child.status['location'] = location
child.generate_name()
child.status['deme'] = pop_name
Populations[pop_name].agents.append(child)
def postpopulation_control(self, Populations, pop_name): pass
def generation_events(self, Populations, pop_name): pass
def population_report(self, Populations, pop_name):
report_list = []
for organism in Populations[pop_name].agents:
identity = str(organism.status['identity'])
report_list.append(identity)
return '\n'.join(report_list)
def database_report(self, con, cur, start_time,
Populations, World, generation_count):
try:
dose.database_report_populations(con, cur, start_time,
Populations, generation_count)
except: pass
try:
dose.database_report_world(con, cur, start_time,
World, generation_count)
except: pass
def deployment_scheme(self, Populations, pop_name, World): pass
dose.simulate(parameters, simulation_functions)
''.join(org.genome[0].sequence)
for org in Populations[pop_name].agents
]
identities = [
org.status['identity'] for org in Populations[pop_name].agents
]
locations = [
str(org.status['location']) for org in Populations[pop_name].agents
]
demes = [org.status['deme'] for org in Populations[pop_name].agents]
return '\n'.join(sequences)
def database_report(self, con, cur, start_time, Populations, World,
generation_count):
try:
dose.database_report_populations(con, cur, start_time, Populations,
generation_count)
except:
pass
try:
dose.database_report_world(con, cur, start_time, World,
generation_count)
except:
pass
def deployment_scheme(self, Populations, pop_name, World):
pass
dose.simulate(parameters, simulation_functions)
def simulation_worker(parameters, eb):
class SimulationFunctions(dose.dose_functions):
def organism_movement(self, populations, pop_name, world):
pass
def organism_location(self, populations, pop_name, world):
pass
def ecoregulate(self, world):
pass
def update_ecology(self, world, x, y, z):
pass
def update_local(self, world, x, y, z):
pass
def report(self, world):
pass
def fitness(self, populations, pop_name):
pass
def mutation_scheme(self, organism):
organism.genome[0].rmutate(parameters["mutation_type"],
parameters["additional_mutation"])
def prepopulation_control(self, populations, pop_name):
pass
def mating(self, populations, pop_name):
pass
def postpopulation_control(self, populations, pop_name):
pass
def generation_events(self, populations, pop_name):
pass
def population_report(self, populations, pop_name):
sequences = [
''.join(org.genome[0].sequence)
for org in populations[pop_name].agents
]
identities = [
org.status['identity'] for org in populations[pop_name].agents
]
locations = [
str(org.status['location'])
for org in populations[pop_name].agents
]
demes = [
org.status['deme'] for org in populations[pop_name].agents
]
return '\n'.join(sequences)
def database_report(self, con, cur, start_time, populations, world,
generation_count):
try:
dose.database_report_populations(con, cur, start_time,
populations, generation_count)
except:
pass
try:
dose.database_report_world(con, cur, start_time, world,
generation_count)
except:
pass
def deployment_scheme(self, populations, pop_name, world):
pass
if not os.path.exists('logs'):
os.makedirs('logs')
sys.stdout = open("logs/" + str(os.getpid()) + ".log", "w")
dose.simulate(parameters, SimulationFunctions, eb)
