That's a hard problem. If you have some material like that with a clear recording, the only good commercial solution that I know of is Melodyne, and he's not saying how he does it. In theory you just look for multiple peaks in the FFT, but this is much easier said than done.

i built a plogue bidule patch before melodyne rolled out "dna" and it is extremely difficult to get the optimal fft parameters to get an accurate conversion. i cant imagine an algorithm that would get it right from analyzing the sample would be any less difficult. ableton's and cubase's options are pretty rough too. i am a drummer though, i am just trying to make up for my ears.