$seq_dumper = Bio::EnsEMBL::Utils::SeqDumper;

  # don't dump snps or repeats
  $seq_dumper->disable_feature_type('repeat');
  $seq_dumper->disable_feature_type('variation');

  # dump EMBL format to STDOUT
  $seq_dumper->dump( $slice, 'EMBL' );

  # dump GENBANK format to a file
  $seq_dumper->dump( $slice, 'GENBANK', 'out.genbank' );

  # dump FASTA format to a file
  $seq_dumper->dump( $slice, 'FASTA', 'out.fasta' );

  my $self = shift;

  my ($sec, $min, $hour, $mday,$mon, $year) = localtime(time());

  my $month = ('JAN', 'FEB', 'MAR', 'APR', 'MAY', 'JUN', 'JUL',
	       'AUG', 'SEP', 'OCT', 'NOV', 'DEC')[$mon];
  $year += 1900;
  
  return "$mday-$month-$year";

  my $self   = shift;
  my $slice  = shift;
  my $FH     = shift;
  my $FORMAT = shift;

  #use only the core database to dump features (except for bloody snps)
  my $lite = $slice->adaptor->db->remove_db_adaptor('lite');

  my $meta = $slice->adaptor->db->get_MetaContainer;
  my $species = $meta->get_Species;

  #lump file handle and format string together for simpler method calls
  my @ff = ($FH, $FORMAT);
  my $value;

  #source
  my $classification = join(', ', $species->classification);
  $self->write(@ff,'source', "1.." . $slice->length());
  $self->write(@ff,''      , '/organism="'.$species->binomial . '"');
  $self->write(@ff,''      , '/db_xref="taxon:'.$meta->get_taxonomy_id().'"');

  #
  # Transcripts & Genes
  #
  my @gene_slices;
  if($self->is_enabled('gene')) {
    push @gene_slices, $slice;
  }

  # Retrieve slices of other database where we need to pull genes from

  my $gene_dbs = {'vegagene' => 'vega',
                  'estgene'  => 'estgene'};

  foreach my $gene_type (keys %$gene_dbs) {
    if($self->is_enabled($gene_type)) {
      my $db = $self->get_database($gene_dbs->{$gene_type});
      if($db) {
        my $sa = $db->get_SliceAdaptor();
        push @gene_slices, $sa->fetch_by_name($slice->name());
      } else {
        warning("A [". $gene_dbs->{$gene_type} ."] database must be " .
                "attached to this SeqDumper\n(via a call to " .
                "attach_database) to retrieve genes of type [$gene_type]");
      }
    }
  }

  foreach my $gene_slice (@gene_slices) {
    foreach my $gene (@{$gene_slice->get_all_Genes(undef,undef, 1)}) {
      $value = $self->features2location( [$gene] );
      $self->write( @ff, 'gene', $value );
      $self->write( @ff, "", '/gene='.$gene->stable_id() );


      if(defined($gene->display_xref)){
	$self->write( @ff, "",'/locus_tag="'.$gene->display_xref->display_id.'"');
      }
      my $desc = $gene->description;
      if(defined($desc) and $desc ne ""){
	$desc =~ s/\"//; 
	$self->write( @ff, "", '/note="'.$gene->description.'"');
      }



      foreach my $transcript (@{$gene->get_all_Transcripts}) {
        my $translation = $transcript->translation;

        # normal transcripts get dumped differently than pseudogenes
        if($translation) {
          #normal transcript
          $value = $self->features2location($transcript->get_all_Exons);
          $self->write(@ff, 'mRNA', $value);
          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"');
          $self->write(@ff,''
                       ,'/note="transcript_id='.$transcript->stable_id().'"');

          # ...and a CDS section
          $value = 
            $self->features2location($transcript->get_all_translateable_Exons);
          $self->write(@ff,'CDS', $value);
          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"'); 
          $self->write(@ff,'', '/protein_id="'.$translation->stable_id().'"');
          $self->write(@ff,''
                       ,'/note="transcript_id='.$transcript->stable_id().'"');

          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
            $value = '/db_xref="'.$dbl->dbname().':'.$dbl->display_id().'"';
            $self->write(@ff, '', $value);
          }

