Sorry, I didn't include all my code, because it is long and not very good!

Just in case you think I am not trying to do it myself see the attached

#!/usr/bin/perl
 
use strict;
use warnings;
use HBV;

my $machine="PC";
my ($inputDataPath, $outputDataPath,$inPathForScript,$outPathForScript
+) = HBV::PathFinder($machine);

my $origfile = $outputDataPath. qw(individualAlleles\HLA-A-1_HBe_Analy
+sis.txt);  # HLA-A-1_HBe_Analysis.txt
open (IN, $origfile) or die "cannot open $origfile";


my @columns;
my $count = 0;
my @genotypeAndAllele;
my @binders;
my @lineCount;
my $bitBinder;
my @bitBinder;
my @copybinders;

while (my $line = <IN>){
    chomp $line;
    if ($line =~/^([A-Z]{9}).*(IOH.{7}).*([1-9].?).*(HLA.{8})/){
    push @genotypeAndAllele,$4.' '.$2;
    push @lineCount,$3;
    }

    if ($line =~/^([A-Z]{9})/){
        push @binders, $1;
        @copybinders = @binders;
    }
}

foreach my $el (@lineCount){
    for (my $i=0; $i <$el; $i++){
    my $bit = $binders[$i];
    $bitBinder .= $bit." ";
    }
    push @bitBinder, $bitBinder;
    $bitBinder='';
    splice @binders,0,$el;
}

my %alleleProtein;
foreach my $item (@genotypeAndAllele){
    $alleleProtein{$item}++;
}

my %bindersHash;
foreach my $item (@copybinders){
    $bindersHash{$item}++;
}


my %genoBinderAlleleHash; @genoBinderAlleleHash{@genotypeAndAllele} = 
+@bitBinder;
foreach my $keys (sort {$a cmp $b} keys (%genoBinderAlleleHash)){
print "$keys \($alleleProtein{$keys}\) = $genoBinderAlleleHash{$keys}\
+n";
}

foreach my $keys (sort {$bindersHash{$b} <=> $bindersHash{$a}} (keys (
+%bindersHash))){
print "$keys = $bindersHash{$keys}\n";
}
[download]

Sorry to have bothered you