use strict;
use warnings;

 my @files = map{$_->[0]}


##</code><code>##

 my @files = map{$_->[0]}
 sort{
      $a->[1] <=> $b->[1]
             ||
      $a->[2] <=> $b->[2]    
             ||
      $a->[3] <=> $b->[3]  
    }
 map{[$_,/.+?_A\.(.+?)-(.+?)-(\d+)\..+$/]}<DATA>;


##</code><code>##

print $_,$/ for @files;

__DATA__
abcd1_abc_123456.abc1a_A.201307282200-2300-1.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-2.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-3.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-4.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-1.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-2.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-3.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-4.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-5.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-10.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-11.gz
abcd1_abc_123456.abc1a_A.201307282300-2400-12.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-10.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-11.gz
abcd1_abc_123456.abc1a_A.201307282200-2300-12.gz


##</code><code>##

foreach (@files) {
my $file = $_;