Bio::Graphics::Glyph::UsereContriBio::Graphics::Glyph::processed_transcript(3)NAMEBio::Graphics::Glyph::processed_transcript - The sequence ontology
transcript glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
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."
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 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 -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 -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.
-implied_utrs implies the -adjust_exons option.
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.
perl v5.14.1Bio::Graphics::Glyph::processed_transcript(3)
