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

💖 NAME 💖

okay so bestie, welcome to Bio::G...::gene(3pm) — it's a page from the User Contributed Perl Documentation and it's literally all about Bio::Graphics::Glyph::gene, a GFF3-compatible gene glyph. no cap. 🧬✨

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🌸 SYNOPSIS 🌸

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

like, that's the whole synopsis, go read those two if you want the lore 📚🫶

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🦋 DESCRIPTION 🦋

So this glyph is the one you pull out when you're drawing genes that might have alternatively-spliced transcripts. 🎀 The different isoforms get stacked on top of each other and share one single label and description that applies to the whole entire stack — main character energy, honestly. 👑

Each individual transcript's name is optionally printed to the left of the transcript glyph, if you want that. 💅

Transcripts (that's the splice isoforms) get drawn using the processed_transcript glyph. The CDS features are drawn in the background color, and the UTRs are drawn in an alternate color that you pick with the utr_color option. Also! You can make the UTRs thinner than the CDS by setting the "thin_utr" option. skinny legend behavior 🍓

This glyph is designed to work properly with GFF3-style three-tier genes, where:

• the top level feature has the Sequence Ontology type "gene"
• the second level feature(s) have the SO type "mRNA"
• the third level feature(s) have the SO type "CDS", "five_prime_utr" and "three_prime_utr"

Subparts named "UTR" are also honored, periodt. ✨

The feature can contain other subparts too (think exon, intron, translation), but ngl they're currently ignored unless you supply the sub_part option. If you do use the sub_part option, that feature type gets used and the CDS and UTR features get excluded. This could be used for specifying that exons be used instead, for example. 👀

Oh and this glyph is a subclass of processed_transcript, so it recognizes all the same options. inherited the whole wardrobe fr 💜

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✨ OPTIONS ✨

These following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. 🌈

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

In addition, the gene glyph recognizes the following glyph-specific options: 🎀

• -label_transcripts — Flag. If true, then the display name of each transcript will be drawn to the left of the transcript glyph. Default is undef (false).
• -thin_utr — Flag. If true, UTRs will be drawn at 2/3 of the height of CDS segments. Default is undef (false).
• -utr_color — Color of UTR segments. Default is Gray #D0D0D0.
• -decorate_introns — Draw strand with little arrows on the intron. Default is undef (false).

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💀 BUGS 💀

The SO terms are hard-coded. 😭 They should be more flexible and should recognize ISA relationships. like... they know. they said it. we move.

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🔥 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 👑 the whole friend group fr

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🌟 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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okay that's the whole page bestie, you ate that 💅✨ this was Bio::G...::gene(3pm) from perl v5.30.0, dated 2019-11-25 — go forth and draw some gorgeous three-tier genes, iykyk 🦋💖🌈