In general I'd recommend avoiding the pattern while(chomp(<$handle>)) because it often suffers from issues (another explanation).
You might also want to consider using a module for prompting.
use IO::Prompt 'prompt';
my $resp = prompt("Foo? ", -yn);
my $term = Term::ReadLine->new;
my $line = $term->readline("Bar? ");
Or even this (the advantage being ExtUtils::MakeMaker is a core module, even though it has a completely different purpose):
use ExtUtils::MakeMaker 'prompt';
my $value = prompt("Quz?","n");
The module does have another advantage: "If prompt() detects that it is not running interactively and there is nothing on STDIN or if the PERL_MM_USE_DEFAULT environment variable is set to true, the $default will be used without prompting. This prevents automated processes from blocking on user input."
Update 2020-11-30: See also the more powerful IO::Prompter, simple example here.