from environment import Environment
from sampler import Sampler
from random import randint
import networkx as nx
for i in range(500):
# We allow ourselves to start with between 1 and 3 viruses
num_viruses = randint(1, 4)
# We allow ourselves to finish with between 20 and 50 viruses
max_num_viruses = randint(20, 50)
e = Environment(num_viruses=num_viruses, virus_type='influenza')
for j in range(max_num_viruses):
if len(e.GetViruses()) < max_num_viruses:
virus = e.GetRandomVirus()
e.ReplicateVirus(virus, date=j)
e.MutateVirus()
else:
break
s = Sampler()
s.SampleVirusesFromEnvironment(e, 'all')
s.DumpSequences(run_number=i)
G = s.GenerateNetwork()
nx.write_gpickle(G,
"Simulated Networks/Run %s Transmission Tree.gpickle" % i)
from sampler import Sampler
from random import randint, random
from numpy.random import normal
import networkx as nx
for i in range(500):
# We allow ourselves to start with between 1 and 3 viruses
num_viruses = randint(1, 4)
# We allow ourselves to finish with between 20 and 50 viruses
max_num_viruses = randint(20, 50)
e = Environment(num_viruses=num_viruses, virus_type='influenza')
for j in range(max_num_viruses):
if len(e.GetViruses()) < max_num_viruses:
cointoss = random()
if cointoss < 0.7:
virus = e.GetRandomVirus()
e.ReplicateVirus(virus, date=j)
e.MutateVirus()
elif cointoss > 0.3 and len(e.GetViruses()) > 2:
e.RandomlyReassortTwoViruses(mutate=True, date=i)
else:
break
s = Sampler(directory_prefix='Simulated Reassortant Sequences')