Receiving Character Controller Input from Other Program

I have a program that is supposed to send key presses to my Unity game. The code is:

SendKeys.SendWait("w 1000")

which sends keypresses of "w" to the Unity game window. I am using the default first person character controller and I would like to be able to control it from this program. However instead of moving the character forward like the "w" button normally would it causes my character to jump up and down in place. This happens regardless of which button I choose to send (none of these are the jump button). Does anyone know why this is and how I can fix it?