If you can use modules you might like the following solution:

#!/usr/local/bin/perl
#
use strict;
use warnings;
use Set::IntSpan::Fast;

my @sequence_numbers = map {int($_)} (<DATA>);

my $set = Set::IntSpan::Fast->new();
$set->add_range(1,9999);
$set->invert();
$set->add(@sequence_numbers);
$set->invert();
print $set->as_string() . "\n";

__DATA__
9996 
9998 
9999 
0001 
0003 
0005
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Which produces:

2,4,6-9995,9997
[download]