          $value = '/translation="'.$transcript->translate()->seq().'"';
          $self->write(@ff, '', $value);
        } else {
          #pseudogene
          $value = $self->features2location($transcript->get_all_Exons);
          $self->write(@ff, 'misc_RNA', $value);
          $self->write(@ff,''   , '/gene="'.$gene->stable_id().'"');
          foreach my $dbl (@{$transcript->get_all_DBLinks}) {
            $value = '/db_xref="'.$dbl->dbname().':'.$dbl->primary_id().'"';
            $self->write(@ff, '', $value);
          }
          $self->write(@ff,''   , '/note="'.$transcript->biotype().'"');
          $self->write(@ff,''
                       ,'/note="transcript_id='.$transcript->stable_id().'"');
        }
      }
    }

    # exons
    foreach my $gene (@{$gene_slice->get_all_Genes(undef,undef,1)}) {
      foreach my $exon (@{$gene->get_all_Exons}) {
        $self->write(@ff,'exon', $self->features2location([$exon]));
        $self->write(@ff,''    , '/note="exon_id='.$exon->stable_id().'"');
      }
    }
  }

  #
  # genscans
  #
  if($self->is_enabled('genscan')) {
    my @genscan_exons;
    foreach my $transcript(@{$slice->get_all_PredictionTranscripts(undef,1)}) {
      my $exons = $transcript->get_all_Exons();
      push @genscan_exons, @$exons;
      $self->write(@ff, 'mRNA', $self->features2location($exons));
      $self->write(@ff, '', '/product="'.$transcript->translate()->seq().'"');
      $self->write(@ff, '', '/note="identifier='.$transcript->stable_id.'"');
      $self->write(@ff, '', '/note="Derived by automated computational' .
		   ' analysis using gene prediction method:' .
		   $transcript->analysis->logic_name . '"');
    }
  }

  #
  # snps
  #
  if($self->is_enabled('variation') && $slice->can('get_all_VariationFeatures')) {
#    $slice->adaptor->db->add_db_adaptor('lite', $lite) if $lite;

    foreach my $snp (@{$slice->get_all_VariationFeatures}) {
      my $ss = $snp->start;
      my $se = $snp->end;
      #skip snps that hang off edge of slice
      next if($ss < 1 || $se > $slice->length); 

      $self->write(@ff, 'variation', "$ss..$se");
      $self->write(@ff, ''         , '/replace="'.$snp->allele_string.'"'); 
      #$self->write(@ff, ''         , '/evidence="'.$snp->status.'"'); 
      my $rs_id = $snp->variation_name();
      my $db = $snp->source();
#      foreach my $link ($snp->each_DBLink) {
#        my $id = $link->primary_id;
#        my $db = $link->database;
        $self->write(@ff, '', "/db_xref=\"$db:$rs_id\""); 
#      }
    }

#    $slice->adaptor->db->remove_db_adaptor('lite') if $lite;
  }

  #
  # similarity features
  #
  if($self->is_enabled('similarity')) {
    foreach my $sim (@{$slice->get_all_SimilarityFeatures}) {
      $self->write(@ff, 'misc_feature', $self->features2location([$sim]));
      $self->write(@ff, ''       , '/note="match: '.$sim->hseqname.
		  ' : '.$sim->hstart.'..'.$sim->hend.'('.$sim->hstrand.')"');
    }
  }

  #
  # repeats
  #
  if($self->is_enabled('repeat')) {
    my $rfs = $slice->get_all_RepeatFeatures();

    foreach my $repeat (@$rfs) {
      $self->write(@ff, 'repeat_region', $self->features2location([$repeat]));
      $self->write(@ff, ''    , '/note="' . $repeat->repeat_consensus->name.
		   ' repeat: matches ' . $repeat->hstart.'..'.$repeat->hend .
		   '('.$repeat->hstrand.') of consensus"');
    }

  }

  #
  # markers
  #
  if($self->is_enabled('marker') && $slice->can('get_all_MarkerFeatures')) {
    foreach my $mf (@{$slice->get_all_MarkerFeatures}) {
      $self->write(@ff, 'STS', $self->features2location([$mf]));
      if($mf->marker->display_MarkerSynonym) {
        $self->write(@ff, ''   , '/standard_name="' .
                     $mf->marker->display_MarkerSynonym->name . '"');
      }


