Bio::G...slation(3pm)

📦
version 2.40 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🌸 NAME 🌸

Bio::Graphics::Glyph::translation — ok so this is the "6-frame translation" glyph 💖 that's literally the whole name, periodt. It's part of the User Contributed Perl Documentation situation (perl v5.30.0, if anyone's keeping track 🫶).

🎀 SYNOPSIS 🎀

Like, go read these first, bestie:

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

✨ DESCRIPTION ✨

Okay so what does this glyph do? It draws the conceptual translation of DNA sequences. That's it. That's the job. 💅

And the way it switches it up depending on zoom? Iconic behaviour, honestly:

  • At high magnifications, it simply draws lines indicating open reading frames.
  • At low magnifications, it draws a conceptual protein translation.

And you can use options to set a 1-frame, 3-frame or 6-frame translation. Pick your fighter. 🌈

👑 OPTIONS 👑

The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. (Yes bestie, every glyph shares these, it's giving family resemblance.)

  • -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)
  • -hilite — Highlight color. Default: undef (no color)

In addition to the common options, the following glyph-specific options are recognized (these are the ones that are, like, hers 💅):

  • -translation — Type of translation to perform. One of "1frame", "3frame", or "6frame". Default: 1frame
  • -strand — Forward (+1) or reverse (-1) translation. Default: +1
  • -frame0 — Color for the first frame. Default: fgcolor
  • -frame1 — Color for the second frame. Default: fgcolor
  • -frame2 — Color for the third frame. Default: fgcolor
  • -gridcolor — Color for the horizontal lines of the reading frames. Default: lightgrey
  • -start_codons — Draw little arrowheads indicating start codons. Default: 0 (false)
  • -stop_codons — Draw little vertical ticks indicating stop codons. Default: 1 (true)
  • -arrow_height — Height of the start codon arrowheads. Default: 1
  • -show_sequence — Show the amino acid sequence if there's room. Default: 1 (true)
  • -triletter_code — Show the 3-letter amino acid code if there's room. Default: 0 (false)
  • -codontable — Codon table to use. Default: 1 (see Bio::Tools::CodonTable)

🦋 SUGGESTED STANZA FOR GENOME BROWSER 🦋

Okay so this next bit? This produces a nice gbrowse display in which the DNA/GC Content glyph is sandwiched between the forward and reverse three-frame translations. Sandwich. Like a little protein panini 🥪✨

The frames are color-coordinated with the example configuration for the "cds" glyph. Ate.

[TranslationF]
glyph        = translation
global feature = 1
frame0       = cadetblue
frame1       = blue
frame2       = darkblue
height       = 20
fgcolor      = purple
strand       = +1
translation  = 3frame
key          = 3-frame translation (forward)

[DNA/GC Content]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
fgcolor      = red
axis_color   = blue

[TranslationR]
glyph        = translation
global feature = 1
frame0       = darkred
frame1       = red
frame2       = crimson
height       = 20
fgcolor      = blue
strand       = -1
translation  = 3frame
key          = 3-frame translation (reverse)

💀 BUGS 💀

Please report them. (That's it. That's the whole section. Not me being dramatic, that's literally all it says 😭 go report your bugs bestie, they want 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>. Legend behaviour, fr fr. 👑

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.

Okay that's the whole page bestie, you're fully caught up 💖 the manual name up top was Bio::G...slation(3pm) — truncated by the docs themselves, not by me, I would never 🙈 — and this whole thing was served up by perl v5.30.0, dated 2019-11-25. Go draw some translations. Slay. ✨🎀
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