#!/usr/bin/env perl -l

use strict;
use warnings;

my $all_aref = [ [qw{id1 seq1}], [qw{id2 seq2}], [qw{id3 seq4}] ];
my $filter_aref = [ [qw{id1 seq1}], [qw{id3 seq3}] ];
my %filter_hash;
$filter_hash{$_->[0]}{$_->[1]} = 1 for @$filter_aref;

for (@$all_aref) {
    if (exists $filter_hash{$_->[0]}) {
        print "ID $_->[0] in filter";
        if (exists $filter_hash{$_->[0]}{$_->[1]}) {
            print "SEQ $_->[1] in filter for ID $_->[0]";
        }
        else {
            print "SEQ $_->[1] not in filter for ID $_->[0]";
        }
    }
    else {
        print "ID $_->[0] not in filter";
    }
}