NAME

Bio::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.

AUTHOR

Lincoln Stein <lstein@cshl.org>