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

💖 Bio::G...script(3pm) — bestie edition 💖

okay so you found the Bio::G...script(3pm) page, which lives under User Contributed Perl Documentation, and honestly? iconic. this is the manual for Bio::Graphics::Glyph::processed_transcript, and I'm gonna walk you through every single line of it like we're texting at 1am. no skips. no "you get the gist." we're doing the whole thing. 🫶

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✨ NAME ✨

Bio::Graphics::Glyph::processed_transcript — the sequence ontology transcript glyph. that's the whole name bestie, say it with your chest. 👑

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✨ SYNOPSIS ✨

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

that's it. that's the synopsis. she's low maintenance. go read those two if you want the full lore. 📚

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✨ DESCRIPTION ✨

so this glyph? she's the one you call when you're drawing processed transcripts — the ones that have both CDS segments and UTR segments. 💅

here's the vibe:

• the CDS gets drawn in the background color
• the UTRs get drawn in an alternate color, and you pick that color with the utr_color option
• and if you want your UTRs to be skinnier than your CDS (a little waist action ✨), set the thin_utr option

for this glyph to actually do the thing you want, you need to hand her a compound Bio::SeqFeature that has subfeatures with primary_tag of "CDS" and "UTR". don't skip this, fr fr.

and you're not even locked into plain old "UTR" — you can get more specific and pass in 5'-UTR, 3'-UTR, or the Sequence Ontology terms untranslated_region, five_prime_untranslated_region, and three_prime_untranslated_region. so many options, so much range. 🌈

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🌸 OPTIONS 🌸

the standard ones every glyph gets 🎀

these are standard across all Glyphs, and if you want the full explanation you go read Bio::Graphics::Glyph. here's the whole list, no gatekeeping:

• -fgcolor — foreground color. default: black 🖤
• -outlinecolor — just a synonym for -fgcolor. same girl, different name.
• -bgcolor — background color. default: turquoise 💎
• -fillcolor — synonym for -bgcolor. again: same energy.
• -linewidth — line width. default: 1
• -height — height of the glyph. default: 10
• -font — the glyph's font. default: gdSmallFont
• -connector — connector type. default: undef (false)
• -connector_color — connector color. default: black
• -label — whether to draw a label. default: undef (false)
• -description — whether to draw a description. default: undef (false)
• -strand_arrow — whether to indicate strandedness. default: undef (false)
• -hilite — highlight color. default: undef (no color)

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and the glyph-specific ones, which the original calls "the alignment glyph" options (typo era, we respect it) 🦋

• -thin_utr — a flag. if it's true, the UTRs get drawn at 2/3 of the height of the CDS segments. default: undef (false)
• -utr_color — the color of UTR segments. default: Gray #D0D0D0
• -decorate_introns — draws the strand with little arrows on the intron. default: undef (false)
• -adjust_exons — fixes exons so they don't overlap UTRs. default: undef (false)
• -implied_utrs — whether UTRs should be implied from exon and CDS features. default: undef (false)
• -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. 👑

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ok but what do those last two actually do 👀

-adjust_exons — you need this when your features have exons (SO type exon) that overlap with the UTRs (SO types five_prime_UTR and three_prime_UTR). with this on, the exon parts of the glyph get clipped so they don't overlap the UTR parts. tidy. ✂️

-implied_utrs — you need this one when there are no explicit UTR features at all. in that case, the UTRs get derived by subtracting the positions of CDS subfeatures from the positions of exon subfeatures. and heads up, bestie:

-implied_utrs implies the -adjust_exons option. it comes as a package deal, no a la carte. 🎁

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🐛 BUGS 🐛

Please report them.

(that's the entire section. she's brief. she's honest. she said "please." 😭)

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👀 SEE ALSO 👀

go read all of these, i'm not summarising, i'm listing:

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

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💜 AUTHOR 💜

Lincoln Stein <lstein@cshl.org> — we love a legend. 🫶

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, you ate it, you read it, you're basically a bioinformatics main character now. 👑💅✨

this was perl v5.30.0, dated 2019-11-25, served up fresh under Bio::G...script(3pm). mwah. 🎀