Bio::EnsEMBL::Pipeline::SeqFetcher::BioIndex

    my $obj = Bio::EnsEMBL::Pipeline::SeqFetcher::BioIndex->new(
								-db    => $db
							     );
    my $seq = $obj->get_Seq_by_acc($acc);

  Object to retrieve sequences as Bio::Seq, using getseqs by James Cuff. Sequences are fetched from a 
database previously formatted with makeindex

  my ($self, $dbs) = @_;
  if (!defined($self->{'_db'})) {
    $self->{'_db'} = [];
  }
  if (defined $dbs){
    if (ref($dbs) eq 'ARRAY') {
      foreach my $db(@$dbs){
	$self->throw("are you sure that $db has been formatted with DBIndex? Some files are missing\n") 
	  unless (-d "$db" && -e "$db/config.dat" && -e "$db/fileids.dat");
	
	my $index =  new Bio::EnsEMBL::Pipeline::SeqFetcher::DBIndex(-database => $db);

	$self->index($index);

	push (@{$self->{'_db'}},$db);
      }
    }
  }
  return (@{$self->{'_db'}});

  my ($self, $acc) = @_;

  if (!defined($acc)) {
    $self->throw("No accession input");
  }  
  
  my $seq;

  foreach my $index ($self->index) {

    my $entry = $index->get_Seq_by_id($acc);

    if ($entry ne "") {
      print "Entry\n";
      my ($idstr,$seqstr) = split(/\n/,$entry,2);
      my ($id,$desc) = split(/ /,$idstr,2);

      $id =~ s/^>//;
      
      $seqstr =~ s/\n//g;
      
      my $seq =  new Bio::Seq(-id      => $acc,
			      -display_id => $acc,
			      -seq    => $seqstr);
      return $seq;
    }
  }
  return;

  my $self = @_;
  return undef;
}

1;

  my ($self,$arg) = @_;


  if (!defined ($self->{_index})) {
    $self->{_index} = [];
  }

  if (defined($arg)) {
    push(@{$self->{_index}},$arg);
  }
  return @{$self->{_index}};

  my ($class, @args) = @_;
  my $self = bless {}, $class;

  my ($db) = $self->_rearrange(['DB'], @args);

  # expect an array of dbs
  $self->throw("Expected a reference to an array of db [" . ref($db) . "]\n") unless ref($db) eq 'ARRAY';
  if (defined $db) {
    $self->db($db);
  }
  
  return $self; # success - we hope!