Population(100, self.canv, self.targetPos, self.obstPos)
self.LIFESPAN = DNA().LIFESPAN
self.cnt = 0
self.win.mainloop()
def create_initial_population(self):
"""
Create an initial population consisting of *population_size*
primitive neural networks with an input-output structure
"""
for individual_i in range(self.population_size):
individual_dna = DNA(Settings.INPUT_SHAPE, Settings.OUTPUT_SHAPE)
individual_dna.create_primitive_structure()
individual_fitness = self.build_and_train_network(individual_dna)
self.population.append(individual_dna)
self.fitness.append(individual_fitness)
self.best_generations_fitness.append(min(self.fitness))
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem5')
solution_dir = os.path.join("Problems", "Problem5Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
pattern = case[0]
genome = case[1]
dna = DNA(genome)
pattern_indices = dna.get_pattern_indices(pattern)
if pattern_indices != case_output:
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + pattern_indices)
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output), len(test_cases)):
usage.start()
case = test_cases[test_i]
pattern = case[0]
genome = case[1]
dna = DNA(genome)
pattern_indices = dna.get_pattern_indices(pattern)
usage.end()
writer.write_data(test_i + 1, pattern_indices, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + pattern + "\n" + genome)
print("\n\nOutput")
print("=====")
print(pattern_indices)
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def generate_population(self):
self.population = []
for i in range(self.population_size):
# generating DNA of an individual
self.population.append(DNA(len(self.target)))
# generating random genes of an individual
self.population[i].generate_random_genes()
self.generation += 1
def import_from_json(self, load):
self.handler.load_file(load)
self.json_object = self.handler.get_data()
self.name = self.json_object["name"]
self.uid = self.json_object["uid"]
self.parents = self.json_object["parents"]
self.personality = self.json_object["personality"]
self.color = self.json_object["color"]
self.happiness = self.json_object["happiness"]
strand = self.json_object["dna"]
self.dna = DNA(strand)
self.handler.close()
logger.logging.info("---Importing Pudgi---")
logger.logging.info("UID: " + str(self.uid))
logger.logging.info("Name: " + self.name)
logger.logging.info("Color: " + self.color)
logger.logging.info("Personality: " + self.personality)
logger.logging.info("Parents: " + str(self.parents))
def reproduction(self):
new_population = []
for i in range(self.population_size):
individual = DNA.cross_over(self.parents, len(self.target))
individual.mutate(self.mutation_rate)
new_population.append(individual)
self.population = new_population
self.generation += 1
def generatePopulation(self):
for i in range(self.populationSize):
#Creates a new dna object
dna = deepcopy(DNA())
gene = GenePolygon(_canvasSize=self.canvasSize)
dna.createGenes(gene=gene, n=self.geneCount)
#Creates a new member with the dna
member = Member(_dna=dna)
#Adds the member to the population
self.population.addMember(member)
def initialize_genes(self, dna):
if dna is not None:
self.dna = dna
else:
self.dna = DNA(4)
self.probability_of_turn = self.dna.get_gene(0) * 0.1 / 100
self.angle_of_rotation = self.dna.get_gene(1) / 255 * self.TWO_PI
self.speed = self.dna.get_gene(2) / 255.0 * 10
self.probability_turn_direction = self.dna.get_gene(3) / 255.0 * 10
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem9')
solution_dir = os.path.join("Problems", "Problem9Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
genome = case[0]
k = case[1][0]
d = case[1][1]
dna = DNA(genome)
k_mers = dna.most_frequent_missmatched_k_mer(int(k), int(d))
if set(case_output) != set(k_mers):
raise Exception("Output not matched!\nExpecting: " +
str(case_output) + "\nFound: " + str(k_mers))
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem17')
solution_dir = os.path.join("Problems", "Problem17Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
dna = test_cases[train_i][0]
k = test_cases[train_i][1][0]
score_matrix = test_cases[train_i][1][1]
case_output = output[train_i]
most_probable_k_mer = DNA(dna).get_most_probable_k_mer(int(k), score_matrix)
if most_probable_k_mer != case_output:
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + str(most_probable_k_mer))
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output) - 1, len(test_cases)):
usage.start()
dna = test_cases[test_i][0]
k = test_cases[test_i][1][0]
score_matrix = test_cases[test_i][1][1]
most_probable_k_mer = DNA(dna).get_most_probable_k_mer(int(k), score_matrix)
usage.end()
writer.write_data(test_i + 1, most_probable_k_mer, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + str(dna) + "\n" + str(k) + "\n" + str(score_matrix))
