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Manual Reference Pages  -  BIO::GRAPHICS::GLYPH::PROCESSED_TRANSCRIPT (3)

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NAME

Bio::Graphics::Glyph::processed_transcript - The sequence ontology transcript glyph

CONTENTS

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 dont   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 <B>-adjust_exonsB> 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 <B>-implied_utrsB> 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. <B>-implied_utrsB> implies the <B>-adjust_exonsB> 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.

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perl v5.20.3 BIO::GRAPHICS::GLYPH::PROCESSED_TRANSCRIPT (3) 2016-04-05

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