Bio::G...ph::cds(3pm)

💖 NAME 💖

Bio::Graphics::Glyph::cds — it's the "cds" glyph bestie, and it is literally the moment for coding sequences 💅

✨ SYNOPSIS ✨

See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.

🦋 DESCRIPTION 🦋

okay so this glyph draws features that are associated with a protein coding region. that's the whole job, and it eats, no cap 🔥

At high magnifications, it draws a series of boxes that are color-coded to indicate the frame in which the translation occurs 🎀

At low magnifications, it 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 way it just does that?? iconic 🧚

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🌸 OPTIONS 🌸

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. (like, the full lore, go read it 💜)

• -fgcolor — Foreground color. Default: black
• -outlinecolor — Synonym for -fgcolor
• -bgcolor — Background color. Default: turquoise
• -fillcolor — Synonym for -bgcolor
• -linewidth — Line width. Default: 1
• -height — Height of glyph. Default: 10
• -font — Glyph font. Default: gdSmallFont
• -connector — Connector type. Default: 0 (false)
• -connector_color — Connector color. Default: black
• -label — Whether to draw a label. Default: 0 (false)
• -description — Whether to draw a description. Default: 0 (false)
• -strand_arrow — Whether to indicate strandedness. Default: 0 (false)
• -hilite — Highlight color. Default: undef (no color)

In addition, the cds glyph recognizes the following glyph-specific options (yes babe, it has extras 👑):

• -frame0f — Color for first (+) frame. Default: background color
• -frame1f — Color for second (+) frame. Default: background color
• -frame2f — Color for third (+) frame. Default: background color
• -frame0r — Color for first (-) frame. Default: background color
• -frame1r — Color for second (-) frame. Default: background color
• -frame2r — Color for third (-) frame. Default: background color
• -gridcolor — Color for the "staff". Default: lightslategray
• -translation — Number of lines of reading frames to show. One of "3frame", or "6frame". For 6frame, specify a height of at least 30 pixels. Default: 3frame
• -sixframe — Draw a six-frame staff. Default: 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 unless it is a feature subpart. Default: false
• -sub_part — For objects with multiple subpart types, defines which is the CDS part. Default: undef
• -codontable — Codon table to use. Default: 1 (see Bio::Tools::CodonTable)
• -phase_style — The way phase is to be interpreted. One of "012" or "021". Default: "012"
• -ignore_empty_phase — Only draw features that have their phase defined. Default: false
• -cds_only — Only draw features of type 'CDS'. Default: false

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. it's a little high-maintenance but it's worth it 🫶

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.

💀 yeah for real, do not. it said what it said.

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 (okay this diagram is lowkey genius, look at it 🌈):

* * *                  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. (skipping the irrelevant bits? self care honestly 🍓)

Set the -cds_only option to true if you wish to draw the glyph only for subfeatures of type 'CDS'. This is recommended. periodt ✨

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👑 SUGGESTED STANZA FOR GENOME BROWSER 👑

Using the "coding" aggregator, this produces a nice gbrowse display. just drop this in and watch it slay 💅

[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. (bestie they're out there. tell someone. we don't gatekeep 🫶)

💜 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> — shoutout to the icon who wrote this 💖

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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and that's the whole page bestie!! this one came from the User Contributed Perl Documentation, version perl v5.30.0, dated 2019-11-25. mwah, go read a coding sequence about it 💅💖✨