# chop the inputs to remove the trailing \n
my $l = <STDIN>;
chop($l);
.. and so on..
# use while to loop over the lines in the file
open MAPFILE "$sdtfile" or die;
while (<MAPFILE>) {
  my ($date, $time, $lot, $waf, $ts, $sstep, $machine, $prog, $product, $plnfile, $striping) = split(/,/, $_);
  if (..) {
    # rest of the program
  }
}