Python Programming for Biology: Bioinformatics and Beyond

Further considerations

Stopping a program

We have mentioned how a program will stop when an error exception occurs, unless we

specifically  try  to  catch  that  error,  and  how  we  can  manually  trigger  an  exception  using

raise.  However,  it  is  also  possible  to  simply  end  a  program  immediately  at  a  particular

point, perhaps the harshest way to control program flow. This kind of intervention is often

not required. Programs in general will simply end after the Python interpreter reaches the

last of the commands, when there is nothing more to execute. Also, we can conditionally

execute  most  of  a  program  inside  an  if  block,  and  thus  skip  straight  to  the  end  of  a

program  if  a  condition  is  not  met.  However,  there  are  some  circumstances  where  a

program has an indefinite loop, perhaps waiting for specific events, which we might want

to terminate in a deliberate manner. A good example of this is a graphical user interface,

where the program does not simply end, but rather enters an event-driven loop whereby it

waits  to  respond  to  the  user  providing  input  like  typing  at  the  keyboard  or

clicking/touching a graphical item on the screen. In this case the program will continue to

run until the user specifically exits the program, maybe by selecting a ‘Quit’ option from a

menu.

In general a Python program is stopped with the exit() function  from  the  standard  sys

module,  which  naturally  must  be  imported  first.  In  the  following  example,  although  we

have  a  loop  which  would  normally  carry  on  indefinitely,  the  exit()  stops  the  program

entirely at the first iteration:

---

import sys

while True: # Loop indefinitely

sys.exit() # Quit program

print('This never gets executed')

Technically  using  sys.exit  raises  a  SystemExit  exception,  which  in  theory  could  be

intercepted  using  try  and  except,  for  example,  to  run  clean-up  code  (e.g.  deleting

temporary  files  or  saving  session  data  to  disk)  before  re-raising  the  exception  so  the

program  actually  stops.  If  you  really  do  want  a  program  to  stop  without  doing  anything

else and with no chance of interception, then os._exit() can be used instead (taking note of

the underscore and the zero which is an exit code):

import os, sys

try:

sys.exit()

except SystemExit:

print("Exit stopped")

os._exit(0) # Can't be stopped