def test_create_basins_piechart():
try:
primes = get_primes("n5s3")
attractors = compute_attractors(primes, update="asynchronous")
compute_basins(attractors)
fname_image = get_tests_path_out(fname="basins_piechart")
create_basins_piechart(attractors, fname_image=fname_image)
except NameError:
pass
def test_compute_json():
primes = get_primes("n5s3")
fname = get_tests_path_out(fname="n5s3_attrs.json")
attractors = compute_attractors(primes=primes,
update="asynchronous",
fname_json=fname,
max_output=2)
assert attractors
from pyboolnet.phenotypes import compute_phenotypes, compute_phenotype_diagram, create_phenotypes_piechart
from pyboolnet.attractors import compute_attractors
from pyboolnet.repository import get_primes
if __name__ == "__main__":
# compute the commitment diagram
primes = get_primes("arellano_rootstem")
print(sorted(primes))
attractors = compute_attractors(primes, "asynchronous")
markers = ["WOX", "MGP"]
phenotypes = compute_phenotypes(attractors, markers, fname_json="phenos.json")
# inspect marker patterns
for pheno in phenotypes["phenotypes"]:
print(pheno["name"])
print(pheno["pattern"])
# draw diagram
diagram = compute_phenotype_diagram(phenotypes, fname_image="phenos_diagram.pdf")
# draw pie chart
create_phenotypes_piechart(diagram, fname_image="phenos_piechart.pdf")
from pyboolnet.repository import get_primes
from pyboolnet.state_transition_graphs import primes2stg
from pyboolnet.attractors import compute_attractors_tarjan, compute_attractors, find_attractor_state_by_randomwalk_and_ctl
if __name__ == "__main__":
# attractor computation with Tarjan
primes = get_primes("tournier_apoptosis")
stg = primes2stg(primes, "asynchronous")
steady, cyclic = compute_attractors_tarjan(stg)
print(steady)
print(cyclic)
# random walk attractor detection
state = find_attractor_state_by_randomwalk_and_ctl(primes, "asynchronous")
print(state)
# model checking based attractor detection
attrs = compute_attractors(primes, "asynchronous", fname_json="attrs.json")
print(attrs["is_complete"])
for x in attrs["attractors"]:
print(x["is_steady"])
print(x["state"]["str"])
def test_compute_basins():
primes = get_primes("n5s3")
attractors = compute_attractors(primes, update="asynchronous")
compute_basins(attractors)
def attractors(primes):
return compute_attractors(primes, update="asynchronous")
def attractors():
return compute_attractors(primes=get_primes("raf"), update="asynchronous")