def run(self):
self.logToMaster("CreatePevntsFile\n")
opts=self.options
if opts.simulation:
truefile=os.path.join(opts.cnavgout, "true.braney")
truehist=os.path.join(opts.cnavgout, "HISTORIES_0.braney")
subprocess.call("grep -v ^$ %s | gzip > %s" % (truefile, truehist), shell=True)
make_STATS_from_truebraney(truefile, os.path.join(opts.cnavgout, "HISTORY_STATS_0"))
historyScores=histseg.combine_history_statsfiles(opts.cnavgout)
np.savetxt(self.historystatsfile, historyScores, fmt='%d', delimiter='\t')
totalp=histseg.compute_likelihood_histories(historyScores[:,0], historyScores)
events=histseg.get_events_from_cnavgdir(opts.cnavgout, historyScores, totalp)
pickle.dump(events, open(self.pevntsfile, 'wb'), pickle.HIGHEST_PROTOCOL)
def score_and_link_cycles(args):
if args.binwidth:
histseg.Global_BINWIDTH=args.binwidth
if not args.historystats and args.cnavg:
historyScores=histseg.combine_history_statsfiles(args.cnavg)
elif not os.path.isfile(args.historystats) and args.cnavg:
historyScores=histseg.combine_history_statsfiles(args.cnavg)
np.savetxt(args.historystats, historyScores, fmt="%d", delimiter='\t')
elif os.path.isfile(args.historystats):
historyScores=np.loadtxt(args.historystats, dtype=int)
if not historyScores:
sys.exit("Need to use --historystats or --cnavg option")
totalp=0
if args.totalp:
totalp=args.totalp
else:
totalp = histseg.compute_likelihood_histories(historyScores[:,0], historyScores)
allevents=[]
if args.cnavg:
sys.stderr.write("using cnavg dir: %s\n" % (args.cnavg))
allevents=histseg.get_events_from_cnavgdir(args.cnavg, historyScores, totalp)
elif args.inpickle and os.path.isfile(args.inpickle):
sys.stderr.write("using pickle file\n")
allevents=pickle.load(open(args.inpickle, 'rb'))
sys.stderr.write("there are %d events\n" % (len(allevents)))
if args.outpickle:
for event in allevents:
event.trim()
eventfile= open(args.outpickle, 'wb')
pickle.dump(allevents, eventfile, pickle.HIGHEST_PROTOCOL)
if args.events:
eventfile=open(args.events, 'w')
for evnt in allevents:
eventfile.write("%s" % (str(evnt)))
# link the events...
if args.links:
if not allevents:
sys.exit("Need events to link! use --inpickle or --cnavg or --events")
if not totalp:
sys.exit("Need a --totalp or --cnavg or --historystats options")
eventlinks = link_events_by_order_within_histories(allevents)
linkfile=open(args.links, 'w')
for link in eventlinks:
link.likelihood=histseg.compute_likelihood_histories(link.histories, historyScores)
linkfile.write("%s" % (str(link)))