package Bio::Graphics::Glyph::processed_transcript;
use strict;
use base qw(Bio::Graphics::Glyph::transcript2);
use constant DEFAULT_UTR_COLOR => '#D0D0D0';
sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
$self->guess_options if !defined $self->option('implied_utrs')
&& !defined $self->option('adjust_exons');
$self;
}
sub guess_options {
my $self = shift;
my ($exons,$utrs,$cds);
foreach ($self->parts) {
$exons++ if $_->feature->type =~ /exon/i;
$utrs++ if $_->feature->type =~ /utr$/i;
$cds++ if $_->feature->type =~ /^cds/i;
$self->configure(implied_utrs=>1) if $exons && $cds && !$utrs;
$self->configure(adjust_exons=>1) if $exons && $utrs;
}
}
# this option will generate implied UTRs by subtracting the
# CDS features from the exons.
sub create_implied_utrs {
my $self = shift;
return if $self->{'.implied_utrs'}++;
# parts should be ordered from left to right
my @features = sort {$a->start <=> $b->start} map {$_->feature} $self->parts;
my @exons = grep {$_->type =~ /^exon/} @features;
my @cds = grep {$_->type =~ /^CDS/ } @features;
my @old_utr = grep {$_->type =~ /UTR/ } @features;
# if there are already UTRs then we don't modify anything
return if @old_utr;
# if exons or CDS features are missing, then we abandon ship
return unless @exons && @cds;
my $first_cds = $cds[0];
my $last_cds = $cds[-1];
my $strand = $self->feature->strand;
my $factory = $self->factory;
# make the left-hand UTRs
for (my $i=0;$i<@exons;$i++) {
my $start = $exons[$i]->start;
last if $start >= $first_cds->start;
my $end = $first_cds->start > $exons[$i]->end ? $exons[$i]->end : $first_cds->start-1;
my $utr = Bio::Graphics::Feature->new(-start=>$start,
-end=>$end,
-strand=>$strand,
-type=>$strand >= 0 ? 'five_prime_UTR' : 'three_prime_UTR');
unshift @{$self->{parts}},$factory->make_glyph($self->{level}+1,$utr);
}
# make the right-hand UTRs
for (my $i=$#exons; $i>=0; $i--) {
my $end = $exons[$i]->end;
last if $end <= $last_cds->end;
my $start = $last_cds->end < $exons[$i]->start ? $exons[$i]->start : $last_cds->end+1;
my $utr = Bio::Graphics::Feature->new(-start=>$start,
-end=>$end,
-strand=>$strand,
-type=>$strand >= 0 ? 'three_prime_UTR' : 'five_prime_UTR');
push @{$self->{parts}},$factory->make_glyph($self->{level}+1,$utr);
}
}
# Preprocess the glyph to remove overlaps between UTRs and
# exons. The exons are clipped so that UTRs have precedence
sub adjust_exons {
my $self = shift;
return if $self->{'.adjust_exons'}++;
# find everything that is not an exon (utrs and cds's)
my @parts = sort {$a->{left}<=>$b->{left}} $self->parts;
my @exon = grep {$_->feature->type =~ /exon/i} @parts;
my %seen = map {$_=>1} @exon;
my @other = grep {!$seen{$_}} @parts;
my @clipped_parts;
my %positions = map {("$_->{left}:$_->{width}" =>1)} @other;
my @unique_exons = grep {!$positions{"$_->{left}:$_->{width}"}} @exon;
# the first and last exons may need to be clipped if they overlap
# with another feature (CDS or UTR)
my $first_exon = $unique_exons[0];
my $last_exon = $unique_exons[-1];
# deal with left hand side first
my $e_left = $first_exon->{left};
my $e_right = $e_left + $first_exon->{width};
for my $other (@other) {
my $o_left = $other->{left};
my $o_right = $o_left + $other->{width};
next if $e_left > $o_right;
last if $e_right < $o_left;