print("\n\nOutput")
print("=====")
print(most_probable_k_mer)
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem6')
solution_dir = os.path.join("Problems", "Problem6Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
genome = case[0]
k = case[1][0]
l = case[1][1][0]
t = case[1][1][1]
dna = DNA(genome)
clumps_patterns = dna.get_clumps_patterns(int(k), int(t), int(l))
if clumps_patterns.sort() != case_output.sort():
raise Exception("Output not matched!\nExpecting: " +
str(case_output) + "\nFound: " + clumps_patterns)
def setUp(self):
self.dna = DNA()
self.n1 = TestNode('node1')
self.n2 = TestNode('node2')
self.n3 = TestNode('node3')
self.n4 = TestNode('node4')
self.dna.head = self.n1
self.crawler = self.dna.spawn_crawler()
self.crawler.attach_to(self.n1)
def __init__(self,
x: float,
y: float,
dna: DNA = DNA(),
brain_dna: DNA = BrainDNA(),
direction: float = 0.0,
name: str = 'object',
health: int = None):
super().__init__(x, y, dna, direction, name, health=health)
# objective function
self.brain = Brain(brain_dna)
def run(self, target_string):
self.target = DNA(target_string)
self.generations = self._initialise(target_string)
result = []
while True:
next_generation = self.generations[-1].next_generation(self.target)
result.append(self.generations[-1].best_fit())
if result[-1][0] == target_string or len(result) > 1000:
break
self.generations.append(next_generation)
return result
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem7')
solution_dir = os.path.join("Problems", "Problem7Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = np.array(output[train_i])
dna = DNA(case.strip())
min_skew_indices = dna.get_min_skew()
if not np.array_equal(case_output, min_skew_indices):
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + str(min_skew_indices))
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output), len(test_cases)):
usage.start()
case = test_cases[test_i]
dna = DNA(case.strip())
min_skew_indices = dna.get_min_skew()
usage.end()
writer.write_data(test_i + 1, min_skew_indices, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + case + "\n")
print("\n\nOutput")
print("=====")
print(list(min_skew_indices))
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem13')
solution_dir = os.path.join("Problems", "Problem13Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
(k, genome) = test_cases[train_i]
case_output = output[train_i]
dna = DNA(genome)
k_mers = dna.get_k_mers(int(k))
if sorted(case_output) != sorted(k_mers):
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + str(k_mers))
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output), len(test_cases)):
usage.start()
(k, genome) = test_cases[test_i]
dna = DNA(genome)
k_mers = dna.get_k_mers(int(k))
usage.end()
writer.write_data(test_i + 1, k_mers, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + k + "\n" + genome + "\n")
print("\n\nOutput")
print("=====")
print(k_mers)
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem4')
solution_dir = os.path.join("Problems", "Problem4Solution")
data_reader = DataReader(problem_dataset_dir)
test_cases, output = data_reader.get_data()
for train_i in range(0, len(output)):
case = test_cases[train_i]
case_output = output[train_i]
dna = DNA(case)
reverse_complement = dna.reverse_complement()
if reverse_complement != case_output:
raise Exception("Output not matched!\nExpecting: " + str(case_output) + "\nFound: " + reverse_complement)
print("Passed training data..")
writer = DataWriter(solution_dir)
usage = Usage()
for test_i in range(len(test_cases) - len(output), len(test_cases)):
usage.start()
case = test_cases[test_i]
dna = DNA(case)
reverse_complement = dna.reverse_complement()
usage.end()
writer.write_data(test_i + 1, reverse_complement, usage.get_execution_time(), usage.get_memory_usage())
print("\n\nInput:\n" + case)
print("\n\nOutput")
print("=====")
print(reverse_complement)
print("\n")
print("======")
print("Execution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Used: " + str(usage.get_memory_usage()) + " MB")
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem2')
solution_dir = os.path.join("Problems", "Problem2Solution")
data_reader = DataReader(problem_dataset_dir)
training_data, testing_data = data_reader.get_data()
codons_table = data_reader.get_rna_codon_table()
for sample in training_data:
dna_string = sample[0][0]
amino_acid = sample[0][1]
output = sample[1]
dna = DNA(dna_string)
dna.set_codon_table(codons_table)
candidates = dna.get_dna_to_amino_acid_candidates(amino_acid)
if set(candidates) != set(output):
raise Exception("Output not matched!\nExpecting: " + str(output) + "\nFound: " + str(candidates))
print("Passed training data..\n\n")
writer = DataWriter(solution_dir)
usage = Usage()
