Probably a better thought out solution could be made, but I think this may be what you're after. 
#!/usr/bin/perl
use strict;
use warnings;

my %hash = ( 
'abc,def' => {
               ',,,item4' => 1,
               'item1,,,' => 1,
               ',item2,,' => 1
              },
'kln,mno' => {
               ',,,item4' => 1,
               'item1,,,' => 1
              },
);

my %new_hash;
for my $key (keys %hash) {
    my @array;
    for (keys %{ $hash{$key}}) {
        my ($lead_comma,$item) = /^(,*)([^,]+)/;
        $array[ length $lead_comma ] = $item;
    }
    $new_hash{$key} = \@array;
}
use Data::Dumper; print Dumper \%new_hash;

__END__
output from Data::Dumper

$VAR1 = {
          'abc,def' => [
                         'item1',
                         'item2',
                         undef,
                         'item4'
                       ],
          'kln,mno' => [
                         'item1',
                         undef,
                         undef,
                         'item4'
                       ]
        };

[download]

In reply to Re: merge with multiple row with same key by Cristoforo
in thread merge with multiple row with same key by tcheungcm

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.