Hi Sandy_Bio_Perl,

Try something like this:

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

open(my $in_fh, '<', 'input.txt') or die $!;
open(my $out_fh, '>', 'output.txt') or die $!;

my %seen_lines;
while (<$in_fh>)
{
    chomp;
    my @columns = split;
    
    if ($columns[1] and $columns[1] =~ /^HLA-A/)
    {
        my $HLA_Peptide = $columns[1] . $columns[2];
        print $out_fh "$_\n" if (!exists $seen_lines{$HLA_Peptide});
        $seen_lines{$HLA_Peptide} = 1;
    }
    else
    {
        print $out_fh "$_\n";
    }
}
close $out_fh;
close $in_fh;
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