for sample in testing_data:
usage.start()
dna_string = sample[0][0]
amino_acid = sample[0][1]
dna = DNA(dna_string)
dna.set_codon_table(codons_table)
candidates = dna.get_dna_to_amino_acid_candidates(amino_acid)
usage.end()
writer.write_data((dna_string, amino_acid), candidates, usage.get_execution_time(), usage.get_memory_usage())
print("DNA:\n" + dna_string)
print("Protein\n" + amino_acid)
print("\n\nOutput")
print("=====")
print(str(len(candidates)))
for substring in candidates:
print(substring)
print("\n\nExecution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Usage: " + str(usage.get_memory_usage()) + " MB")
class TestGetSequence(unittest.TestCase):
def setUp(self):
self.dna = DNA()
def test_integration_normal(self):
self.dna.in_sequence = "AATGACCT"
expected = "TTACTGGA"
self.dna.get_sequence()
self.assertEqual(self.dna.out_sequence, expected)
def test_integration_mixed_case(self):
self.dna.in_sequence = "aAtgAcCt"
expected = "TTACTGGA"
self.dna.get_sequence()
self.assertEqual(self.dna.out_sequence, expected)
def test_integation_bad_input(self):
self.dna.in_sequence = "1234567"
with self.assertRaises(Exception) as e:
self.dna.get_sequence()
self.assertEqual(e.exception.message, "Not a DNA base")
class tests(test_utils):
def setUp(self):
self.dna = DNA()
self.n1 = TestNode('node1')
self.n2 = TestNode('node2')
self.n3 = TestNode('node3')
self.n4 = TestNode('node4')
self.dna.head = self.n1
self.crawler = self.dna.spawn_crawler()
self.crawler.attach_to(self.n1)
# test inserting (before, after, child)
def test_1_insert_before(self):
self.crawler.add_before(self.n2)
self.check_seq(self.n2, self.n1)
self.assertIsNone(self.n2.dna_node_prev_sib)
self.assertIsNone(self.n1.dna_node_next_sib)
def test_2_insert_after(self):
self.crawler.add_after(self.n2)
self.check_seq(self.n1, self.n2)
self.assertIsNone(self.n1.dna_node_prev_sib)
self.assertIsNone(self.n2.dna_node_next_sib)
def test_3_insert_child(self):
self.crawler.add_child(self.n3)
self.check_child(self.n1, self.n3)
# test removing
def test_4_remove_head(self):
c = self.crawler
c.add_after(self.n2, self.n1)
c.add_after(self.n3, self.n2)
c.remove(self.n1)
self.assertRaises(AssertionError, self.check_seq, self.n1, self.n2)
self.assertIsNone(self.n1.dna_node_next_sib)
def test_5_remove_tail(self):
c = self.crawler
c.add_after(self.n2, self.n1)
c.add_after(self.n3, self.n2)
c.remove(self.n3)
self.assertRaises(AssertionError, self.check_seq, self.n2, self.n3)
self.assertIsNone(self.n3.dna_node_prev_sib)
def test_6_remove_middle(self):
c = self.crawler
c.add_after(self.n2, self.n1)
c.add_after(self.n3, self.n2)
c.remove(self.n2)
self.check_seq(self.n1, self.n3)
self.assertIsNone(self.n2.dna_node_next_sib)
self.assertIsNone(self.n2.dna_node_prev_sib)
def test_7_remove_child(self):
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_after(self.n3, self.n2)
c.remove(self.n2)
self.check_child(self.n1, self.n3)
self.assertIsNone(self.n2.dna_node_parent)
self.assertIsNone(self.n2.dna_node_next_sib)
self.assertIsNone(self.n2.dna_node_prev_sib)
# test low-level traversing
def test_8_traverse_sibs(self):
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_after(self.n3, self.n1)
self.assertIs(self.n1, c.current_node)
self.assertIs(self.n3, c.next_sib())
self.assertIsNone(c.next_sib())
def test_9_traverse_node_flat(self):
c = self.crawler
c.add_after(self.n2, self.n1)
c.add_after(self.n3, self.n2)
self.assertIs(self.n1, c.current_node)
self.assertIs(self.n2, c.next_node())
self.assertIs(self.n3, c.next_node())
self.assertIsNone(c.next_node())
def test_10_traverse_node_wchild(self):
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_after(self.n3, self.n1)
c = self.crawler
self.assertIs(self.n1, c.current_node)
self.assertIs(self.n2, c.next_node())
self.assertIs(self.n3, c.next_node())
self.assertIsNone(c.next_node())
# test crawling
def test_11_crawl_sibs(self):
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_after(self.n3, self.n1)
gen = c.crawl_sibs()
self.assertIs(self.n1, gen.next())
self.assertIs(self.n3, gen.next())
self.assertRaises(StopIteration, gen.next)
def test_12_crawl_flat(self):
c = self.crawler
c.add_after(self.n2, self.n1)
c.add_after(self.n3, self.n2)
gen = c.crawl()
self.assertIs(self.n1, gen.next())
self.assertIs(self.n2, gen.next())
self.assertIs(self.n3, gen.next())
self.assertRaises(StopIteration, gen.next)
def test_13_crawl_wchild(self):
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_after(self.n3, self.n1)
gen = c.crawl()
self.assertIs(self.n1, gen.next())
self.assertIs(self.n2, gen.next())
self.assertIs(self.n3, gen.next())
self.assertRaises(StopIteration, gen.next)
def test_14_crawl_w_mul_children(self):
"""
Tests that when traversing this stucture we correctly jump from n3 to
n4.
