from ROOT import TFile

file = TFile("tree.root",'update')
 
# make directory if it does not exist
dir = file.GetDirectory("dir")
if not dir:
    print ">>> created dir"
    dir = file.mkdir("dir")
 
# make this directory the current one: everything you write will be saved here
dir.cd()

# make tree, histogram, ...
        
file.Write("",TFile.kOverwrite)
file.Close()