def bnet_to_maboss(sbml_filename, cfg_filename=None):
from .gsparser import load
bnd_filename = new_output_file("bnd")
default_cfg_filename = new_output_file("cfg")
bnet_to_bnd_and_cfg(sbml_filename, bnd_filename, default_cfg_filename)
sim = load(
bnd_filename,
cfg_filename if cfg_filename is not None else default_cfg_filename)
if cfg_filename is None:
for node in sim.network:
sim.network.set_istate(node, [1, 0])
return sim
def to_booleannet(model, mode='async'):
bnetfile = new_output_file("booleannet")
assert save(model, bnetfile, "booleannet")
with open(bnetfile, 'r') as f:
rules = f.read()
rules = rules.replace('#BOOLEAN RULES', '')
boolean2 = import_colomoto_tool("boolean2")
return boolean2.Model(rules, mode)
def to_pint(model, simplify=True):
anfile = new_output_file("an")
assert save(model, anfile, "an")
pypint = import_colomoto_tool("pypint")
an = pypint.load(anfile)
if simplify:
an = an.simplify()
return an
def to_minibn(maboss_model):
from colomoto import minibn
bnet_filename = new_output_file("bnet")
with open(bnet_filename, "w") as bnet_file:
for node, rule in maboss_model.get_logical_rules().items():
bnet_file.write("%s, %s\n" % (node, rule))
return minibn.BooleanNetwork.load(bnet_filename)
def to_biolqm(maboss_model):
biolqm = import_colomoto_tool("biolqm")
bnet_filename = new_output_file("bnet")
with open(bnet_filename, "w") as bnet_file:
for node, rule in maboss_model.get_logical_rules().items():
bnet_file.write("%s, %s\n" % (node, rule))
return biolqm.load(bnet_filename)
def to_ginsim(model):
"""
Convert a bioLQM model into an equivalent GINsim model using the
:py:mod:`ginsim` Python module.
Please note that no layout is set for the regulatory graph.
"""
import_colomoto_tool("ginsim")
ginml_file = new_output_file("ginml")
assert save(model, ginml_file, "ginml")
return ginsim.load(ginml_file)
def to_minibn(model):
from colomoto import minibn
if model.isBoolean():
fmt = "bnet"
cls = minibn.BooleanNetwork
else:
fmt = "mnet"
cls = minibn.MultiValuedNetwork
bnfile = new_output_file(fmt)
assert save(model, bnfile, fmt)
with open(bnfile) as data:
return cls(data)
def to_minibn(model, simplify=True, ensure_boolean=False):
from colomoto import minibn
if ensure_boolean or model.isBoolean():
fmt = "bnet"
cls = minibn.BooleanNetwork
else:
fmt = "mnet"
cls = minibn.MultiValuedNetwork
bnfile = new_output_file(fmt)
assert save(model, bnfile, fmt)
with open(bnfile) as data:
bn = cls(data)
if simplify and hasattr(bn, "simplify"):
bn = bn.simplify()
return bn
def to_nusmv(lrg, update_mode="async"):
assert update_mode in ["async", "sync", "complete"], "Unknown update mode"
serv = service("NuSMV")
cfg = serv.getConfig(lrg.getModel())
## configure update mode
d_update = {
"async": cfg.CFG_ASYNC,
"sync": cfg.CFG_SYNC,
"complete": cfg.CFG_COMPLETE,
}
cfg.setUpdatePolicy(d_update[update_mode])
smvfile = new_output_file("smv")
serv.run(cfg, smvfile)
from colomoto.modelchecking import ColomotoNuSMV
return ColomotoNuSMV(smvfile, nusmv_var_state)
def to_nusmv(lrg, update_mode="async"):
assert update_mode in ["async", "sync", "complete"], "Unknown update mode"
serv = service("NuSMV")
cfg = serv.getConfig(lrg.getModel())
## configure update mode
d_update = {
"async": cfg.CFG_ASYNC,
"sync": cfg.CFG_SYNC,
"complete": cfg.CFG_COMPLETE,
}
cfg.setUpdatePolicy(d_update[update_mode])
## configure input nodes
sinit = japi.gs.associated(lrg, "initialState", True)
for inputNode in sinit.getInputNodes():
cfg.addFixedInput(str(inputNode))
smvfile = new_output_file("smv")
serv.run(cfg, smvfile)
from colomoto.modelchecking import ColomotoNuSMV
return ColomotoNuSMV(smvfile, nusmv_var_state)
def to_pyboolnet(model):
bnetfile = new_output_file("bnet")
assert save(model, bnetfile, "bnet")
PyBoolNet = import_colomoto_tool("PyBoolNet")
bn = PyBoolNet.FileExchange.bnet2primes(bnetfile)
return bn
def to_maboss(model):
maboss = import_colomoto_tool("maboss")
maboss_file = new_output_file("bnd")
assert save(model, maboss_file, "bnd")
return maboss.load(maboss_file, "%s.cfg" % maboss_file)
def to_biolqm(self):
bnfile = new_output_file(ext=self.biolqm_format)
with open(bnfile, "w") as f:
f.write(self.source())
biolqm = import_colomoto_tool("biolqm")
return biolqm.load(bnfile)
def biolqm_import(biolqm, lqm):
bnfile = new_output_file(self.biolqm_format)
assert biolqm.save(lqm, bnfile)
with open(bnfile) as fp:
self.import_data(fp)
return True
