I know this should be pretty easy, but for the life of me I can't quite get it to work.

I have a program (lets call it trjconv) calling it from the command line has the following structure

trjconv -f (file one) -s (file 2) -o (output)

Once it loads it requires me to enter a selection, which is always "1".

I need to run this command roughly 500 times, and it is an absolute pain to have the computer on my lap the whole time just so I can press 1 and enter every 45 seconds.

At this point I'll use just about anything to automate this process (though I prefer awk or sed since I am working on learning them).

Thank you for any and all help.

It depends a bit on the program in question and if it correctly handles piped input, but try this:

This really isn't an optimal job for awk or sed, if the simple answer above doesn't work i would suggest trying expect, it is built for exactly that kind of automation. You could also look at autoexpect, but this would be a pretty trivial expect script.

how about echo 1 | trjconf ...

Echo worked. Thanks.

-Problem Solved-

You can also add ` < <(yes 1)' to the end of the command.

I use this for commands like cp and mv with "interactive" options.
If you want to answer "no" since a non-zero replay is the same, you can get colorful and put a smiley in your command:
mv -vi source/* dest/ < <(

If echo worked then yes should work, the only issue I see with using echo is it's only going to execute one time and then it will sit there forever, although in retrospect I may have misread your issue. If you need multiple 1's inputed use yes, if you need a single 1 inputed use echo. If you're running the same command 500 times you might want to put it in a loop and do the echo/yes as appropriate.