def main():
args = initParser()
myProj = MultiCactusProject()
myProj.readXML(args['cactus_project'])
# for now we do not support appending at the script level
print 'rm -f {0}'.format(args['HAL_file_path'])
system('rm -f {0}'.format(args['HAL_file_path']))
# some quick stats
totalTime = time.time()
totalAppendTime = 0
# traverse tree to make sure we are going breadth-first
tree = myProj.mcTree
# find subtree if event specified
event = args['event']
rootNode = None
if event is not None:
assert event in tree.nameToId and not tree.isLeaf(tree.nameToId[event])
rootNode = tree.nameToId[event]
for node in tree.breadthFirstTraversal(rootNode):
genomeName = tree.getName(node)
if genomeName in myProj.expMap:
experimentFilePath = myProj.expMap[genomeName]
experiment = ExperimentWrapper(
ET.parse(experimentFilePath).getroot())
outgroups = experiment.getOutgroupEvents()
expTreeString = NXNewick().writeString(experiment.getTree())
assert len(expTreeString) > 1
assert experiment.getHALPath() is not None
assert experiment.getHALFastaPath() is not None
cmdline = "time halAppendCactusSubtree \'{0}\' \'{1}\' \'{2}\' \'{3}\'".format(
experiment.getHALPath(), experiment.getHALFastaPath(),
expTreeString, args['HAL_file_path'])
if len(outgroups) > 0:
cmdline += " --outgroups {0}".format(",".join(outgroups))
if args["cacheBytes"] is not None:
cmdline += " --cacheBytes {0}".format(args["cacheBytes"])
if args["cacheMDC"] is not None:
cmdline += " --cacheMDC {0}".format(args["cacheMDC"])
if args["cacheRDC"] is not None:
cmdline += " --cacheRDC {0}".format(args["cacheRDC"])
if args["cacheW0"] is not None:
cmdline += " --cacheW0 {0}".format(args["cacheW0"])
if args["chunk"] is not None:
cmdline += " --chunk {0}".format(args["chunk"])
if args["deflate"] is not None:
cmdline += " --deflate {0}".format(args["deflate"])
print cmdline
appendTime = time.time()
system(cmdline)
appendTime = time.time() - appendTime
totalAppendTime += appendTime
# print "time of above command: {0:.2f}".format(appendTime)
totalTime = time.time() - totalTime
print "total time: {0:.2f} total halAppendCactusSubtree time: {1:.2f}".format(
totalTime, totalAppendTime)
def main():
args = initParser()
myProj = MultiCactusProject()
myProj.readXML(args['cactus_project'])
# for now we do not support appending at the script level
print 'rm -f {0}'.format(args['HAL_file_path'])
system('rm -f {0}'.format(args['HAL_file_path']))
# some quick stats
totalTime = time.time()
totalAppendTime = 0
# traverse tree to make sure we are going breadth-first
tree = myProj.mcTree
# find subtree if event specified
event = args['event']
rootNode = None
if event is not None:
assert event in tree.nameToId and not tree.isLeaf(tree.nameToId[event])
rootNode = tree.nameToId[event]
for node in tree.breadthFirstTraversal(rootNode):
genomeName = tree.getName(node)
if genomeName in myProj.expMap:
experimentFilePath = myProj.expMap[genomeName]
experiment = ExperimentWrapper(ET.parse(experimentFilePath).getroot())
outgroups = experiment.getOutgroupEvents()
expTreeString = NXNewick().writeString(experiment.getTree())
assert len(expTreeString) > 1
assert experiment.getHALPath() is not None
assert experiment.getHALFastaPath() is not None
cmdline = "time halAppendCactusSubtree \'{0}\' \'{1}\' \'{2}\' \'{3}\'".format(experiment.getHALPath(), experiment.getHALFastaPath(), expTreeString, args['HAL_file_path'])
if len(outgroups) > 0:
cmdline += " --outgroups {0}".format(",".join(outgroups))
if args["cacheBytes"] is not None:
cmdline += " --cacheBytes {0}".format(args["cacheBytes"])
if args["cacheMDC"] is not None:
cmdline += " --cacheMDC {0}".format(args["cacheMDC"])
if args["cacheRDC"] is not None:
cmdline += " --cacheRDC {0}".format(args["cacheRDC"])
if args["cacheW0"] is not None:
cmdline += " --cacheW0 {0}".format(args["cacheW0"])
if args["chunk"] is not None:
cmdline += " --chunk {0}".format(args["chunk"])
if args["deflate"] is not None:
cmdline += " --deflate {0}".format(args["deflate"])
print cmdline
appendTime = time.time()
system(cmdline)
appendTime = time.time() - appendTime
totalAppendTime += appendTime
# print "time of above command: {0:.2f}".format(appendTime)
totalTime = time.time() - totalTime
print "total time: {0:.2f} total halAppendCactusSubtree time: {1:.2f}".format(totalTime, totalAppendTime)
