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use strict;
use warnings;
...
   chr( ( ord($1) - ord('a') + $rot + 26 ) % 26 + ord('a') )
/ge;
print("$message\n");

use strict;
use warnings;
...
chomp(my $message = lc(<>));
eval "\$message =~ tr/$src/$dst/;";
print("$message\n");

use strict;
use warnings;
...
chomp(my $message = lc(<>));
$message = $tr->($message);
print("$message\n");