Yes, PIPE and prog are meant to be talking about the same process. oh dear .. i have a lot to learn here.
OK ... well eventually I would like this program to be run as a cgi itself yes. But I'm not going to be running another cgi from this script, its a C program. Everything is on the same server, so perhaps I could run them locally then.
Thanks for the tips so far.
As for how I would run the program on the command line normally .. well I would type in the name of the program to start .. and then a prompt comes up asking me for the text file to process.

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