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my %gene = ();
foreach (@gene_score) {
...
  $gene{$_->[0]}->{stop} = $_->[2];
  $gene{$_->[0]}->{chr} = $_->[3];
}

%gene = ( gene_name_0 => { score => 'score_0',
                           start => 'start_0',
...
          gene_name_1 => { score => 'score_1',
          ...
        );