You only show 2 columns of input data, but your code seems to expect 10 columns ($fields[9]). If I just assume 2 columns (what choice do I have?), you could stuff your input into an Hash-of-Hashes data structure as follows: 
use strict;
use warnings;
use Data::Dumper;

my %clone_hash;

while (<DATA>) {
    my ($key, $value) = split;
    my $grade = ($value =~ /^pass[1-3]$/) ? 'good' : 'bad';
    $clone_hash{$key}{$grade}++;
}
print Dumper(\%clone_hash);

__DATA__
Eif2b2    fail
Eif2b2    pass5
Eif2b2    fail
Eif2b2    pass2
Eif2b2    fail
Eif2b2    pass4
Eif2b2    fail
49334    fail
49334    fail
49334    pass1
49334    fail
49334    pass4
Oxct1    pass4
Oxct1    fail
Oxct1    pass4
Oxct1    fail

[download]

which prints out (unsorted): 

$VAR1 = {
          'Eif2b2' => {
                        'good' => 1,
                        'bad' => 6
                      },
          '49334' => {
                       'good' => 1,
                       'bad' => 4
                     },
          'Oxct1' => {
                       'bad' => 4
                     }
        };

[download]

In reply to Re: processing key value pairs of a hash by toolic
in thread processing key value pairs of a hash by lomSpace

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