I think this is usually done in two steps: audio>midi and then midi>notation. Some of the audio>midi software works OK for a single-note (monophonic) line, but the recognition of midi note pitches from polyphonic (multi-note, multi-instrument) audio is inevitably a lot less accurate (to put it mildly). A lot depends on the instrumentation in the audio file. Complex instruments with lots of harmonics are harder to work with than e.g. a simple pure flute sound. Maybe Intelliscore, Wavemid or WIDI?

Shotcut.