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diff variant_effect_predictor/Bio/SeqIO/game.pm @ 0:1f6dce3d34e0

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author mahtabm
date Thu, 11 Apr 2013 02:01:53 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqIO/game.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,672 @@
+# $Id: game.pm,v 1.26.2.1 2003/06/28 22:23:15 jason Exp $
+#
+# BioPerl module for Bio::SeqIO::game
+#
+# Cared for by Brad Marshall <bradmars@yahoo.com>
+#
+# Copyright Ewan Birney & Lincoln Stein & Brad Marshall
+#
+# You may distribute this module under the same terms as perl itself
+# _history
+# June 25, 2000     written by Brad Marshall 
+#
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqIO::game - Parses GAME XML 0.1 and higher into and out of Bio::Seq objects.  
+
+=head1 SYNOPSIS
+
+To use this module you need XML::Parser, XML::Parser::PerlSAX
+and XML::Writer.
+
+Do not use this module directly.  Use it via the Bio::SeqIO class.
+
+=head1 DESCRIPTION
+
+This object can transform Bio::Seq objects to and from bioxml seq,
+computation, feature and annotation dtds,versions 0.1 and higher.
+These can be found at http://www.bioxml.org/dtds/current.  It does
+this using the idHandler, seqHandler and featureHandler modules you
+should have gotten with this one.
+
+The idea is that any bioxml features can be turned into bioperl
+annotations.  When Annotations and computations are parsed in, they
+gain additional info in the bioperl SeqFeature tag attribute.  These
+can be used to reconstitute a computation or annotation by the bioxml
+with the bx-handler module when write_seq is called.
+
+If you use this to write SeqFeatures that were not generated from
+computations or annotations, it will output a list of bioxml features.
+Some data may be lost in this step, since bioxml features just have a
+span, type and description - nothing about the anlysis performed.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this
+and other Bioperl modules. Send your comments and suggestions preferably
+ to one of the Bioperl mailing lists.
+Your participation is much appreciated.
+
+  bioperl-l@bioperl.org        - Technical bioperl discussion
+  bioxml-dev@bioxml.org        - Technical discussion - Moderate volume
+  bioxml-announce@bioxml.org   - General Announcements - Pretty dead
+  http://www.bioxml.org/MailingLists/         - About the mailing lists
+
+=head1 AUTHOR - Brad Marshall & Ewan Birney & Lincoln Stein
+
+Email: bradmars@yahoo.com
+       birney@sanger.ac.uk
+       lstein@cshl.org
+
+
+=head1 CONTRIBUTORS
+
+Jason Stajich E<lt>jason@bioperl.orgE<gt>
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+package Bio::SeqIO::game;
+use vars qw(@ISA);
+use strict;
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::SeqIO;
+use Bio::SeqIO::game::seqHandler;
+use Bio::SeqIO::game::featureHandler;
+use Bio::SeqIO::game::idHandler;
+use XML::Parser::PerlSAX;
+use Bio::SeqFeature::Generic;
+use XML::Writer;
+
+use Bio::Seq;
+
+@ISA = qw(Bio::SeqIO);
+
+
+sub _initialize {        
+  my($self,@args) = @_;
+  $self->SUPER::_initialize(@args);
+  my $xmlfile           = "";
+  $self->{'counter'}    = 0;
+  $self->{'id_counter'} = 1;  
+  $self->{'leftovers'}  = undef;
+  $self->{'header'}     = undef;
+  $self->{'chunkable'}  = undef;
+  $self->{'xmldoc'}     = undef;
+
+  $self->_export_subfeatures(1);
+  $self->_group_subfeatures(1);
+  $self->_subfeature_types('exons', 'promoters','poly_A_sites',
+			   'utrs','introns','sub_SeqFeature');
+  
+  # filehandle is stored by superclass _initialize
+}
+
+
+=head2 _export_subfeatures
+
+ Title   : _export_subfeatures
+ Usage   : $obj->_export_subfeatures
+ Function: export all subfeatures (also in the geneprediction structure)
