def main():
print "time_evol module is the main code."
EDGE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-edges-new-names.dat'
NODE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-nodes-new-names.dat'
net = inet.read_network_from_file(EDGE_FILE, NODE_FILE)
nodes_list = inet.build_nodes_list(NODE_FILE)
timeSeriesData = ensemble_time_series(net, nodes_list, 2, 8)#, Nbr_States=2, MAX_TimeStep=20)
# initState = 1
# biStates = decimal_to_binary(nodes_list, initState)
biStates = {'cdk-2/cyclinE':1, 'cki-1':1, 'cdc-14/fzy-1':1, 'fzr-1':1, 'cdk-1/cyclinB':0, 'lin-35/efl-1/dpl-1':1, 'cul-1/lin-23':0, 'cdc-25.1':0}
dec_init = binary_to_decimal(nodes_list, biStates, Nbr_States=2)
print 'initial state', biStates
print 'cdk-2/cyclinE', timeSeriesData['cdk-2/cyclinE'][dec_init]
print 'cki-1', timeSeriesData['cki-1'][dec_init]
print 'cdc-14/fzy-1', timeSeriesData['cdc-14/fzy-1'][dec_init]
print 'fzr-1', timeSeriesData['fzr-1'][dec_init]
print 'cdk-1/cyclinB', timeSeriesData['cdk-1/cyclinB'][dec_init]
print 'lin-35/efl-1/dpl-1', timeSeriesData['lin-35/efl-1/dpl-1'][dec_init]
print 'cul-1/lin-23', timeSeriesData['cul-1/lin-23'][dec_init]
print 'cdc-25.1', timeSeriesData['cdc-25.1'][dec_init]
decStateTransMap = net_state_transition(net, nodes_list)
# nx.write_graphml(decStateTransMap, '/Users/Kelle Dhein/C.-elegans/ElegansGraph.graphml')
plt.show()
attractors = find_attractor(decStateTransMap)
print attractors
def main(args):
## to obtain biological sequence for the Fission Yeast Cell-Cycle Net starting from biological inital state
EDGE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-edges-new-names.dat'
NODE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-nodes-new-names.dat'
BIO_INIT_FILE = '../data/fission-net/fission-net-bioSeq-initial.txt'
net = inet.read_network_from_file(EDGE_FILE, NODE_FILE)
nodes_list = inet.build_nodes_list(NODE_FILE)
#input_file_name1 = 'time-series/%s-step%d-trans0.dat'%(network_index, maxStep)
#input_file1 = open( input_file_name1, 'r')
Nbr_Initial_States = np.power(2,len(nodes_list))
maxStep = 20
Nbr_States = 2
historyLength = 5
result_ai = open('../results/fission-net/ai-step%d-trans0-h%d.dat'%(maxStep, historyLength),'w')
result_te = open('../results/fission-net/te-step%d-trans0-h%d.dat'%(maxStep, historyLength),'w')
timeSeries = tev.time_series(net, nodes_list, Nbr_Initial_States, Nbr_States, MAX_TimeStep=20)
print 'AI'
AI = {}
for n in nodes_list:
AI[n] = info.compute_AI(timeSeries[n], historyLength, Nbr_Initial_States, Nbr_States)
result_ai.write('%s\t%f\n'%(n, AI[n]))
print n, AI[n]
print 'done AI'
print 'TE'
TE = defaultdict(float)
for v in nodes_list:
for n in nodes_list:
TE[(v, n)] = info.compute_TE(timeSeries[v], timeSeries[n], historyLength, Nbr_Initial_States, Nbr_States)
result_te.write('%s\t%s\t%f\n'%(v, n,TE[(v, n)] ))
print v, n, TE[(v, n)]
print 'done TE'
def main():
print "updating_rule module is the main code."
EDGE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-edges-new-names.dat'
NODE_FILE = 'C:\Users\Kelle Dhein\C.-elegans\example\SES591_SampleCode\data\elegans\elegans-net-nodes-new-names.dat'
net = inet.read_network_from_file(EDGE_FILE, NODE_FILE)
#prevState = {'a':0.0, 'b':0.0, 'c':1.0}
prevState = {'cdk-2/cyclinE':1.0, 'cki-1':1.0, 'cdc-14/fzy-1':1.0, 'fzr-1':1.0, 'cdk-1/cyclinB':0.0, 'lin-35/efl-1/dpl-1':1.0, 'cul-1/lin-23':0.0, 'cdc-25.1':0.0}
# prevState['cdk-2/cyclinE'] = float(sys.argv[1])
# prevState['cki-1'] = float(sys.argv[2])
# prevState['cdc-14/fzy-1'] = float(sys.argv[3])
# prevState['fzr-1'] = float(sys.argv[4])
# prevState['cdk-1/cyclinB'] = float(sys.argv[5])
# prevState['lin-35/efl-1/dpl-1'] = float(sys.argv[6])
# prevState['cul-1/lin-23'] = float(sys.argv[7])
# prevState['cdc-25.1'] = float(sys.argv[8])
print "network state @ previous step", OrderedDict(sorted(prevState.items(), key=lambda t: t[0]))
currState = sigmoid_updating(net, prevState)
print "network state @ current step", OrderedDict(sorted(currState.items(), key=lambda t: t[0]))
