Ejemplos de read_init_from_file en Python

Ejemplo n.º 1

Archivo: attractor_analysis.py Proyecto: SES591/Mammalian-Cell-Cycle-Tessa-

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

Ejemplo n.º 2

Archivo: time_evol.py Proyecto: SES591/Mammalian-Cell-Cycle-Tessa-

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)

Ejemplo n.º 3

Archivo: time_evol.py Proyecto: SES591/C.-elegans

    
    ## 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()