      #grep out synonyms without a source
      my @synonyms = @{$mf->marker->get_all_MarkerSynonyms};
      @synonyms = grep {$_->source } @synonyms;
      foreach my $synonym (@synonyms) {
        $self->write(@ff, '', '/db_xref="'.$synonym->source.
                     ':'.$synonym->name.'"');
      }
      $self->write(@ff, '', '/note="map_weight='.$mf->map_weight.'"');
    }
  }

  #
  # contigs
  #
  if($self->is_enabled('contig')) {
    foreach my $segment (@{$slice->project('seqlevel')}) {
      my ($start, $end, $slice) = @$segment;
      $self->write(@ff, 'misc_feature',
                   $start .'..'. $end);
      $self->write(@ff, '', '/note="contig '.$slice->seq_region_name .
		   ' ' . $slice->start . '..' . $slice->end .
		    '(' . $slice->strand . ')"');
    }
  }

  $slice->adaptor->db->add_db_adaptor('lite', $lite) if $lite;

  my ($self, $name, $db) = @_;

  $name || throw("name arg is required");
  unless($db && ref($db) && $db->isa('Bio::EnsEMBL::DBSQL::DBAdaptor')) {
    throw("db arg must be a Bio::EnsEMBL::DBSQL::DBAdaptor not a [$db]");
  }

  $self->{'attached_dbs'}->{$name} = $db;

  my ($self, $type) = @_;
  
  $type || throw("type arg is required");

  if(exists($self->{'feature_types'}->{$type})) {
    $self->{'feature_types'}->{$type} = 0;
  } else {
    warning("unknown feature type '$type'\n" .
	    "valid types are: " . join(',', keys %{$self->{'feature_types'}}));
  }

  my ($self, $slice, $format, $outfile, $seq) = @_;

  $format || throw("format arg is required");
  $slice  || throw("slice arg is required");

  my $dump_handler = $DUMP_HANDLERS->{uc($format)};

  unless($dump_handler) {
    throw("No dump handler is defined for format $format\n");
  }


  my $FH = IO::File->new;;
  if($outfile) {
    $FH->open(">>$outfile") or throw("Could not open file $outfile");
  } else {
    $FH =\* STDOUT;
    #mod_perl did not like the following
    #$FH->fdopen(fileno(STDOUT), "w") 
    #  or throw("Could not open currently selected output filehandle " .
    #		      "for writing");
  }
  
  &$dump_handler($self, $slice, $FH, $seq);

  $FH->close if ($outfile); #close if we were writing to a file

  my $self = shift;
  my $slice = shift;
  my $FH   = shift;
  my $SEQ = shift;

  my $len = $slice->length;

  my $version;
  my $acc;

  my $cs = $slice->coord_system();
  my $name_str = $cs->name() . ' ' . $slice->seq_region_name();
  $name_str .= ' ' . $cs->version if($cs->version);

  my $start = $slice->start;
  my $end   = $slice->end;

  #determine if this slice is the entire seq region
  #if it is then we just use the name as the id
  my $slice_adaptor = $slice->adaptor();
  my $full_slice =
    $slice->adaptor->fetch_by_region($cs->name,
                                    $slice->seq_region_name,
                                    undef,undef,undef,
                                    $cs->version);


  my $entry_name = $slice->seq_region_name();



  if($full_slice->name eq $slice->name) {
    $name_str .= ' full sequence';
    $acc = $slice->seq_region_name();
    my @acc_ver = split(/\./, $acc);
    if(@acc_ver == 2) {
      $acc = $acc_ver[0];
      $version = $acc_ver[0] . '.'. $acc_ver[1];
    } elsif(@acc_ver == 1 && $cs->version()) {
      $version = $acc . '.'. $cs->version();
    } else {
      $version = $acc;
    }
  } else {
    $name_str .= ' partial sequence';
    $acc = $slice->name();
    $version = $acc;
  }

  $acc = $slice->name();



  #line breaks are allowed near the end of the line on ' ', "\t", "\n", ',' 
  $: = ("\t\n -,");

  #############
  # dump header
  #############

  my $EMBL_HEADER = 
'@<   ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~
';

