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use Bio::Graphics::Glyph::segments;
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use Bio::Graphics::Util qw(frame_and_offset);
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use Bio::Tools::CodonTable;
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use Bio::Graphics::Glyph::translation;
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@ISA = qw(Bio::Graphics::Glyph::segmented_keyglyph Bio::Graphics::Glyph::translation);
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use base qw(Bio::Graphics::Glyph::segmented_keyglyph Bio::Graphics::Glyph::translation);
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my %default_colors = qw(
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frame0f cornflowerblue
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my %swap_phase = ( 0 => 0,
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sub connector { 0 };
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$self->{sixframe} = $self->option('sixframe')
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unless exists $self->{sixframe};
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return $self->{sixframe};
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return $self->{sixframe} if exists $self->{sixframe};
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my $sixframe = $self->option('sixframe');
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$sixframe = $self->option('translation') eq '6frame' unless defined $sixframe;
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return $self->{sixframe} = $sixframe;
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sub require_subparts {
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my $rs = $self->option('require_subparts');
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@parts = $self if !@parts && $self->level == 0 && !$self->require_subparts;
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my $fits = $self->protein_fits;
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my $strand = $self->feature->strand || 1;
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# draw the staff (musically speaking)
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my ($x1,$y1,$x2,$y2) = $self->bounds($left,$top);
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my $line_count = $self->sixframe ? 6 : 3;
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my $height = ($y2-$y1)/$line_count;
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my $grid = $self->gridcolor;
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for (0..$line_count-1) {
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my $offset = $y1+$height*$_+1;
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$gd->line($x1,$offset,$x2,$offset,$grid);
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if ($self->level == 0) {
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my ($x1,$y1,$x2,$y2) = $self->bounds($left,$top);
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my $line_count = $self->sixframe ? 6 : 3;
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my $height = ($y2-$y1)/$line_count;
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my $grid = $self->gridcolor;
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for (0..$line_count-1) {
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my $offset = $y1+$height*$_+1;
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$gd->line($x1,$offset,$x2,$offset,$grid);
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# with three-frame translation, the position of the arrows changes depending on
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# the strand of the feature. With six-frame translation, we draw the first three
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# staff lines with an arrow to the right, and the second three to the left
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my $forward = ($line_count == 6) ? ($_ < 3) : ($strand > 0);
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$gd->line($x2,$offset,$x2-2,$offset-2,$grid);
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$gd->line($x2,$offset,$x2-2,$offset+2,$grid);
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$gd->line($x1,$offset,$x1+2,$offset-2,$grid);
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$gd->line($x1,$offset,$x1+2,$offset+2,$grid);
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$self->{cds_part2color} ||= {};
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my $fill = $self->bgcolor;
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my $strand = $self->feature->strand;
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# figure out the colors of each part
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# sort minus strand features backward
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$codon_table = 1 unless defined $codon_table;
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my $translate_table = Bio::Tools::CodonTable->new(-id=>$codon_table);
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my $ignore_undef_phase = $self->ignore_undef_phase;
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my $ignore_non_cds = $self->ignore_non_cds;
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my $broken_phase = $self->phase_style eq '021';
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for (my $i=0; $i < @parts; $i++) {
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my $part = $parts[$i];
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my $feature = $part->feature;
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my $pos = $strand > 0 ? $feature->start : $feature->end;
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my $phase = eval {$feature->phase} || 0;
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my $type = $feature->method;
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next if ($self->option('sub_part') && $type ne $self->option('sub_part'));
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next if $ignore_non_cds && lc($type) ne 'cds';
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my $pos = $feature->strand >= 0 ? $feature->start : $feature->end;
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my $phase = $feature->can('phase') ? $feature->phase # bioperl uses "frame" but this is incorrect usage
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:$feature->can('frame') ? $feature->frame
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next if $ignore_undef_phase && !defined($phase);
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$phase = $swap_phase{$phase} if $broken_phase;
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my $strand = $feature->strand;
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my ($frame,$offset) = frame_and_offset($pos,
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my $suffix = $strand < 0 ? 'r' : 'f';
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my $key = "frame$frame$suffix";
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$self->{cds_frame2color}{$key} ||= $self->color($key) || $self->default_color($key) || $fill;
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# do in silico splicing in order to find the codon that
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# arises from the splice
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my $protein = $part->feature->translate(undef,undef,$phase,$codon_table)->seq;
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my $seq = $self->get_seq($part->feature->seq);
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my $protein = $seq->translate(undef,undef,$phase,$codon_table)->seq;
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$part->{cds_translation} = $protein;
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length $protein >= $feature->length/3 and last BLOCK;
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($feature->length - $phase) % 3 == 0 and last BLOCK;
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my $next_part = $parts[$i+1]
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$part->{cds_splice_residue} = '?';
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my $next_feature = $next_part->feature or last BLOCK;
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my $next_phase = eval {$next_feature->phase} or last BLOCK;
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my $splice_codon = '';
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my $left_of_splice = substr($feature->seq,-$next_phase,$next_phase);
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my $right_of_splice = substr($next_feature->seq,0,3-$next_phase);
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my $left_of_splice = substr($self->get_seq($feature->seq), -$next_phase, $next_phase);
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my $right_of_splice = substr($self->get_seq($next_feature->seq),0 , 3-$next_phase);
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$splice_codon = $left_of_splice . $right_of_splice;
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length $splice_codon == 3 or last BLOCK;
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my $amino_acid = $translate_table->translate($splice_codon);
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my $height = ($y2-$y1)/$linecount;
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my $offset = $y1 + $height*$frame;
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$offset += ($y2-$y1)/2 if $self->sixframe && $self->strand < 0;
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$offset = $y1 + (($y2-$y1) - ($offset-$y1))-$height if $self->{flip}; # ugh. This works, but I don't know why
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$gd->filledRectangle($x1,$offset,$x2,$offset+2,$color);
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# 2) correct for the phase offset
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my $start = $self->map_no_trunc($feature->start + $self->{cds_offset});
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my $stop = $self->map_no_trunc($feature->end + $self->{cds_offset});
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($start,$stop) = ($stop,$start) if $self->{flip};
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($start,$stop) = ($stop,$start) if $stop < $start; # why does this keep happening?
