Since I need all of the query and answers info on one line in the output, yes, I need to collect them up until I have all of the answers.

here is a more closely working example of the code. I was trying to keep it simple and focus on the memory usage of the hash but here we are.

#!/usr/bin/perl

use warnings;
use strict;
$|++;

use JSON;

my $l;
my @vals;
my $json;
my %pairs;
my %pind;
my %flush;

while (<DATA>) {
    $l = $_;
    chomp $l;
    @vals = split /;/, $l;
    if ($vals[0] =~ /Query/) {
        if (! $pairs{$vals[1]}) {
            $pind{$vals[1]} = 0;
        }
        if (!defined $flush{$vals[1]}) {
                $flush{$vals[1]} = " ";
        } elsif ($flush{$vals[1]} ne $vals[1]) {
                $json = encode_json $pairs{$vals[1]};
                print "DEBUG: Flushing \"complete\" answer\n";
                print $json."\n";
                delete $pairs{$vals[1]};
                $flush{$vals[1]} = $vals[1];
                $pind{$vals[1]} = 0;
        }
        $pairs{$vals[1]}{$vals[2]} = $vals[3];
        $pairs{$vals[1]}{id} = $vals[1];
    } elsif ($vals[0] =~ /Answer/) {
        $pairs{$vals[1]}{$vals[0]}[$pind{$vals[1]}++]{$vals[2]} = $val
+s[3];
    }
}

print "DEBUG: output remaining data ...\n";

foreach my $key (keys %pairs) {
        $json = encode_json $pairs{$key};
        print $json."\n";
}

__DATA__
Query;1;host;www.example.com
Answer;1;ip;1.2.3.4
Query;2;host;www.cnn.com
Query;3;host;www.google.com
Answer;2;ip;2.3.4.5
Answer;2;ip;2.3.4.5
Query;4;host;www.google.com
Answer;4;ip;3.4.5.6
Answer;3;ip;3.4.5.6
Query;2;host;www.example2.com
Answer;4;ip;1.2.4.5
Answer;2;ip;2.3.4.5
[download]

DEBUG: Flushing "complete" answer
{"Answer":[{"ip":"2.3.4.5"},{"ip":"2.3.4.5"}],"id":"2","host":"www.cnn
+.com"}
DEBUG: output remaining data ...
{"Answer":[{"ip":"3.4.5.6"},{"ip":"1.2.4.5"}],"id":"4","host":"www.goo
+gle.com"}
{"Answer":[{"ip":"1.2.3.4"}],"id":"1","host":"www.example.com"}
{"Answer":[{"ip":"3.4.5.6"}],"id":"3","host":"www.google.com"}
{"Answer":[{"ip":"2.3.4.5"}],"id":"2","host":"www.example2.com"}
[download]