Analyse audio stream in Matlab - Best setup?

I wish process audio in a streamed process where I analyse frames of two seconds each during a recording until I have analysed all audio. I have no control over the recording process. I will use Matlab compiler to compile my program and let another user integrate his c-code to execute my program. My idea is the following:

Let him put audio-files of 2 seconds and define the folder where he puts them. The first time he has put a 2 second-file there ("file1") he calls my program. My program reads the first file "file1" and process it. It then tries to read "file2" and pause 100 ms between each try. When it finds "file2" it processes it etc.

Do you think my approach is ok? Is there a better way for compiled programs to be integrated to do streaming in Matlab?