+ Returns : value of _export_subfeatures
+ Args    : newvalue (optional)
+
+=cut
+
+sub _export_subfeatures{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'_export_subfeatures'} = $value;
+    }
+    return $obj->{'_export_subfeatures'};
+
+} 
+
+=head2 _group_subfeatures
+
+ Title   : _group_subfeatures
+ Usage   : $obj->_group_subfeatures
+ Function: Groups all subfeatures in separate feature_sets
+ Returns : value of _group_subfeatures
+ Args    : newvalue (optional)
+
+=cut
+
+sub _group_subfeatures{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'_group_subfeatures'} = $value;
+    }
+    return $obj->{'_group_subfeatures'};
+}
+
+=head2 _subfeature_types
+
+ Title   : _subfeature_types
+ Usage   : $obj->_subfeature_types
+ Function: array of all possible subfeatures, it should be a 
+           name of a function which
+         : returns an arrau of sub_seqfeatures when called: 
+           @array = $feature->subfeaturetype()
+ Returns : array of _subfeature_types
+ Args    : array of subfeature types (optional)
+
+=cut
+
+sub _subfeature_types{
+   my $obj = shift;
+   if( @_ ) {
+      my @values = @_;
+      $obj->{'_subfeature_types'} = \@values;
+    }
+    return @{$obj->{'_subfeature_types'}};
+
+} 
+
+=head2 _add_subfeature_type
+ 
+ Title   : _add_subfeature_type
+ Usage   : $obj->_add_subfeature_type
+ Function: add one possible subfeature, it should be a name of a function which
+         : returns an arrau of sub_seqfeatures when called: @array = $feature->subfeaturetyp()
+ Returns : 1
+ Args    : one subfeature type (optional)
+
+=cut
+
+sub _add_subfeature_type{
+   my $obj = shift;
+   if( @_ ) {
+      my @values = @_;
+      push @{$obj->{'_subfeature_types'}}, @values;
+    }
+    return 1;
+
+} 
+
+
+=head2 next_seq
+
+ Title   : next_seq
+ Usage   : $seq = $stream->next_seq()
+ Function: returns the next sequence in the stream
+ Returns : Bio::Seq object
+ Args    : NONE
+
+=cut
+
+sub next_seq {
+  my $self = shift; 
+
+
+  #  The header is the top level stuff in the XML file.
+  #  IE  before the first <bx-seq:seq> tag.
+  #  If you don't include this in each 'chunk', the
+  #  parser will barf.
+  my $header;
+  unless ($self->{'header'}) {
+    while (my $next_line = $self->_readline) {
+      if($next_line=~/<bx-seq:seq?/) {
+	$header .= $`;
+	$self->{'header'}=$header;
+	$self->{'leftovers'} .= "<bx-seq:seq".$';
+	last;
+      } else {
+	$header .= $next_line;
+      }      
+    }
+    if ($self->{'header'}=~m|<bx-game:flavor>.*chunkable.*</bx-game:flavor>|) {
+      $self->{'chunkable'}=1;
+    }
+    
+  }
+
+  my $not_top_level;
+  my $xmldoc;
+  my $seq;
+  #  If chunkable, we read in the document until the next 
+  #  TOP LEVEL sequence.
+  if ($self->{'chunkable'}) {
+    $xmldoc = $self->{'header'}.$self->{'leftovers'};
+    while (my $next_line = $self->_readline) {
+      # Maintain depth of computations and annotations. 
+      # We only want TOP LEVEL seqs if chunkable.
+      while ($next_line=~ m|<bx-computation:computation|g) {
+	$not_top_level++;
+      }
+      while ($next_line=~ m|<bx-annotation:annotation|g) {
+	$not_top_level++;
+      }
+      while ($next_line=~ m|</bx-computation:computation|g) {
+	$not_top_level--;
+      }
+      while ($next_line=~ m|</bx-annotation:annotation|g) {
+	$not_top_level--;
+      }
+      if($next_line=~/<bx-seq:seq?/) {
+	if (!$not_top_level) {
+	  $xmldoc .= $`;
+	  $self->{'leftovers'} .= "<bx-seq:seq".$';
+	  last;
+	}
+      } else {
+	$xmldoc .= $next_line;
+      }  
+    }
+    #  Make sure the 'doc chunk' has a closing tag 
+    #  to make the parser happy.
+    if (!$xmldoc=~m|</bx-game:game>|){
+      $xmldoc .= "</bx-game:game>";
+    }
+    # Grab the TOP LEVEL seq..