#dgg- need to skip 3prime/right utr for 1exon; end same as exon
last if (@unique_exons == 1 && $o_left > $e_left); #dgg- o_ is 3prime not 5
# clip left hand side; may get clipped into oblivion!
$first_exon->{left} = $o_right + 1;
$first_exon->{width} = $e_right - $first_exon->{left};
}
# deal with right hand side
$e_left = $last_exon->{left};
$e_right = $e_left + $last_exon->{width};
for (my $i=$#other; $i>=0; $i--) {
my $o_left = $other[$i]->{left};
my $o_right = $o_left + $other[$i]->{width};
next if $e_right < $o_left;
last if $e_left > $o_right;
# clip right hand side; may get clipped into oblivion!
#dgg- !! this always clips to oblivion: $last_exon->{width} = ($e_left - 1) - $last_exon->{left};
$last_exon->{width} = $o_left - $last_exon->{left}; #dgg-
}
$self->{parts} = [ grep {$_->width > 0} sort {$a->{left}<=>$b->{left}} (@other,@unique_exons)];
}
sub fixup_glyph {
my $self = shift;
return unless $self->level == 0;
$self->create_implied_utrs if $self->option('implied_utrs');
$self->adjust_exons if $self->option('implied_utrs') || $self->option('adjust_exons');
}
sub draw {
my $self = shift;
$self->fixup_glyph();
$self->SUPER::draw(@_);
return unless $self->thin_utr;
my $gd = shift;
my ($dx,$dy) = @_;
my $bgcolor = $self->bgcolor;
my @parts = $self->parts;
for (my $i = 0; $i < @parts; $i++) {
if ($i >= 1 && ($parts[$i-1]->is_utr != $parts[$i]->is_utr)) {
next unless $parts[$i-1]->end+1 == $parts[$i]->start;
my ($x1,$y1,$x2,$y2) = $parts[$i]->bounds($dx,$dy+$self->top+$self->pad_top);
my $height = $parts[$i-1]->is_utr ?
$parts[$i-1]->height
: $parts[$i]->height;
my $center = ($y1+$y2)/2;
$gd->line($x1,$center-$height/2,$x1,$center+$height/2,$bgcolor); # erase
}
}
}
sub boxes {
my $self = shift;
$self->fixup_glyph();
$self->SUPER::boxes(@_);
}
sub is_utr {
my $self = shift;
return $self->feature->primary_tag =~ /UTR|untranslated_region/i;
}
sub thin_utr {
my $self = shift;
$self->option('thin_utr');
}
sub utr_color {
my $self = shift;
return $self->SUPER::bgcolor if $self->thin_utr;
return $self->color('utr_color') if $self->option('utr_color');
return $self->factory->translate_color(DEFAULT_UTR_COLOR);
}
sub height {
my $self = shift;
my $height = $self->SUPER::height;
return $height unless $self->thin_utr;
return $self->is_utr ? int($height/1.5+0.5) : $height;
}
sub pad_top {
my $self = shift;
my $pad_top = $self->SUPER::pad_top;
return $pad_top unless $self->thin_utr && $self->is_utr;
return $pad_top + int(0.167*$self->SUPER::height + 0.5);
}
sub bgcolor {
my $self = shift;
return $self->SUPER::bgcolor unless $self->is_utr;
return $self->utr_color;
}
sub connector {
my $self = shift;
return 'quill' if $self->option('decorate_introns');
return $self->SUPER::connector(@_);
}
sub _subfeat {
my $self = shift;
return $self->SUPER::_subfeat(@_) unless ref($self) && $self->{level} == 0 && $self->option('one_cds');
my $feature = shift;
my @subparts = $feature->get_SeqFeatures(qw(CDS five_prime_UTR three_prime_UTR UTR));
# The CDS and UTRs may be represented as a single feature with subparts or as several features
# that have different IDs. We handle both cases transparently.
my @result;
foreach (@subparts) {
if ($_->primary_tag =~ /CDS|UTR/i) {
my @cds_seg = $_->get_SeqFeatures;
if (@cds_seg > 0) { push @result,@cds_seg } else { push @result,$_ }
} else {
push @result,$_;
}
}
return @result;
}
1;
__END__
=head1 NAME
Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph
=head1 SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
=head1 DESCRIPTION
This glyph is used for drawing processed transcripts that have both
CDS and UTR segments. The CDS is drawn in the background color, and
the UTRs are drawn in an alternate color selected by the utr_color
option. In addition, you can make the UTRs thinner than the CDS by
setting the "thin_utr" option.
