I see. OK, that answers one question, but it is not clear from what you have posted so far what constitutes a "test". Is a 'test" the same as a "file"? You still haven't posted any sample data with the expected output from that data. That would be helpful in trying to understand your situation.

Also, are you aware of how fragile it is to try to handle comma-separated values manually by just splitting? Use Text::CSV! (In fact you could encapsulate this whole program into a Text::CSV after_parse callback, but that's a different story...)

Assuming that one file is one test, testing one href, and that you do *not* want multiple hashes each keyed with 'test', but just one, with one listing for each group, maybe you could use something like:

use strict;
use warnings;
use feature 'say';

use JSON;

my $results = {};

for my $href ('root') {
    my $by_group = {};

    while (my $line = <DATA>) {
        my ( $key, $group, $value, $version, $file, $count ) = split(/
+,/, $line);

        push @{ $by_group->{ $group } }, $value;
    }

    my $test = [];
    for my $group ( keys %{ $by_group } ) {
        push @{ $test }, { group => $group, values => $by_group->{ $gr
+oup } }
    }

    $results->{ $href } = $test;
}

say JSON->new->pretty->canonical->encode($results);

__DATA__
bla,ABC,6.13.00,bla,bla,bla
bla,XYZ,1234,bla,bla,bla
bla,XYZ,tcsh,bla,bla,bla
bla,WEA,6.13.00,bla,bla,bla
bla,BAB,ASDAS,bla,bla,bla
bla,BAB,12312321,bla,bla,bla
bla,SADA,6.13.00,bla,bla,bla
bla,SADA,12312321,bla,bla,bla
[download]

$ perl oved.pl
{
   "root" : [
      {
         "group" : "BAB",
         "values" : [
            "ASDAS",
            "12312321"
         ]
      },
      {
         "group" : "ABC",
         "values" : [
            "6.13.00"
         ]
      },
      {
         "group" : "XYZ",
         "values" : [
            "1234",
            "tcsh"
         ]
      },
      {
         "group" : "WEA",
         "values" : [
            "6.13.00"
         ]
      },
      {
         "group" : "SADA",
         "values" : [
            "6.13.00",
            "12312321"
         ]
      }
   ]
}
[download]

Hope this helps!