+    if ($xmldoc =~ m|</bx-seq:seq|) {
+      my $handler = Bio::SeqIO::game::idHandler->new();
+      my $options = {Handler=>$handler};
+      my $parser  = XML::Parser::PerlSAX->new($options);
+      $self->{'seqs'} = $parser->parse(Source => { String => $xmldoc });
+    } else { # No sequences.
+      return 0;
+    }
+    # Get the seq out of the array.
+    $seq = @{$self->{'seqs'}}[0];
+  # If not chunkable,
+  # only read document into memory once!
+  } elsif (!$self->{'xmldoc'}) {
+    $self->{'xmldoc'}=$self->{'header'}.$self->{'leftovers'};
+    while (my $next_line = $self->_readline) {
+      $self->{'xmldoc'} .= $next_line;
+    }
+    $xmldoc=$self->{'xmldoc'};
+    # Get the seq id index.
+    if ($xmldoc =~ m|</bx-seq:seq|) {
+      my $handler = Bio::SeqIO::game::idHandler->new();
+      my $options = {Handler=>$handler};
+      my $parser  = XML::Parser::PerlSAX->new($options);
+      $self->{'seqs'} = $parser->parse(Source => { String => $xmldoc });
+      $seq = shift @{$self->{'seqs'}};
+    } else { # No sequences.
+      return 0;
+    }
+    my $seq = @{$self->{'seqs'}}[0];
+  # if we already have the doc in memory, 
+  # just get the doc.
+  } elsif ($self->{'xmldoc'}) {
+    $xmldoc=$self->{'xmldoc'};
+    $seq = shift @{$self->{'seqs'}};
+  }
+  #  If there's more sequences:
+  if ($seq) {
+    # Get the next seq.
+    my $handler = Bio::SeqIO::game::seqHandler->new(-seq => $seq);
+    my $options = {Handler=>$handler};
+    my $parser  = XML::Parser::PerlSAX->new($options);
+    my $pseq = $parser->parse(Source => { String => $xmldoc });
+    # get the features.
+    my $fhandler = Bio::SeqIO::game::featureHandler->new($pseq->id(),
+							 $pseq->length(), 
+							 $pseq->alphabet());
+    $options = {Handler=>$fhandler};
+    
+    $parser = XML::Parser::PerlSAX->new($options);
+    my $features = $parser->parse(Source => { String => $xmldoc });
+    my $seq = Bio::Seq->new();
+    # Build the Bioperl Seq and return it.
+    foreach my $feature (@{$features}) {
+      $seq->add_SeqFeature($feature);
+    }
+    $seq->primary_seq($pseq);
+    return $seq;
+  } else {
+    return 0;
+  }
+}
+
+=head2 next_primary_seq
+
+ Title   : next_primary_seq
+ Usage   : $seq = $stream->next_primary_seq()
+ Function: returns the next primary sequence (ie no seq_features) in the stream
+ Returns : Bio::PrimarySeq object
+ Args    : NONE
+
+=cut
+
+sub next_primary_seq {
+  my $self=shift;
+
+  #  The header is the top level stuff in the XML file.
+  #  IE  before the first <bx-seq:seq> tag.
+  #  If you don't include this in each 'chunk', the
+  #  parser will barf.
+  my $header;
+  unless ($self->{'header'}) {
+    while (my $next_line = $self->_readline) {
+      if($next_line=~/<bx-seq:seq?/) {
+	$header .= $`;
+	$self->{'header'}=$header;
+	$self->{'leftovers'} .= "<bx-seq:seq".$';
+	last;
+      } else {
+	$header .= $next_line;
+      }      
+    }
+    if ($self->{'header'}=~m|<bx-game:flavor>.*chunkable.*</bx-game:flavor>|) {
+      $self->{'chunkable'}=1;
+    }
+      
+  }
+
+  my $not_top_level = 0;
+  my $xmldoc;
+  my $seq;
+  #  If chunkable, we read in the document until the next 
+  #  TOP LEVEL sequence.
+  if ($self->{'chunkable'}) {
+    $xmldoc = $self->{'header'}.$self->{'leftovers'};
+    while (my $next_line = $self->_readline) {
+      # Maintain depth of computations and annotations. 
