[LAU] midi capture of external hardware over usb

Hi all, I have a Korg Oasys synth that has some digital based drums, and a Jomox xbase 999 analog drum machine, which also has an analog filter. I'd like to use some of the preset drum patterns on the Oasys as a starting point, and play them on the Jomox via midi and run the output thru the analog filter. Problem is: The MIDI notes on the jomox aren't the same as the kit I want to use in the Oasys. I have a midisport 2x2 that works fine in linux (opensuse 11.2) . I have jackd seemingly running properly. I'd like to capture the MIDI coming out of the Oasys, capture it on linux into perhaps a midi file, and then edit the notes so that they match the kit on the Jomox. If that plan makes sense, once I get to that point I could use any midi sequencer to get the pattern to the jomox. Can anyone give me some advice on this? Googling brought me to Qtractor and CSound for midi capture, but they don't seem to be the right tool for midi capture over usb. If they are, any pointers would be helpful.