def test_launch_model():
from models import readREINfile
from launch_model import model2igraph, launch_model
from grn_solver import grn_solver
from grn_inference import getState
print("------- START TEST")
print("Test model2igraph:")
print(">>> With non-coloured nodes:")
C = ["Gene_" + str(i) for i in range(3)]
Idef = [[C[1], C[2], "+"], [C[0], C[2], "-"]]
Iopt = [[C[0], C[0], "+"], [C[1], C[0], "+"], [C[2], C[1], "-"]]
resList = [[["Is", "011"]] + [["R", 10]]*3]
P = [[]*3]
model2igraph(0, resList, C, Idef, Iopt, P, plotIt=True, verbose=True)
print(">>> With coloured nodes:")
P = [["-", "+"], ["-"], ["+"]]
model2igraph(0, resList, C, Idef, Iopt, P, plotIt=True, verbose=True)
print("Test launch_model:")
print("On toy model:")
[C, CRM, length, Idef, Iopt, R, E, typeT, solmax, KO, FE, uniqueness, limreg, P, Fixpoint] = readREINfile(model="toy/model_expanded.net", experiments="toy/observations.spec")
res = grn_solver(C, CRM, length, Idef, Iopt, R, E, typeT, 1, KO, FE, uniqueness, limreg, P, Fixpoint)
try:
[resList, _, _] = res
except:
resList = None
if (resList):
## Random generation of state ##
#q0 = [randint(0, 1) for i in range(len(C))]
q0 = ["0", "1", "1", "0", "1"]
print("Test on first model found:")
modelID = 0
printStates([[">>> Initial state :", [["q0", q0]]]], 0, C)
sstep = 6
print(">>> Number of steps: " + str(sstep))
print(">>> Not steady state:")
states = launch_model(modelID, C, CRM, resList, Idef, Iopt, R, q0,
sstep, typeT, KO, FE, P)
for i in range(len(states)):
printStates(states, i, C)
print("\n")
print(">>> Steady state:")
states = launch_model(modelID, C, CRM, resList, Idef, Iopt, R, q0,
sstep, typeT, KO, FE,
P, steadyStates=True)
for i in range(len(states)):
printStates(states, i, C)
print("------- END TEST")
def call_run(model=full_toy_model,
experiments=full_toy_experiments,
simplify=False,
visualize=False):
from models import readREINfile
from grn_solver import grn_solver
from get_grfs import get_grfs, write_grfs, simplify_grfs
if (visualize):
from launch_model import model2igraph
[
C, CRM, length, Idef, Iopt, R, E, typeT, solmax, KO, FE, uniqueness,
limreg, P, Fixpoint
] = readREINfile(model, experiments)
res = grn_solver(C,
CRM,
length,
Idef,
Iopt,
R,
E,
typeT,
solmax,
KO,
FE,
uniqueness,
limreg,
P,
Fixpoint,
verbose=False)
try:
[resList, s, regInt] = res
except:
return (res)
title = "result_" + model.split("/")[0] + "_" + model.split("/")[1]
grfsList = [get_grfs(C, res, regInt) for res in resList]
write_grfs(grfsList, title=title)
print("MSG: Wrote GRFs in " + title + ".txt")
if (simplify):
for m in range(1, len(grfsList) + 1):
simplify_grfs(title=title + "_model" + str(m) + ".txt")
print("MSG: Simplified functions.")
if (visualize):
for modelID in range(len(resList)):
print("MSG: Close plot to resume.")
model2igraph(modelID, resList, C, Idef, Iopt, P, plotIt=True)
return (s)
P = [""] * len(C)
if (not resList):
addGRF = False
R = [["?"]] * len(C)
resList = [[['Is', [1] * len(Iopt)]] + [[C[i], R[i][0]]
for i in range(len(C))]
]
else:
addGRF = True
## Boolean addGRF is set to True iff. indices corresponding to GRF ##
## templates should be printed ##
model2igraph(0,
resList,
C,
Idef,
Iopt,
P,
model=sys.argv[2] + "_" + emodel,
plotIt=True,
addGRF=addGRF)
else:
print("-- START")
if (len(Iopt) > 0):
print("Solving abstract model...")
[resList, _, _] = grn_solver(C,
CRM,
length,
Idef,
Iopt,
R,
E,