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use strict;
use warnings;

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

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

print $_,$/ for @files;

...
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

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