#!/usr/bin/env perl

use strict;
use warnings;

my ($group_size, $group) = (2, 0);
local $/ = "\n>";

while (<DATA>) {
    print '*** Filename: XYZ_', ++$group, "\n" unless ($. - 1) % $group_size;
    chop;
    print '>' unless $. == 1;
    print; 
}

print "\n";

__DATA__
>b_comp_seq1
ACGCGGGGGAATTT
>b_comp_seq_2
ACGGGCTTTCACC
>b_comp_seq3
ACGCGGGGGAATTT
>b_comp_seq_4
ACGGGCTTTCACC

##</code><code>##

*** Filename: XYZ_1
>b_comp_seq1
ACGCGGGGGAATTT
>b_comp_seq_2
ACGGGCTTTCACC
*** Filename: XYZ_2
>b_comp_seq3
ACGCGGGGGAATTT
>b_comp_seq_4
ACGGGCTTTCACC