You could always just start doing what you're trying to do and set up and alarm handler.

$SIG{ALRM}      =       sub { die "timeout" };
eval {
       alarm(300);
       # do stuff here
       alarm(0);
};

if($@) {
       if($@ =~ /timeout/) {
           #
           #  Call our alrm_hdlr subroutine, we were hung up
           #
           alrm_hdlr();
       } else {
           alarm(0);
           die;
       }
}

# continue on, manipulate data, etc...

sub alrm_hdlr {
      # Handle the fact that we got hung up
}
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