+      # We only want TOP LEVEL seqs if chunkable.
+      while ($next_line=~ m|<bx-computation:computation|g) {
+	$not_top_level++;
+      }
+      while ($next_line=~ m|<bx-annotation:annotationn|g) {
+	$not_top_level++;
+      }
+      while ($next_line=~ m|</bx-computation:computation|g) {
+	$not_top_level--;
+      }
+      while ($next_line=~ m|</bx-annotation:annotationn|g) {
+	$not_top_level--;
+      }
+      if($next_line=~/<bx-seq:seq?/) {
+	if (!$not_top_level) {
+	  $xmldoc .= $`;
+	  $self->{'leftovers'} .= "<bx-seq:seq".$';
+	  last;
+	}
+      } else {
+	$xmldoc .= $next_line;
+      }  
+    }
+    #  Make sure the 'doc chunk' has a closing tag 
+    #  to make the parser happy.
+    if (!$xmldoc=~m|</bx-game:game>|){
+      $xmldoc .= "</bx-game:game>";
+    }
+    # Grab the TOP LEVEL seq..
+    if ($xmldoc =~ m|</bx-seq:seq|) {
+      my $handler = Bio::SeqIO::game::idHandler->new();
+      my $options = {Handler=>$handler};
+      my $parser  = XML::Parser::PerlSAX->new($options);
+      $self->{'seqs'} = $parser->parse(Source => { String => $xmldoc });
+    } else { # No sequences.
+      return 0;
+    }
+    $seq = @{$self->{'seqs'}}[0];
+  # If not chunkable,
+  # only read document into memory once!
+  } elsif (!$self->{'xmldoc'}) {
+    $self->{'xmldoc'}=$self->{'header'}.$self->{'leftovers'};
+    while (my $next_line = $self->_readline) {
+      $self->{'xmldoc'} .= $next_line;
+    }
+    $xmldoc=$self->{'xmldoc'};
+    # Get the seq id index.
+    if ($xmldoc =~ m|</bx-seq:seq|) {
+      my $handler = Bio::SeqIO::game::idHandler->new();
+      my $options = {Handler=>$handler};
+      my $parser  = XML::Parser::PerlSAX->new($options);
+      $self->{'seqs'} = $parser->parse(Source => { String => $xmldoc });
+      $seq = shift @{$self->{'seqs'}};
+    } else { # No sequences.
+      return 0;
+    }
+    my $seq = @{$self->{'seqs'}}[0];
+  # if we already have the doc in memory, 
+  # just get the doc.
+  } elsif ($self->{'xmldoc'}) {
+    $xmldoc=$self->{'xmldoc'};
+    $seq = shift @{$self->{'seqs'}};
+  }
+
+  #print $xmldoc;
+    
+  if ($seq) {
+    # Get the next seq.
+    my $handler = Bio::SeqIO::game::seqHandler->new(-seq => $seq);
+    my $options = {Handler=>$handler};
+    my $parser  = XML::Parser::PerlSAX->new($options);
+    my $pseq = $parser->parse(Source => { String => $xmldoc });
+    return $pseq;
+  } else {
+    return 0;
+  }
+}
+
+
+=head2 write_seq
+
+ Title   : write_seq
+ Usage   : Not Yet Implemented! $stream->write_seq(@seq)
+ Function: writes the $seq object into the stream
+ Returns : 1 for success and 0 for error
+ Args    : Bio::Seq object
+
+
+=cut
+
+sub write_seq {
+    my ($self,@seqs) = @_;
+
+    my $bxfeat  = "http://www.bioxml.org/dtds/current/feature.dtd";
+    my $bxann   = "http://www.bioxml.org/dtds/current/annotation.dtd";
+    my $bxcomp  = "http://www.bioxml.org/dtds/current/computation.dtd";
+    my $bxgame  = "http://www.bioxml.org/dtds/current/game.dtd";
+    my $bxlink  = "http://www.bioxml.org/dtds/current/link.dtd";
+    my $bxseq   = "http://www.bioxml.org/dtds/current/seq.dtd";
+
+    my $writer = new XML::Writer(OUTPUT      => $self->_fh || \*STDOUT,
+				 NAMESPACES  => 1,
+				 DATA_MODE   => 1,
+				 DATA_INDENT => 4,
+				 PREFIX_MAP  => {
+				     ''     => '', # to keep undef warnings away in XML::Writer, fill in with something as a default prefix later?
