networks['A']['thresholds'] = {("rr","gg"):1, ("rr","bb"):2, ("bb","gg"):1, ("gg","gg"):1}
combis = [(False, False), (True, False), (False, True)] # low, medium, high
ALformulas = ["?(left: left.frozen(gg)&left.max(gg)=0)", "?(middle: middle.frozen(gg)&middle.min(gg)=1)",
"?(right: right.frozen(gg)&right.max(gg)=0)"]
for letter in 'A': # in C, unfortunately green is the input gene
print "===================================================================================="
print "Considering network:", networks[letter]['name']
interactions = networks[letter]['interactions']
edges = interactions.keys()
thresholds = networks[letter]['thresholds']
IG = nx.DiGraph()
IG.add_edges_from(edges)
mc = dict_to_model(interactions, thresholds=thresholds, add_morphogene=True)
smallmc = dict_to_model(interactions, thresholds=thresholds, add_morphogene=False)
lpss = mc._psc._localParameterSets
print len(mc._psc), "parameter sets."
gpss = mc._psc.get_parameterSets()
countaccepted = 0
countrejected = 0
for gps in gpss:
#print gps
subgps = dict((combi, encode_gps_full(subparset(gps, is_m1_in=combi[0], is_m2_in=combi[1]))) for combi in combis)
parameter_set_IG_list = [decode_gps_full(subgps[combi]) for combi in combis]
parameter_sets = [elem[0] for elem in parameter_set_IG_list]
accepted = all(filter_byAL(smallmc, parameter_sets[i], ALformulas[i]) for i in range(3))*1
if accepted:
import cPickle
from _02_regnet_generator import dict_to_model
from _03_database_functions import export_STG
if __name__=='__main__':
net = {('rr', 'bb'):'+', ('bb', 'rr'):'+'}
mc = dict_to_model(net, add_morphogene=True, thresholds=None)
print "found", len(mc._psc), "parameter sets."
gpss = mc._psc.get_parameterSets()
for gps in gpss:
print gps
print "exporting example STG..."
export_STG(mc, gps, filename="example_network_STG.gml", initialRules=None)
print "done."
pstotal = 0
for nwkey in networks:
#print "===================================================================================="
#print nwkey, networks[nwkey]
# disable following to keep overregulated networks
if networks[nwkey][('bb', 'rr')]!='0' and networks[nwkey][('gg', 'rr')]!='0' and networks[nwkey][('rr', 'rr')]!='0':
if nwkey in non:
print "i am making a mistake at", nwkey
sys.exit()
print "network", nwkey, "is overregulated, skipping."
continue # we skip if rr is overregulated (too slow)
current += 1
#if nwkey<start_nwkey or nwkey>=start_nwkey+tocheck: continue
print "===================================================================================="
print "considering nwkey:", nwkey
mc = dict_to_model(networks[nwkey], add_morphogene)
npsc = len(mc._psc)
print nwkey, ":", npsc, "parameter sets."
pstotal += npsc
print nwkey, ":", pstotal, "parameter sets in total."
gpss = mc._psc.get_parameterSets()
count_accepted = 0
for gps in gpss:
# decompose gps code into 3 small gps codes
subgps = dict((combi, encode_gps_full(subparset(gps, is_m1_in=combi[0], is_m2_in=combi[1]))) for combi in combis)
accepted = d[subgps[combis[0]]][0] and d[subgps[combis[1]]][1] and d[subgps[combis[2]]][0] # d[][2] (the one with 'instable') is not used here
#print accepted
if accepted:
count_accepted += 1
results = [count_accepted, npsc, count_accepted*1.0/npsc]
print net #, networks[net]['interactions']
graph_number = lookup_graph_number(networks[net]['interactions'])
iso_graph_number = lookup_iso_rep(graph_number)
print iso_graph_number
print crs[str(iso_graph_number)]
print "========================================="
print "AL model checking"
crs = shelve.open(combined_results_shelvenames[0])
numbers = {7747:'A', 7423:'B', 7969:'E', 9349:'D', 14284:'F'} # TODO: this should be generated by the above loop (simple)
combis = [(False, False), (True, False), (False, True)] # low, medium, high
ALformulas = ["?(left: left.frozen(gg)&left.max(gg)=0)", "?(middle: middle.frozen(gg)&middle.min(gg)=1)",
"?(right: right.frozen(gg)&right.max(gg)=0)"]
for number in numbers:
mc = dict_to_model(allnetworks[number], add_morphogene=True)
smallmc = dict_to_model(allnetworks[number], add_morphogene=False)
gpss = mc._psc.get_parameterSets()
count_accepted = 0
for gps in gpss:
#print gps
subgps = dict((combi, encode_gps_full(subparset(gps, is_m1_in=combi[0], is_m2_in=combi[1]))) for combi in combis)
parameter_set_IG_list = [decode_gps_full(subgps[combi]) for combi in combis]
parameter_sets = [elem[0] for elem in parameter_set_IG_list]
#print parameter_sets
accepted = all(filter_byAL(smallmc, parameter_sets[i], ALformulas[i]) for i in range(3))*1
if accepted:
print "accepting:", gps
#export_STG(mc, gps, filename=str(number).zfill(5)+"_"+encode_gps(gps, base=10)+".gml", initialRules=None)
export_STG(mc, gps, filename="_"+numbers[number]+"_"+encode_gps(gps, base=10)+".gml", initialRules=None)