Option 1:

while (@ref) {
  my $k = shift(@ref);
  $out{$k} = [ shift(@ref), shift(@ref) ];
}
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while (@ref) {
  $out{$_} = [ shift(@ref), shift(@ref) ] for shift(@ref);
}
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Option 2: Change your SQL to something like SELECT key, value1, key, value2, then do:

push @{ $out{shift(@ref)} }, shift(@ref) while (@ref);
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