Exemplo n.º 1
0
def addNewHistory(histories,
                  index,
                  file=None,
                  stats=None,
                  braney=None,
                  tree=None):
    # Just do not process if run time > MAX_TIMER_LENGTH
    if time.time() > TIMER_END:
        return histories

    # Generate new history from the last one
    newHistory = chooseNewHistory(histories[-1],
                                  TEMPERATURE,
                                  depth=1,
                                  index=index)
    # DEBUG
    #if debug.TRIGGER_TEST:
    #	newHistory.validate()
    #	debug.TRIGGER_TEST = False

    c = newHistory.rearrangementCost()
    FH = flattened.flattenGraph(newHistory)
    S = FH.simplifyStubsAndTrivials()
    F = S.removeLowRatioEvents(debug.RATIO_CUTOFF)
    O = ordered.OrderedHistory(F)

    if stats is not None:
        stats.write("%s\n" % newHistory.stats())
    if braney is not None:
        # The + 1 takes into account the fact that history 0 is the one created initially,
        # the MCMC histories start at index 1
        braney.write("%s\n" % O.braneyText(index + 1, c))
    if tree is not None:
        tree.write("%s\n" % O.newick())
    if file is None:
        histories.append(newHistory)
        return histories
    else:
        # Really, who need to pickle files when there's a perfectly good zipped braney file next to it?
        #pickle.dump(newHistory, file)
        # Cheap trick: only store minimal and latest histories
        if sum(c) / 2 < sum(histories[0].rearrangementCost()) / 2:
            # Memory optimization trick -> Frees unused matrices and overlap tables
            histories[0].embalmDeadHistories(newHistory)
            return [newHistory]
        else:
            return [histories[0], newHistory]
Exemplo n.º 2
0
def addNewHistory(histories, index, file=None, stats=None, braney=None, tree=None):
	# Just do not process if run time > MAX_TIMER_LENGTH
	if time.time() > TIMER_END:
		return histories
	
	# Generate new history from the last one
	newHistory = chooseNewHistory(histories[-1], TEMPERATURE, depth=1, index=index)
	# DEBUG
	#if debug.TRIGGER_TEST:
	#	newHistory.validate()
	#	debug.TRIGGER_TEST = False

	c = newHistory.rearrangementCost()
	FH = flattened.flattenGraph(newHistory)
	S = FH.simplifyStubsAndTrivials()
	F = S.removeLowRatioEvents(debug.RATIO_CUTOFF)
	O = ordered.OrderedHistory(F)

	if stats is not None:
		stats.write("%s\n" % newHistory.stats())
	if braney is not None:
		# The + 1 takes into account the fact that history 0 is the one created initially,
		# the MCMC histories start at index 1
		braney.write("%s\n" % O.braneyText(index + 1, c))
	if tree is not None:
		tree.write("%s\n" % O.newick())
	if file is None: 
		histories.append(newHistory)
		return histories 
	else:
		# Really, who need to pickle files when there's a perfectly good zipped braney file next to it?
		#pickle.dump(newHistory, file)
		# Cheap trick: only store minimal and latest histories
		if sum(c)/2 < sum(histories[0].rearrangementCost())/2:
			# Memory optimization trick -> Frees unused matrices and overlap tables
			histories[0].embalmDeadHistories(newHistory)
			return [newHistory]
		else:
			return [histories[0], newHistory]
Exemplo n.º 3
0
def main():
	options = _parseOptions()

	sampleGraphCycles.TEMPERATURE = options.temp

	if options.dir is not None:
		if not os.path.exists(options.dir):
			os.mkdir(options.dir)
		os.chdir(options.dir)

	if options.index is None:
		## Initial graph construction
		G = _parseGraph(options)
		B = balancedAVG.BalancedAVG(G)
		C = cactus.Cactus(B)
		pickle.dump(C, open('CACTUS', "wb"))
	else:
		H = None

		if options.debug:
			## Picking up from where we started
			OC = pickle.load(open('CACTUS_%i' % options.index))
			random.setstate(pickle.load(open("STATE_%i" % options.index)))
		elif options.cont:
			## Picking up from where we stopped
			OC = pickle.load(open('CACTUS_%i' % options.index))
			## Going through all the histories to the last in file 
			file= open('HISTORIES_%i' % (options.index))
			while True:
				try:
					H = pickle.load(file)
				except:
					break
			file.close()
		else:
			## Just moving from there 
			pickle.dump(random.getstate(), open("STATE_%i" % options.index, "wb"))
			C = pickle.load(open('CACTUS'))

			## Sampling possible cactus
			NC = normalized.NormalizedCactus(C)
			if debug.RATIO_TO_OFFSET:
				BC = balancedCactus.BalancedCactus(NC)
			else:
				BC = NC
			OC = oriented.OrientedCactus(BC)

			## Saving sampled cactus
			pickle.dump(OC, open('CACTUS_%i' % options.index, "wb"))
		

		# Moving into historical space
		if options.integer:
			debug.INTEGER_HISTORY = True
		if H is None:
			H = cycleCover.initialHistory(OC)
		FH = flattened.flattenGraph(H)
		S = FH.simplifyStubsAndTrivials()
		F = S.removeLowRatioEvents(debug.RATIO_CUTOFF)
		O = ordered.OrderedHistory(F)

		# Preparing file for progressive write
		if options.cont:
			stats_file = open("HISTORY_STATS_%li" % options.index, "a")
			pickle_file = open('HISTORIES_%i' % options.index, "ab")
			braney_file = gzip.open("HISTORIES_%i.braney" % options.index, "a")
		else:
			stats_file = open("HISTORY_STATS_%li" % options.index, "w")
			pickle_file = open('HISTORIES_%i' % options.index, "wb")
			braney_file = gzip.open("HISTORIES_%i.braney" % options.index, "w")
		stats_file.write("%s\n" % H.stats())
		#pickle.dump(H, pickle_file)
		braney_file.write("%s\n" % O.braneyText(0, H.rearrangementCost()))
		#tree_file = open("HISTORY_TREES_%li" % options.index, "w")
		#tree_file.write("%s\n" % O.newick())
		tree_file = None

		# Sampling
		for i in range(options.size):
			H2 = copy.copy(H)
			# Shuffle events
			for event in list(H.parent):
				H2.correctSchedulingError(event)
			H = H2
			stats_file.write("%s\n" % H.stats())
			FH = flattened.flattenGraph(H)
			S = FH.simplifyStubsAndTrivials()
			F = S.removeLowRatioEvents(debug.RATIO_CUTOFF)
			O = ordered.OrderedHistory(F)
			braney_file.write("%s\n" % O.braneyText(i+1, H.rearrangementCost()))

		# Cleaning up
		stats_file.close()
		pickle_file.close()
		braney_file.close()
		#tree_file.close()

		## Removing temp file
		if os.path.exists("STATE_%i" % options.index):
			os.remove("STATE_%i" % options.index)