$_ eq 's' ? $OPER='s' : $OPER='c';

That's a priority issue. Try:

However, your code has a worse problem: mo strict nor warnings. As a consequence, your usage of lc is useless without you noticing it:

print "Field 1 & 2 Separate or Combined? ";
chomp($_=<STDIN>);
lc($_);
$_ eq 's' ? $OPER='s' : $OPER='c';
print "OPER $OPER\n";
__END__
Field 1 & 2 Separate or Combined? S
OPER c
[download]

Try this fixed version:

use strict;
use warnings;

print "Field 1 & 2 Separate or Combined? ";
chomp ($_ = <STDIN>);
my $OPER = lc eq 's' ? 's' : 'c';
print "OPER $OPER\n";
[download]