# prepare_run.pl

open my $file, '+<', 'main.pl'; #your original script we will replace keywords
open my $run, '+>', 'run.pl'; #newly created script that we will execute below

print "Enter left side of s///: ";
chomp(my $LeftSide = <STDIN>);

print "Enter right side of s///: ";
chomp(my $RightSide = <STDIN>);

while(my $line = <$file>){
print $run $line if $line !~ /.*search_here.*/ || /.*replace_here.*/;
print $run $line if $line =~ s/(.*)search_here(.*)/$1$LeftSide$2/ && 	$line =~ s/(.*)replace_here(.*)/$1$RightSide$2/;
}

close($file);
close($run);

system("run.pl"); #or whatever the the equivalent of your OS.