Untested:
%data;
$data{$_[0]}{$_[1]} = [@{$_}[2,3]] for @$query2;
foreach my $row (@$query) {
no warnings 'uninitialized';
$$row[2] -= $data{$$row[0]}{$$row[1]}[0];
$$row[3] -= $data{$$row[0]}{$$row[1]}[1];
local $" = ",";
print "@$row\n";
}
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