  #ID and moltype
  # HTG = High Throughput Genome division, probably most suitable
  #       and it would be hard to come up with another appropriate division
  #       that worked for all organisms (e.g. plants are in PLN but human is
  #       in HUM).
  my $VALUE = "$entry_name    standard; DNA; HTG; $len BP.";
  $self->write($FH, $EMBL_HEADER, 'ID', $VALUE);  
  $self->print( $FH, "XX\n" );

  #Accession
  $self->write($FH, $EMBL_HEADER, 'AC', $acc);
  $self->print( $FH, "XX\n" );

  #Version
  $self->write($FH, $EMBL_HEADER, 'SV', $version);
  $self->print( $FH, "XX\n" );

  #Date
  $self->write($FH, $EMBL_HEADER, 'DT', $self->_date_string);
  $self->print( $FH, "XX\n" );

  my $species   = $slice->adaptor->db->get_MetaContainer->get_Species();

  #Description
  $self->write($FH, $EMBL_HEADER, 'DE', $species->binomial .
               " $name_str $start..$end annotated by Ensembl");
  $self->print( $FH, "XX\n" );

  #key words
  $self->write($FH, $EMBL_HEADER, 'KW', '.');
  $self->print( $FH, "XX\n" );

  #Species
  my $species_name = $species->binomial();
  if(my $cn = $species->common_name()) {
    $species_name .= " ($cn)";
  }

  $self->write($FH, $EMBL_HEADER, 'OS', $species_name);

  #Classification
  my @cls = $species->classification;
  shift @cls; #shift off species name
  $self->write($FH, $EMBL_HEADER, 'OC', join('; ', reverse(@cls)) . '.');
  $self->print( $FH, "XX\n" );
  
  #References (we are not dumping refereneces)

  #Database References (we are not dumping these)

  #comments
  foreach my $comment (@COMMENTS) {
    $self->write($FH, $EMBL_HEADER, 'CC', $comment);
    $self->print( $FH, "XX\n" );
  }

  ####################
  #DUMP FEATURE TABLE
  ####################
  $self->print( $FH, "FH   Key             Location/Qualifiers\n" );

  my $FEATURE_TABLE = 
'FT   ^<<<<<<<<<<<<<<<^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~
';
  $self->_dump_feature_table($slice, $FH, $FEATURE_TABLE);  

  #write an XX after the feature tables
  $self->print( $FH, "XX\n" );

  ###################
  #DUMP SEQUENCE
  ###################

  if(!defined($SEQ)){
    $SEQ = $slice->seq();
  }
#  my $SEQ     = $slice->seq();
  my $length  = length($SEQ);
  my $a_count = $SEQ =~ tr/aA/aA/;
  my $c_count = $SEQ =~ tr/cC/cC/;
  my $t_count = $SEQ =~ tr/tT/tT/;
  my $g_count = $SEQ =~ tr/gG/gG/;
  my $other_count = $length - $a_count - $c_count - $t_count - $g_count;

  my $value = "Sequence $length BP; $a_count A; $c_count C; " .
    "$g_count G; $t_count T; $other_count other;";
  $self->write($FH, $EMBL_HEADER, 'SQ', $value);

  $self->write_embl_seq($FH,\$ SEQ);


  $self->print( $FH, "//\n" );

  # Set formatting back to normal
  $: = "\n -";

  my $self = shift;
  my $slice = shift;
  my $FH   = shift;

  my $id       = $slice->seq_region_name;
  my $seqtype  = 'dna';
  my $idtype   = $slice->coord_system->name;
  my $location = $slice->name;
  my $start = 1;
  my $end = $slice->length();

  my $header = ">$id $seqtype:$idtype $location\n";
  $self->print( $FH, $header );

  #set the formatting to FASTA
  my $FORMAT = '^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
';

  #chunk the sequence in 60kb chunks to use less memory
  my $cur = $start;
  while($cur < $end) {
    my $to = $cur + 59_999;
    $to = $end if($to > $end); 
    my $seq = $slice->subseq($cur, $to);
    $cur = $to + 1;
    $self->write($FH, $FORMAT, $seq);
  }

  my ($self, $slice, $FH, $SEQ) = @_;