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# ($start,$stop) = ($stop,$start) if $self->{flip};
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my @residues = split '',$self->{cds_translation};
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my $x = $strand > 0 ? $start + $i * $pixels_per_residue
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: $stop - $i * $pixels_per_residue;
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next unless ($x >= $x1 && $x <= $x2);
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$x -= $fontwidth + 1 if $self->{flip}; # align right when flipped
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$gd->char($font,$x+1,$y,$residues[$i],$color);
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-hilite Highlight color undef (no color)
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In addition, the alignment glyph recognizes the following
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glyph-specific options:
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Option Description Default
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------ ----------- -------
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-frame0f Color for first (+) frame background color
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-frame1f Color for second (+) frame background color
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-frame2f Color for third (+) frame background color
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-frame0r Color for first (-) frame background color
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-frame1r Color for second (-) frame background color
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-frame2r Color for third (-) frame background color
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-gridcolor Color for the "staff" lightslategray
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-sixframe Draw a six-frame staff 0 (false; usually draws 3 frame)
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In addition, the cds glyph recognizes the following glyph-specific
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Option Description Default
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------ ----------- -------
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-frame0f Color for first (+) frame background color
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-frame1f Color for second (+) frame background color
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-frame2f Color for third (+) frame background color
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-frame0r Color for first (-) frame background color
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-frame1r Color for second (-) frame background color
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-frame2r Color for third (-) frame background color
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-gridcolor Color for the "staff" lightslategray
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-translation Number of lines of reading 3frame
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frames to show. One of
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"3frame", or "6frame".
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For 6frame, specify a height
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of at least 30 pixels.
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-sixframe Draw a six-frame staff 0 (false; usually draws 3 frame)
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-translation, which essentially
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-require_subparts
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Don't draw the reading frame 0 (false)
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Don't draw the reading frame 0 false
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unless it is a feature
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-codontable Codon table to use 1 (see Bio::Tools::CodonTable)
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-sub_part For objects with multiple undef
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subpart types, defines which
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-codontable Codon table to use 1 (see Bio::Tools::CodonTable)
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-phase_style The way phase is to be
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interpreted. One of "012"
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-ignore_empty_phase false
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Only draw features that have
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-cds_only Only draw features of type false
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This glyph is more sensitive to the underlying data model than usual,
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so there are a few additional options to use to help adapt the glyph
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to different environments.
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The -require_subparts option is suggested when rendering spliced
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transcripts which contain multiple CDS subparts. Otherwise, the glyph
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phantom reading frame will appear). For unspliced sequences, do *not*
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use -require_subparts.
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The -phase_style controls how the value returned by the phase() or
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frame() methods is to be interpreted. The official interpretation is
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that the phase value indicates the offset into the feature at which
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the reading frame starts -- e.g. a phase of "2" means the reading
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frame starts after skipping two bases from the beginning of the
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feature. However, many GFF2 format feature files interpret this field
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to mean the position reading frame of the first base of the feature --
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e.g. a phase of "2" means that the reading frame starts after skipping
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just one base from the beginning of the feature. Specify "012" to
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interpret the phase field in the correct way, and "021" to interpret
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the phase field in the legacy way. The default is "012."
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Here is how the option names were chosen:
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* * * Base the reading frame starts on
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0 1 2 PHASE REPRESENTED CORRECTLY
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0 2 1 PHASE REPRESENTED IN THE LEGACY WAY
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Set the -ignore_empty_phase option to true if you wish to skip
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subfeatures that do not have a defined phase() or frame(). This is useful
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if you are rendering exons that have both translated and untranslated
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parts, and you wish to skip the untranslated parts.
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Set the -cds_only option to true if you wish to draw the glyph only
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for subfeatures of type 'CDS'. This is recommended.
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=head1 SUGGESTED STANZA FOR GENOME BROWSER
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Using the "coding" aggregator, this produces a nice gbrowse display.
added
removed
Bio/Graphics/Glyph/cds.pm
