Hi toolic!
I have tried several different ways to trying to get the 'bad' values from
the hash of hashes. Some compile and others don't. The lit online is not
clear to me. In my code you will see where I commented out my most
recent attempt at printing the 'bad'.

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;


=cut
open( my $in, "c:/Documents and Settings/mydir/Desktop/current/mart_ex
+port.txt" );
open( my $out, ">c:/Documents and Settings/mydir/Desktop/current/clone
+_qual_counts.txt" );

my $first_line = <$in>;
chomp $first_line;

my %clone_hash;
print $out "clone\tgood\tbad\n";
while (<$in>)
{
    chomp;
    my @fields = split /\t/;         
    my ($gene_symbol, $esc_qc) = ($fields[1], $fields[8]);
    #use regex to extend to a hash of hashes to separate good and bad 
+clone counts
    my $grade = ($esc_qc =~ /^pass[1-3]$/) ? 'good' : 'bad';
    $clone_hash{$gene_symbol}{$grade}++;
}
for (keys %clone_hash) {
    #print $out "$_ \t $clone_hash{$_}{good}\n" if exists $clone_hash{
+$_}{good};
    print $out "$_ \t$clone_hash{$_}{good}\n" if exists $clone_hash{$_
+}{good};
    #print $out "\t$clone_hash{$_}->{'bad'}\n";
}
#print Dumper(\%clone_hash);

close ($in);
close ($out);
[download]

It is apparent that I am new to hash of hashes. I humbly appreciate you help.
LomSpace