You have an extra level introduced in the push @all and you need to flush @temp2: 

        elsif ( $line =~ /\^+/xms ) {
            push @all, @temp2;
            @temp2 = ();
        }

[download]

With both sets of changes applied to your original code it now prints:

$VAR1 = {
          'mus09r' => [
                        [
                          'AGAGAAAG 1',
                          '7',
                          '0.142138988325903',
                          '3',
                          '0',
                          [
                            '7.66666666666667',
                            '1,-424,CAGAGACAGGGGAGAGATAG',
                            '1,-338,AAGAGAAAGGGAGGAGAGGC',
                            '1,-349,AAGAGGGGAGGAAGAGAAAG'
                          ]
                        ],
                        [
                          'AGAGAAAG 1',
                          '7',
                          '0.142138988325903',
                          '3',
                          '0',
                          [
                            '7.66666666666667',
                            '1,-337,AGAGAAAGGGAGGAGAGGCA',
                            '1,-348,AGAGGGGAGGAAGAGAAAGG',
                            '1,-423,AGAGACAGGGGAGAGATAGA'
                          ]
                        ],
                        [
                          'AGAAACAG 1',
                          '7',
                          '1.36112386682747',
                          '4',
                          '4',
                          [
                            '7.66666666666667',
                            '1,-383,TGAGAAACAG',
                            '1,-319,CAAGAAACAG',
                            '0,-457,CTTGAAACAG'
                          ]
                        ]
                      ]
        };

[download]
DWIM is Perl's answer to Gödel

In reply to Re^3: Problem of Duplicating an Array while Parsing Text by GrandFather
in thread Problem of Duplicating an Array while Parsing Text by monkfan

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