Any method for running your IPython code using a standard Python interpreter is going to be a little complicated. For example, see this question, with one of the answers illustrating the call to IPython's 'magic' methods to do a shell command:
from IPython.terminal.embed import InteractiveShellEmbed
ipshell = InteractiveShellEmbed()
ipshell.dummy_mode = True
ipshell.magic("%timeit abs(-42)")
The much easier option would be to simply use the IPython interpreter to run your saved script. You need to make sure that each shell command is preceded by a %, as this indicates a 'magic' command. Should be a simple find-and-replace task, as I doubt you are using too many shell commands. If there are a lot of different shell commands to prefix with % you could also write a short script to do this work for you. You also need to ensure that your script has the extension .ipy.
script.ipy:
%cd ..
%ls
x = "My script!"
print(x)
To run script from terminal:
>>> ipython script.ipy