def main(): EDGE_FILE = '../data/fission-net/fission-net-edges.txt' NODE_FILE = '../data/fission-net/fission-net-nodes.txt' 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) bio_initStates = inet.read_init_from_file(BIO_INIT_FILE) decStateTransMap = net_state_transition(net, nodes_list) attractors = find_attractor(decStateTransMap) print attractors
def main(): ''' print "time_evol module is the main code." ## to import a network of 3-node example EDGE_FILE = '../data/example/example-net-edges.dat' NODE_FILE = '../data/example/example-net-nodes.dat' net = inet.read_network_from_file(EDGE_FILE, NODE_FILE) nodes_list = inet.build_nodes_list(NODE_FILE) ## to obtain time series data for all possible initial conditions for 3-node example network timeSeriesData = ensemble_time_series(net, nodes_list, 2, 10)#, Nbr_States=2, MAX_TimeStep=20) initState = 1 biStates = decimal_to_binary(nodes_list, initState) print 'initial state', biStates ## to print time series data for each node: a, b, c starting particualr decimal inital condition 1 print 'a', timeSeriesData['a'][1] print 'b', timeSeriesData['b'][1] print 'c', timeSeriesData['c'][1] ## to obtain and visulaize transition map in the network state space decStateTransMap = net_state_transition(net, nodes_list) nx.draw(decStateTransMap) plt.show() ## to find fixed point attractors and limited cycle attractors with given transition map. attractors = find_attractor(decStateTransMap) print attractors ''' ## to obtain biological sequence for the Fission Yeast Cell-Cycle Net starting from biological inital state EDGE_FILE = '../data/fission-net/fission-net-edges.txt' NODE_FILE = '../data/fission-net/fission-net-nodes.txt' #BIO_INIT_FILE = '../data/fission-net/fission-net-bioSeq-initial.txt' 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) bio_initStates = inet.read_init_from_file(BIO_INIT_FILE) outputFile = '../results/fission-net/fission-net-bioSeq.txt' bioSeq = biological_sequence(net, nodes_list, bio_initStates, outputFile)
## to obtain and visulaize transition map in the network state space decStateTransMap = net_state_transition(net, nodes_list) nx.draw(decStateTransMap) plt.show() ## to find fixed point attractors and limited cycle attractors with given transition map. attractors = find_attractor(decStateTransMap) print attractors ''' ## to obtain biological sequence for the Fission Yeast Cell-Cycle Net starting from biological inital state EDGE_FILE = '../data/fission-net/fission-net-edges.txt' NODE_FILE = '../data/fission-net/fission-net-nodes.txt' <<<<<<< HEAD #BIO_INIT_FILE = '../data/fission-net/fission-net-bioSeq-initial.txt' ======= BIO_INIT_FILE = '../data/fission-net/fission-net-bioSeq-initial.txt' >>>>>>> origin/master net = inet.read_network_from_file(EDGE_FILE, NODE_FILE) nodes_list = inet.build_nodes_list(NODE_FILE) bio_initStates = inet.read_init_from_file(BIO_INIT_FILE) outputFile = '../results/fission-net/fission-net-bioSeq.txt' bioSeq = biological_sequence(net, nodes_list, bio_initStates, outputFile) if __name__=='__main__': main()