  #line breaks are allowed near the end of the line on ' ', "\t", "\n", ',' 
  $: = "\t\n -,";

  my $GENBANK_HEADER = 
'^<<<<<<<<<  ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';

  my $GENBANK_SUBHEADER =
'  ^<<<<<<<  ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';

  my $GENBANK_FT =
'     ^<<<<<<<<<<<<<< ^<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<~~
';

  my $version;
  my $acc;

  my $cs = $slice->coord_system();

  my $name_str = $cs->name() . ' ' . $slice->seq_region_name();

  $name_str .= ' ' . $cs->version if($cs->version);

  #determine if this slice is the entire seq region
  #if it is then we just use the name as the id
  my $slice_adaptor = $slice->adaptor();
  my $full_slice =
    $slice->adaptor->fetch_by_region($cs->name,
                                    $slice->seq_region_name,
                                    undef,undef,undef,
                                    $cs->version);


  my $entry_name = $slice->seq_region_name();

  if($full_slice->name eq $slice->name) {
    $name_str .= ' full sequence';
    $acc = $slice->seq_region_name();
    my @acc_ver = split(/\./, $acc);
    if(@acc_ver == 2) {
      $acc = $acc_ver[0];
      $version = $acc_ver[0] . $acc_ver[1];
    } elsif(@acc_ver == 1 && $cs->version()) {
      $version = $acc . $cs->version();
    } else {
      $version = $acc;
    }
  } else {
    $name_str .= ' partial sequence';
    $acc = $slice->name();
    $version = $acc;
  }

  $acc = $slice->name();     # to keep format consistent for all

  my $length = $slice->length;
  my $start = $slice->start();
  my $end   = $slice->end();

  my $date = $self->_date_string;

  my $species = $slice->adaptor->db->get_MetaContainer->get_Species;


  #LOCUS
  my $tag   = 'LOCUS';
  my $value = "$entry_name $length bp DNA HTG $date";
  $self->write($FH, $GENBANK_HEADER, $tag, $value);

  #DEFINITION
  $tag   = "DEFINITION";
  $value = $species->binomial . 
    " $name_str $start..$end reannotated via EnsEMBL";
  $self->write($FH, $GENBANK_HEADER, $tag, $value);

  #ACCESSION
  $self->write($FH, $GENBANK_HEADER, 'ACCESSION', $acc);

  #VERSION
  $self->write($FH, $GENBANK_HEADER, 'VERSION', $version);

  # KEYWORDS
  $self->write($FH, $GENBANK_HEADER, 'KEYWORDS', '.');

  # SOURCE
  $self->write($FH, $GENBANK_HEADER, 'SOURCE', $species->common_name());

  #organism
  my @cls = $species->classification();
  shift @cls;
  $self->write($FH, $GENBANK_SUBHEADER, 'ORGANISM', $species->binomial);
  $self->write($FH, $GENBANK_SUBHEADER, '', join('; ', reverse @cls) . ".");

  #refereneces

  #comments
  foreach my $comment (@COMMENTS) {
    $self->write($FH, $GENBANK_HEADER, 'COMMENT', $comment);
  }

  ####################
  # DUMP FEATURE TABLE
  ####################
  $self->print( $FH, "FEATURES             Location/Qualifiers\n" );
  $self->_dump_feature_table($slice, $FH, $GENBANK_FT);

  ####################
  # DUMP SEQUENCE
  ####################

  if(!defined($SEQ)){
    $SEQ = $slice->seq();
  }
#  my $SEQ       = $slice->seq();
  my $a_count = $SEQ =~ tr/aA/aA/;
  my $c_count = $SEQ =~ tr/cC/cC/;
  my $t_count = $SEQ =~ tr/tT/tT/;
  my $g_count = $SEQ =~ tr/gG/gG/;
  my $bp_length = length($SEQ);
  my $other_count = $bp_length - $a_count - $c_count - $t_count - $g_count;

  $tag   = 'BASE COUNT';
  $value = "$a_count a $c_count c $g_count g $t_count t";
  $value .= " $other_count n" if($other_count);
  $self->write($FH, $GENBANK_HEADER, $tag, $value);
  $self->print( $FH, "ORIGIN\n" );

  $self->write_genbank_seq($FH,\$ SEQ);

