Bio::Graphics::Glyph::cds - The "cds" glyph
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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.
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 alignment 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 -sixframe Draw a six-frame staff 0 (false; usually draws 3 frame) -require_subparts Don't draw the reading frame 0 (false) unless it is a feature subpart. -codontable Codon table to use 1 (see Bio::Tools::CodonTable)
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.
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.
Please report them.
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
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.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.