#!/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;