def setUp(self):
self.bn1 = bonesis.BooleanNetwork({"a": "b", "b": "c", "c": 1})
self.bn2 = bonesis.BooleanNetwork({"a": "b", "b": "c", "c": "c"})
self.data = {}
for a in [0, 1]:
for b in [0, 1]:
for c in [0, 1]:
self.data[f"{a}{b}{c}"] = {"a": a, "b": b, "c": c}
def main_reprogramming():
ap = ArgumentParser()
ap.add_argument("bnet_file",
help="file specifying the Boolean network in bnet format")
ap.add_argument(
"marker",
help="Marker specification (partial configuration) - JSON format")
ap.add_argument("max_size",
type=int,
help="Maximum number of perturbation")
ap.add_argument(
"--reachable-from",
help=
"Initial configuration for source-marker reprogramming - JSON format")
ap.add_argument("--fixpoints",
action="store_true",
help="Reprogram fixed points only")
ap.add_argument(
"--allow-no-fixpoint",
action="store_true",
help="When reprogramming fixed points, allow having no fixed points")
ap.add_argument("--exclude", help="Perturbation blacklist - JSON format")
ap.add_argument("--limit", type=int, help="Maximum number of solutions")
ap.add_argument("--verbose", action="store_true")
ap.add_argument("--parallel", "-t", default=1, help="Parallel solving")
args = ap.parse_args()
bonesis.settings["quiet"] = not args.verbose
bonesis.settings["parallel"] = args.parallel
f = bonesis.BooleanNetwork(args.bnet_file)
M = json.loads(args.marker)
k = args.max_size
meth_prefix = ""
meth_suffix = ""
meth_args = (f, M, k)
meth_kwargs = {}
if args.exclude:
meth_kwargs["exclude"] = json.loads(args.exclude)
if args.reachable_from:
z = json.loads(args.reachable_from)
meth_prefix = "source_"
meth_args = (f, z, M, k)
if args.fixpoints:
meth_suffix = "_fixpoints"
meth_kwargs["at_least_one"] = not args.allow_no_fixpoint
from bonesis import reprogramming
meth = f"{meth_prefix}marker_reprogramming{meth_suffix}"
meth = getattr(reprogramming, meth)
it = meth(*meth_args, **meth_kwargs)
has_one = False
if args.limit:
it = islice(it, args.limit)
for sol in it:
has_one = True
print(sol)
if not has_one:
print("No solution", file=sys.stderr)
def main_attractors():
ap = ArgumentParser()
ap.add_argument("bnet_file",
help="file specifying the Boolean network in bnet format")
ap.add_argument("--fixpoints-only",
action="store_true",
help="Enumerate only fixed points")
args = ap.parse_args()
dom = bonesis.BooleanNetwork(args.bnet_file)
bo = bonesis.BoNesis(dom)
x = bo.cfg() if args.fixpoints_only else bo.hypercube()
bo.fixed(x)
publish = print
for sol in x.assignments():
publish(sol)
import bonesis
f = bonesis.BooleanNetwork({
"a": "c & (!a | !b)",
"b": "c & a",
"c": "a|b|c",
})
bo = bonesis.BoNesis(f)
x = bo.cfg()
~bo.obs({
"a": 1,
"b": 0,
"c": 0
}) >= bo.in_attractor(x) != bo.obs({
"a": 1,
"b": 1
})
for v in x.assignments():
print(v)
import bonesis
dom = bonesis.InfluenceGraph.complete("abc", sign=1, exact=True, loops=False)
dom2 = bonesis.BooleanNetwork({"a": "c", "b": "a", "c": "b"})
bo = bonesis.BoNesis(dom)
"""
x = bo.cfg()
bo.in_attractor(x)
for i, sol in enumerate(x.assignments()):
print(i, sol)
"""
#h = bo.hypercube({"a": 1})
h = bo.hypercube()
bo.fixed(h)
bo.aspmodel.make()
print(str(bo.aspmodel))
assert bo.is_satisfiable()
for i, sol in enumerate(h.assignments()):
print(i, sol)
import bonesis
dom = bonesis.BooleanNetwork({"a": "a", "b": "a & c", "c": "!b"})
data = {
"never_b": {
"b": 0
},
}
bo = bonesis.BoNesis(dom, data)
bad_control = bo.Some()
with bo.mutant(bad_control) as m:
m.fixed(bo.obs("never_b"))
for res in bad_control.complementary_assignments():
print(res)