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]
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]
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)
