#!/usr/bin/env perl

use strict;
use warnings;

while (<DATA>) {
    if (/^>/) {
        print "\n" unless $. == 1;
        print;
    }
    else {
        chomp;
        print;
    }
}

print "\n";

__DATA__
>chunk1
c1_line1
c1_line2
c1_line3
>chunk2
c2_line1
c2_line2
c2_line3

##</code><code>##

>chunk1
c1_line1c1_line2c1_line3
>chunk2
c2_line1c2_line2c2_line3