For this glyph to produce the desired results, you should pass it a
compound Bio::SeqFeature that has subfeatures of primary_tag "CDS" and
"UTR". In fact, you may give it more specific types of UTR, including
5'-UTR, 3'-UTR, or the Sequence Ontology terms "untranslated_region,"
"five_prime_untranslated_region," and
"three_prime_untranslated_region."
=head2 OPTIONS
The following options are standard among all Glyphs. See
L<Bio::Graphics::Glyph> for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type undef (false)
-connector_color
Connector color black
-label Whether to draw a label undef (false)
-description Whether to draw a description undef (false)
-strand_arrow Whether to indicate undef (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the alignment glyph recognizes the following
glyph-specific options:
Option Description Default
------ ----------- -------
-thin_utr Flag. If true, UTRs will undef (false)
be drawn at 2/3 of the
height of CDS segments.
-utr_color Color of UTR segments. Gray #D0D0D0
-decorate_introns
Draw strand with little arrows undef (false)
on the intron.
-adjust_exons Fix exons so that they don't undef (false)
overlap UTRs
-implied_utrs Whether UTRs should be implied undef (false)
from exons and CDS features
-one_cds Some databases (e.g. FlyBase) represent their
transcripts as having a single CDS that is
broken up into multiple parts. Set this to
true to display this type of feature.
The B<-adjust_exons> option is needed to handle features in which the
exons (SO type "exon") overlaps with the UTRs (SO types
"five_prime_UTR" and "three_prime_UTR"). The exon parts of the glyph
will be clipped so that it doesn't overlap with the UTR parts.
The B<-implied_utrs> option is needed if there are no explicit UTR
features. In this case, UTRs are derived by subtracting the positions
of "CDS" subfeatures from the positions of "exon" subfeatures.
B<-implied_utrs> implies the B<-adjust_exons> option.
=head1 BUGS
Please report them.
=head1 SEE ALSO
L<Bio::Graphics::Panel>,
L<Bio::Graphics::Glyph>,
L<Bio::Graphics::Glyph::arrow>,
L<Bio::Graphics::Glyph::cds>,
L<Bio::Graphics::Glyph::crossbox>,
L<Bio::Graphics::Glyph::diamond>,
L<Bio::Graphics::Glyph::dna>,
L<Bio::Graphics::Glyph::dot>,
L<Bio::Graphics::Glyph::ellipse>,
L<Bio::Graphics::Glyph::extending_arrow>,
L<Bio::Graphics::Glyph::generic>,
L<Bio::Graphics::Glyph::graded_segments>,
L<Bio::Graphics::Glyph::heterogeneous_segments>,
L<Bio::Graphics::Glyph::line>,
L<Bio::Graphics::Glyph::pinsertion>,
L<Bio::Graphics::Glyph::primers>,
L<Bio::Graphics::Glyph::rndrect>,
L<Bio::Graphics::Glyph::segments>,
L<Bio::Graphics::Glyph::ruler_arrow>,
L<Bio::Graphics::Glyph::toomany>,
L<Bio::Graphics::Glyph::transcript>,
L<Bio::Graphics::Glyph::transcript2>,
L<Bio::Graphics::Glyph::translation>,
L<Bio::Graphics::Glyph::triangle>,
L<Bio::DB::GFF>,
L<Bio::SeqI>,
L<Bio::SeqFeatureI>,
L<Bio::Das>,
L<GD>
=head1 AUTHOR
Lincoln Stein E<lt>lstein@cshl.orgE<gt>
Copyright (c) 2001 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut