def run(self, name, datafiles, goldnet_file):
import numpy
os.chdir(os.environ["gene_path"])
datastore = ReadData(datafiles[0], "steadystate")
for file in datafiles[1:]:
datastore.combine(ReadData(file, "steadystate"))
datastore.normalize()
settings = {}
settings = ReadConfig(settings)
# TODO: CHANGE ME
settings["global"]["working_dir"] = os.getcwd() + '/'
# Setup job manager
print "Starting new job manager"
jobman = JobManager(settings)
# Make GENIE3 jobs
genie3 = GENIE3()
genie3.setup(datastore, settings, name)
print "Queuing job..."
jobman.queueJob(genie3)
print jobman.queue
print "Running queue..."
jobman.runQueue()
jobman.waitToClear()
print "Queue finished"
job = jobman.finished[0]
print job.alg.gene_list
print job.alg.read_output(settings)
jobnet = job.alg.network
print "PREDICTED NETWORK:"
print job.alg.network.network
print jobnet.original_network
if goldnet_file != None:
goldnet = Network()
goldnet.read_goldstd(goldnet_file)
print "GOLD NETWORK:"
print goldnet.network
print jobnet.analyzeMotifs(goldnet).ToString()
print jobnet.calculateAccuracy(goldnet)
return jobnet.original_network
def run(self, ko_file, wt_file, ts_file=None, kd_file=None, name=None):
import numpy
os.chdir(os.environ["gene_path"])
print "Reading in knockout data"
knockout_storage = ReadData(ko_file, "knockout")
knockout_storage.normalize()
wildtype_storage = ReadData(wt_file, "wildtype")
wildtype_storage.normalize()
knockdown_storage = ReadData(kd_file, "knockdown")
knockdown_storage.normalize()
wildtype_storage.combine(knockdown_storage)
timeseries_storage = None
if ts_file != None:
timeseries_storage = ReadData(ts_file, "timeseries")
for ts in timeseries_storage:
ts.normalize()
settings = {}
settings = ReadConfig(settings)
# TODO: CHANGE ME
settings["global"]["working_dir"] = os.getcwd() + '/'
# Setup job manager
print "Starting new job manager"
jobman = JobManager(settings)
# Make MCZ jobs
mczjob = MCZ()
mczjob.setup(knockout_storage, wildtype_storage, settings, timeseries_storage, name)
print "Queuing job..."
jobman.queueJob(mczjob)
print jobman.queue
print "Running queue..."
jobman.runQueue()
jobman.waitToClear()
print "Queue finished"
job = jobman.finished[0]
print job.alg.gene_list
print job.alg.read_output(settings)
jobnet = job.alg.network
print "PREDICTED NETWORK:"
print job.alg.network.network
print jobnet.original_network
return jobnet.original_network
dexcombined.combine(dex_storage2)
no3_storage = no3_1_storage
no3_storage.combine(no3_2_storage)
no3_storage.combine(no3_3_storage)
cnlo_no3_storage.combine(no3_storage)
#all_storage.combine(cnlo_no3_storage)
#dex_storage.combine(cnlo_storage)
#dex_storage.combine(no3_storage)
#dex_storage.normalize()
no3_storage.normalize()
cnlo_storage.normalize()
cnlo_no3_storage.normalize()
#all_storage.normalize()
ts_storage = [kno3_1, kno3_2, kno3_3, kno3_4]
#for s in ts_storage:
#s.normalize()
# Setup job manager
jobman = JobManager(settings)
# Make BANJO jobs
#mczjob = MCZ()
#mczjob.setup(knockout_storage, wildtype_storage, settings, timeseries_storage, knockdown_storage, "MCZ")
#jobman.queueJob(mczjob)
#kd_file = settings["global"]["large_network_knockdown_file"].split() #ts_file = settings["global"]["large_network_timeseries_file"].split() #wt_file = settings["global"]["large_network_wildtype_file"].split() # Read data into program # Where the format is "FILENAME" "DATATYPE" knockout_storage = ReadData(ko_file[0], "knockout") knockdown_storage = ReadData(kd_file[0], "knockdown") timeseries_storage = ReadData(ts_file[0], "timeseries") wildtype_storage = ReadData(wt_file[0], "wildtype") wildtype_storage.combine(knockout_storage) wildtype_storage.combine(knockdown_storage) wildtype_storage.combine(timeseries_storage) wildtype_storage.normalize() knockout_storage.normalize() # Setup job manager jobman = JobManager(settings) # Make BANJO jobs mczjob = MCZ() mczjob.setup(knockout_storage, wildtype_storage, settings, None, "mcz-test-run-1") jobman.queueJob(mczjob) print jobman.queue jobman.runQueue() jobman.waitToClear()