+				     $bxfeat => 'bx-feature',
+				     $bxann =>  'bx-annotation',
+				     $bxcomp => 'bx-computation',
+				     $bxgame => 'bx-game',
+				     $bxlink => 'bx-link',
+				     $bxseq =>  'bx-seq'
+				     });
+    $writer->xmlDecl("UTF-8");
+    $writer->doctype("bx-game:game", 'game', $bxgame);
+    $writer ->startTag ([$bxgame, 'game']);
+    $writer->startTag  ([$bxgame, 'flavor']);
+    $writer->characters('chunkable');
+    $writer->endTag    ([$bxgame, 'flavor']);
+
+    foreach my $seq (@seqs) {
+	$writer->startTag([$bxseq, 'seq'], 
+			  [$bxseq, 'id'] => $seq->display_id,
+			  [$bxseq, 'length'] => $seq->length,
+			  [$bxseq, 'type'] => $seq->alphabet);
+	if ($seq->length > 0) {
+	    $writer->startTag([$bxseq, 'residues']);
+	    $writer->characters($seq->seq);
+	    $writer->endTag([$bxseq, 'residues']);
+	}
+	$writer->endTag([$bxseq, 'seq']);
+
+	my @feats = $seq->all_SeqFeatures;
+
+	my $features;
+	foreach my $feature (@feats) {
+	    if ($feature->has_tag('annotation_id')) {
+		my @ann_id = $feature->each_tag_value('annotation_id');
+		push (@{$features->{'annotations'}->{$ann_id[0]}}, $feature);
+	    } elsif ($feature->has_tag('computation_id')) {
+		my @comp_id = $feature->each_tag_value('computation_id');
+		push (@{$features->{'computations'}->{$comp_id[0]}}, $feature);
+	    } else {
+		push (@{$features->{'everybody_else'}}, $feature);
+	    }
+	}
+	foreach my $key (keys %{$features->{'annotations'}}) {
+	    $writer->startTag([$bxann, 'annotation'],
+			      [$bxann, 'id']=>$key
+			      );
+	    $writer->startTag([$bxann, 'seq_link']);
+	    $writer->startTag([$bxlink, 'link']);
+	    $writer->emptyTag([$bxlink, 'ref_link'],
+			      [$bxlink, 'ref'] => $seq->display_id());
+	    $writer->endTag([$bxlink, 'link']);
+	    $writer->endTag([$bxann, 'seq_link']);					   
+	    $self->__draw_feature_set($writer, $seq, $bxann, "", @{$features->{'annotations'}->{$key}});
+	    $writer->endTag([$bxann, 'annotation']);
+	}
+
+	foreach my $key (keys %{$features->{'computations'}}) {
+	    $writer->startTag([$bxcomp, 'computation'],
+			      [$bxcomp, 'id']=>$key
+			      );
+	    $writer->startTag([$bxcomp, 'seq_link']);
+	    $writer->startTag([$bxlink, 'link']);
+	    $writer->emptyTag([$bxlink, 'ref_link'],
+			      [$bxlink, 'ref'] => $seq->display_id());
+	    $writer->endTag([$bxlink, 'link']);
+	    $writer->endTag([$bxcomp, 'seq_link']);
+	    $self->__draw_feature_set($writer, $seq, $bxcomp, "", @{$features->{'computations'}->{$key}});   
+	    $writer->endTag([$bxcomp, 'computation']);
+	}
+	foreach my $feature (@{$features->{'everybody_else'}}) {
+	    $self->__draw_feature($writer, $feature, $seq, "", 
+				  $self->_export_subfeatures());
+	}
+    }
+    $writer->endTag([$bxgame, 'game']);
+
+    $self->flush if $self->_flush_on_write && defined $self->_fh;
+    return 1;
+}
+
+
+#these two subroutines are very specific!
