The best example of audio data manipulating GPIO pins is the [LightshowPi][1] project. Experience in Python, especially NumPy is tantamount for the success of such a project. Audio input and output is done with the [pyalsaaudio][2] module.

TL,DR: Learn the mathematics behind the Fast Fourier Transform, learn NumPy.

[1]: http://www.lightshowpi.org
[2]: https://github.com/larsimmisch/pyalsaaudio/