my $setup = "./setup";
my $answerFile = "./AnswerFile";
my $logFile = "./log";

open (IN, "<$answerFile") || die "can't open $answerFile: $!";
my @answerFile = <IN>;
close IN;

my $i=0; 
open (SETUP, "| $setup") || die "can't run $setup: $!";
while(<SETUP>)
{
   # stuff gets printed out then a question is displayed
   # want to answer the question from $answerFile
   # perhaps:
   print SETUP $answerFile[$i++];
}
close SETUP;