+
+sub __draw_feature_set {
+    my ($self, $writer, $seq, $namespace, $parent, @features) = @_;
+    my ($feature_set_id);
+
+    my $bxfeat = "http://www.bioxml.org/dtds/current/feature.dtd";
+
+    if ($self->_export_subfeatures() && $self->_group_subfeatures()) {
+	$feature_set_id = $self->{'id_counter'}; $self->{'id_counter'}++;
+	$writer->startTag([$namespace, 'feature_set'],
+			  [$namespace, 'id'] => $feature_set_id);
+	foreach my $feature (@features) {
+	    $self->__draw_feature($writer, $feature, $seq, $parent , 0);  
+	}
+	$writer->endTag([$namespace, 'feature_set']);
+	foreach my $feature (@features) {
+	    foreach my $subset ($self->_subfeature_types()) {
+		if (my @subfeatures = eval ( '$feature->' . $subset . '()' )) {
+		    my @id = $feature->each_tag_value('id');
+		    $self->__draw_feature_set($writer, $seq, $namespace, $id[0], @subfeatures);     
+		}
+	    }	        
+	}
+
+    } else {
+	$feature_set_id = $self->{'id_counter'}; $self->{'id_counter'}++;
+	$writer->startTag([$namespace, 'feature_set'],
+			  [$namespace, 'id'] => $feature_set_id);
+	foreach my $feature (@features) {
+	    $self->__draw_feature($writer, $feature, $seq, "" , $self->_export_subfeatures());
+	}
+	$writer->endTag([$namespace, 'feature_set']);
+    }
+}
+
+
+sub __draw_feature {
+    my ($self, $writer, $feature, $seq, $parent, $recursive) = @_;
+    my ($subfeature, $subset, @subfeatures, $score, $score_val, $score_no);
+    my $bxfeat = "http://www.bioxml.org/dtds/current/feature.dtd";
+    
+    if (!$feature->has_tag('id')) {
+	$feature->add_tag_value('id', $self->{'id_counter'});
+	$self->{'id_counter'}++;
+    }
+    
+    my @id = $feature->each_tag_value('id');
+    if ($parent) {
+	$writer->startTag([$bxfeat, 'feature'],
+			  [$bxfeat, 'id'] => $id[0]
+			  );
+    } else {
+	$writer->startTag([$bxfeat, 'feature'],
+			  [$bxfeat, 'id'] => $id[0],
+			  [$bxfeat, 'parent'] => $parent
+			  );
+    }    
+    $writer->startTag([$bxfeat, 'type']);
+    $writer->characters($feature->primary_tag());
+    $writer->endTag([$bxfeat, 'type']);
+    foreach $score ($feature->all_tags()) {
+	next if ($score eq 'id');
+	$writer->startTag([$bxfeat, 'score'],
+			  [$bxfeat, 'type'] => $score 
+			  );
+	$score_no = 0;
+	foreach $score_val ($feature->each_tag_value($score)) {
+	    next unless defined $score_val;
+	    $writer->characters(' ') if ($score_no > 0);
+	    $writer->characters($score_val);
+	    $score_no++;
+	}
+	$writer->endTag([$bxfeat, 'score']);
+    }
+
+    $writer->startTag([$bxfeat, 'seq_relationship'],
+		      [$bxfeat, 'seq'] => $seq->display_id,
+		      [$bxfeat, 'type'] => 'query'
+		      );
+
+    $writer->startTag([$bxfeat, 'span']);
+    $writer->startTag([$bxfeat, 'start']);
+    $writer->characters($feature->start());
+    $writer->endTag([$bxfeat, 'start']);
+    $writer->startTag([$bxfeat, 'end']);
+    $writer->characters($feature->end());
+    $writer->endTag([$bxfeat, 'end']);
+    $writer->endTag([$bxfeat, 'span']);
+    $writer->endTag([$bxfeat, 'seq_relationship']);
+    $writer->endTag([$bxfeat, 'feature']);
+
+    #proces subseqfeature's, exons, introns, promotors, whatever...
+    if ($recursive) {
+	foreach $subset ($self->_subfeature_types()) {
+	    #determine if it exists
+	    if (@subfeatures = eval ( '$feature->' . $subset . '()' )) {
+		foreach $subfeature (@subfeatures) {
+		    $self->__draw_feature ($writer, $subfeature, $seq, $id[0], 1);
+		}        
+	    }
+	}
+    }
+}
+
+1;
+