n1 -- n2 -- n3
|
n4
"""
c = self.crawler
c.add_child(self.n2, self.n1)
c.add_child(self.n3, self.n2)
c.add_after(self.n4, self.n1)
gen = c.crawl()
self.assertIs(self.n1, gen.next())
self.assertIs(self.n2, gen.next())
self.assertIs(self.n3, gen.next())
self.assertIs(self.n4, gen.next())
self.assertRaises(StopIteration, gen.next)
def setUp(self):
self.dna = DNA()
class Creature:
TWO_PI = 6.283185
#location (x, y) and window_size (width, height)
def __init__(self, location, window_size, image, batch, dna = None):
self.window_width, self.window_height = window_size
self.initialize_image(image, batch)
self.initialize_genes(dna)
self.initialize_attributes(location)
def initialize_image(self, image, batch):
self.sprite = pyglet.sprite.Sprite(image, batch=batch)
self.sprite.image.anchor_x = self.sprite.width / 2
self.sprite.image.anchor_y = self.sprite.height / 2
self.sprite_boundary_width = self.sprite.width / 2
self.sprite_boundary_height = self.sprite.height / 2
def initialize_genes(self, dna):
if dna is not None:
self.dna = dna
else:
self.dna = DNA(4)
self.probability_of_turn = self.dna.get_gene(0) * 0.1 / 100
self.angle_of_rotation = self.dna.get_gene(1) / 255 * self.TWO_PI
self.speed = self.dna.get_gene(2) / 255.0 * 10
self.probability_turn_direction = self.dna.get_gene(3) / 255.0 * 10
def initialize_attributes(self, location):
self.sprite.x, self.sprite.y = location
self.x_delta = (random() - 0.5) * self.speed
self.y_delta = (random() - 0.5) * self.speed
self.metabolic_rate = self.speed
self.rotation = self.angle_of_rotation
self.life = 200
self.cycles = 0
self.sprite.rotation = -(atan2(self.y_delta, self.x_delta) / self.TWO_PI) * 360
def update(self):
if not self.is_alive():
self.remove_sprite()
return
if self.is_turning():
dir_r = 1
if random() < 0.5:
dir_r = -1
self.rotation = (self.rotation + dir_r * self.angle_of_rotation) % self.TWO_PI
self.x_delta = -sin(self.rotation)
self.y_delta = cos(self.rotation)
self.sprite.rotation = -(atan2(self.y_delta, self.x_delta) / self.TWO_PI) * 360
self.sprite.x = self.sprite.x + self.x_delta
self.sprite.y = self.sprite.y + self.y_delta
if self.is_x_off_map():
self.sprite.x = self.sprite.x - self.x_delta
if self.is_y_off_map():
self.sprite.y = self.sprite.y - self.y_delta
self.life -= self.metabolic_rate
self.cycles += 1
def is_turning(self):
if random() < self.probability_of_turn:
return True
return False
def is_y_off_map(self):
if self.sprite.y < self.sprite_boundary_height or \
self.sprite.y > self.window_height - self.sprite_boundary_height:
return True
return False
def is_x_off_map(self):
if self.sprite.x < self.sprite_boundary_width or \
self.sprite.x > self.window_height - self.sprite_boundary_width:
return True
return False
def get_location(self):
return (self.sprite.x, self.sprite.y)
def add_life(self):
self.life += 100
def is_alive(self):
if self.life <= 0:
return False
return True
def remove_sprite(self):
self.sprite.batch = None
def test_counts_a_nucleotide_only_once(self):
dna = DNA('CGATTGGG')
dna.count('T')
self.assertEqual(2, dna.count('T'))
def initializeChildPopulation(self, numOfChildren):
for i in range(numOfChildren):
self.genotypePopulation.append(DNA.randomGenotype(self.bitsInGenotypes))
def __init__(self, **kw):
super(DNAVis, self).__init__(**kw)
self.dna = DNA()
self.crawler = self.dna.spawn_crawler()
self.bind(size=self.redraw, pos=self.redraw)
def test_dna_counts_do_not_change_after_counting_uracil(self):
dna = DNA('GATTACA')
dna.count('U')
expected = {"A": 3, "T": 2, "C": 1, "G": 1}
self.assertEqual(expected, dna.nucleotide_counts())
def test_counts_all_nucleotides(self):
s = "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
dna = DNA(s)
expected = {'A': 20, 'T': 21, 'G': 17, 'C': 12}
self.assertEqual(expected, dna.nucleotide_counts())
