Running another program within Matlab

I have a matlab script within which another program needs to be run on several occasions in different parts of matlab script. Matlab is counted as the manager. The following could be schematic of the code.

Here comes the problem. Whenever I run my matlab script in the batch mode, the inner text files generator commands are executed first and the content of the original text file “Realization.txt” is updated. Like before even the original text file (i.e. Realization.txt, see below) being used, its content is updated through text files generator commands in different part inside of the code.

Schematic of the code:

There is an original text file to be used as input of anther program

Realization.txt

The text file is gonna be used here in another program

. . . .

based on the output of another program, update the contents of the text file and save it with the same name

 Realization.txt

The text file is gonna be used here in another program again

. . . .

based on the output of another program, update the contents of the text file and save it with the same name

 Realization.txt

The text file is gonna be used here in another program again

. . .