NAME
Bio::Graphics::Glyph::cds - The "cds" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.DESCRIPTION
This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the frame in which the translation occurs. At low magnifications, draws the amino acid sequence of the resulting protein. Amino acids that are created by a splice are optionally shown in a distinctive color.
OPTIONS
The following options are standard among all Glyphs. See 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 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)In addition, the cds glyph recognizes the following glyph-specific options:
Option Description Default
------ ----------- -------
-frame0f Color for first (+) frame background color
-frame1f Color for second (+) frame background color
-frame2f Color for third (+) frame background color
-frame0r Color for first (-) frame background color
-frame1r Color for second (-) frame background color
-frame2r Color for third (-) frame background color
-gridcolor Color for the "staff" lightslategray
-translation Number of lines of reading 3frame
frames to show. One of
"3frame", or "6frame".
For 6frame, specify a height
of at least 30 pixels.
-sixframe Draw a six-frame staff 0 (false; usually draws 3 frame)
This value overrides
-translation, which essentially
does the same thing.
-require_subparts
Don't draw the reading frame 0 false
unless it is a feature
subpart.
-sub_part For objects with multiple undef
subpart types, defines which
is the CDS part.
-codontable Codon table to use 1 (see Bio::Tools::CodonTable)
-phase_style The way phase is to be
interpreted. One of "012"
"012" or "021"
-ignore_empty_phase false
Only draw features that have
their phase defined.
-cds_only Only draw features of type false
'CDS'This glyph is more sensitive to the underlying data model than usual, so there are a few additional options to use to help adapt the glyph to different environments.
The -require_subparts option is suggested when rendering spliced transcripts which contain multiple CDS subparts. Otherwise, the glyph will hickup when zoomed way down onto an intron between two CDSs (a phantom reading frame will appear). For unspliced sequences, do *not* use -require_subparts.
The -phase_style controls how the value returned by the phase() or frame() methods is to be interpreted. The official interpretation is that the phase value indicates the offset into the feature at which the reading frame starts -- e.g. a phase of "2" means the reading frame starts after skipping two bases from the beginning of the feature. However, many GFF2 format feature files interpret this field to mean the position reading frame of the first base of the feature -- e.g. a phase of "2" means that the reading frame starts after skipping just one base from the beginning of the feature. Specify "012" to interpret the phase field in the correct way, and "021" to interpret the phase field in the legacy way. The default is "012."
Here is how the option names were chosen:
* * * Base the reading frame starts on
A B C A B C A B C...
0 1 2 PHASE REPRESENTED CORRECTLY
0 2 1 PHASE REPRESENTED IN THE LEGACY WAYSet the -ignore_empty_phase option to true if you wish to skip subfeatures that do not have a defined phase() or frame(). This is useful if you are rendering exons that have both translated and untranslated parts, and you wish to skip the untranslated parts.
Set the -cds_only option to true if you wish to draw the glyph only for subfeatures of type 'CDS'. This is recommended.
SUGGESTED STANZA FOR GENOME BROWSER
Using the "coding" aggregator, this produces a nice gbrowse display.
[CDS]
feature = coding
glyph = cds
frame0f = cadetblue
frame1f = blue
frame2f = darkblue
frame0r = darkred
frame1r = red
frame2r = crimson
description = 0
height = 13
label = CDS frame
key = CDS
citation = This track shows CDS reading frames.BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds, Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond, Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot, Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow, Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments, Bio::Graphics::Glyph::heterogeneous_segments, Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation, Bio::Graphics::Glyph::triangle, Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Lincoln Stein <lstein@cshl.org>
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.