I haven't yet worked out what you are doing with the @two array but here is what I have working so far. 

#!perl
use strict;
use warnings;
use autodie;
use Bio::SeqIO;
STDOUT->autoflush(1);

my $gbffpath = 'your path';
opendir DIR, $gbffpath;
my @files = grep {/\.gbff$/ } readdir DIR;
closedir DIR;

foreach my $gbfffile (@files){
  my $in = Bio::SeqIO->new(-file=>$gbffpath.'/'.$gbfffile,
                           -format=>"genbank");
  my $obj = $in->next_seq();
  my @feat = $obj->get_SeqFeatures();
  my $start = 0; my $length = 9;
  foreach my $n  (0..$#feat){
    my $pt    = $feat[$n]->primary_tag();
    $start   += $feat[$n]->start();
    my $end = $start + $length;
    my $subseq = $obj->subseq($start,$end);
    printf "%2d %-10s %2d %2d %s\n",$n,$pt,$start,$end,$subseq;
    $start = $end;
  }
}

[download]
poj

In reply to Re: Trying to get intergenic sequences using BioPerl by poj
in thread Trying to get intergenic sequences using BioPerl by Sosi

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