Ubuntu Manpage: Bio::Graphics::Glyph::cds

Provided by: libbio-graphics-perl_2.40-6_all

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 WAY

Set 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.

AUTHOR