for line in filename:
if (not line.startswith(">")):
sequence = sequence + line
sequence.replace("\n", "")
return sequence
sequence = parse_fasta(fasta)
environment = Environment(0.000000001, 10)
organism = Organism(sequence)
environment.population_list.append(organism)
start = time.clock()
for organism in environment.population_list:
print "-" * 20
print "Current organism: ", organism
organism.transcribe()
organism.translate()
environment.population_list.append(organism.reproduce())
print "Population:", len(environment.population_list)
print environment.population_list
print "-" * 20
if len(environment.population_list) >= environment.carrying_capacity:
break
stop = time.clock()
print environment.population_list
print "Total time taken =", (stop-start), "seconds"
def reproduce(self):
self.children = [Organism.reproduce(p1, p2) for (p1, p2) in zip(self.parents1, self.parents2)]
self.population += self.children
self.population = sorted(self.population, key=lambda org: org.fitness, reverse=True)[:self.pop_size]