  $self->print( $FH, "//\n" );

  # Set formatting back to normal
  $: = "\n -";

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

  $type || throw("type arg is required");

  if(exists($self->{'feature_types'}->{$type})) {
    $self->{'feature_types'}->{$type} = 1;
  } else {
    warning("unknown feature type '$type'\n" .
	  "valid types are: " . join(',', keys %{$self->{'feature_types'}})); 
  }

  my $self = shift;
  my $features = shift;

  my @join = ();

  foreach my $f (@$features) {
    my $slice = $f->slice;
    my $start = $f->start();
    my $end   = $f->end();
    my $strand = $f->strand();

    if($start >= 1 && $end <= $slice->length) {
      #this feature in on a slice and doesn't lie outside the boundary
	
      if($strand == 1) {
        push @join, "$start..$end";
      } else {
        push @join, "complement($start..$end)";
      }
    } else {
      my @fs = ();
      #this feature is outside the boundary of the dump,
      # yet implemented and 'seqlevel' is guaranteed to be 1step
      my $projection = $f->project('seqlevel');
      foreach my $segment (@$projection) {
        my $slice = $segment->[2];
        my $slc_start = $slice->start();
        my $slc_end   = $slice->end();
        my $seq_reg   = $slice->seq_region_name();
        if($slice->strand == 1) {
          push @join, "$seq_reg:$slc_start..$slc_end";
        } else {
          push @join, "complement($seq_reg:$slc_start..$slc_end)";
        }
      }
    }
  }

  my $out = join ',', @join;

  if(scalar @join > 1) {
    $out = "join($out)";
  }

  return $out;

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

  $name || throw("name arg is required");
  
  return $self->{'attached_dbs'}->{$name};

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

  $type || throw("type arg is required");

  if(exists($self->{'feature_types'}->{$type})) {
    return $self->{'feature_types'}->{$type};
  } else {
    warning("unknown feature type '$type'\n" .
	   "valid types are: " . join(',', keys %{$self->{'feature_types'}}));
  }

  my ($caller, $slice) = @_;

  my $class = ref($caller) || $caller;

  my $feature_types = {'gene'        => 1,
		       'genscan'     => 1,
		       'repeat'      => 1,
		       'similarity'  => 1,
		       'variation'   => 1,
		       'contig'      => 1,
		       'marker'      => 1,
		       'estgene'     => 0,
                       'vegagene'    => 0};

  my $self = bless {'feature_types' => $feature_types}, $class;

  return $self;

  my( $self, $FH, $string ) = @_;
  print $FH $string;
}

1;

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

  $name || throw("name arg is required");

  if(exists $self->{'attached_dbs'}->{$name}) {
    return delete $self->{'attached_dbs'}->{$name};
  }

  return undef;

  my ($self, $FH, $FORMAT, @values) = @_;
  
  #while the last value still contains something
  while($values[-1] ne '') {
    formline($FORMAT, @values);
    $self->print( $FH, $^A );
    $^A = '';
  }

  my $self = shift;
  my $FH   = shift;
  my $seq  = shift;
  my $base_total = shift;

  $base_total ||= 0;

  my $EMBL_SEQ = 
'     ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<<@>>>>>>>>>~
';
  #keep track of total and print lines of 60 bases with spaces every 10bp
  my $length = length($$seq);
  my $total = $length - $base_total;
  while($$seq) {
    $total -= 60;
    $total = 0 if($total < 0);
    formline($EMBL_SEQ, 
	     $$seq, $$seq, $$seq, $$seq, $$seq, $$seq, 
	     $length - $total);
    $self->print( $FH, $^A );
    $^A = '';
  }

  my $self = shift;
  my $FH  = shift;
  my $seq = shift;
  my $base_total = shift;

  $base_total ||= 0;

  my $GENBANK_SEQ = 
'@>>>>>>>> ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<< ^<<<<<<<<<~
';

  my $total = -59 + $base_total;
  #keep track of total and print lines of 60 bases with spaces every 10bp
  while($$seq) {
    $total += 60; 
    formline($GENBANK_SEQ,$total, $$seq, $$seq, $$seq, $$seq, $$seq, $$seq);
    $self->print( $FH, $^A );
    $^A = '';
  }

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.