>>> import time
>>> 
>>> def f():
...     for i in 123, 456, 789:
...         print('\r' + ' ' * 5 + '\r' + str(i), end='')
...         time.sleep(1)
...     print()
... 
>>> f()
789  
>>>

 import sys
import time
while True:
    t = time.strftime('%H:%M:%S', time.localtime(time.time()))
    sys.stdout.write('\r%s' % t)
    time.sleep(0.5)