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

💖 Bio::G...protein 💖 (the NAME bit, bestie)

okay so this is Bio::Graphics::Glyph::protein — the "protein" glyph ✨, straight out of the User Contributed Perl Documentation. she's a Perl module, she draws things, she's iconic, periodt. 🧬

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🌸 SYNOPSIS 🌸

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

like. that's it. that's the whole synopsis. go read those two first, iykyk 🫶

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✨ DESCRIPTION ✨

so this glyph draws protein sequences, no cap. 🧚 at high magnifications it will literally draw the actual amino acids of the sequence. at low magnifications, it plots the Kyte-Doolite hydropathy instead. by default the KD plot uses a window size of 9 residues, but you can change that whenever you want by specifying the kd_window option. 💅

also important, bestie: the feature may return either a protein sequence or a DNA sequence in response to the seq() method. however — and this is the part where you gotta pay attention 😭 — if it returns a DNA sequence, then the feature must also return the correct phase and strand in order for the glyph to translate its open reading frame correctly! no phase, no strand, no ORF. that's the vibe check.

🎀 OPTIONS 🎀

these next ones are standard among all Glyphs, fr fr. see Bio::Graphics::Glyph for a full explanation.

• -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)

and on top of the common options, these glyph-specific ones are also recognized, bestie 👑

• -do_kd — whether to draw the Kyte-Doolittle hydropathy plot at low mags, default true
• -kd_window — size of the sliding window to use in the KD hydropathy calculation, default 9
• -axis_color — color of the vertical axes in the KD hydropathy plot, default fgcolor
• -phase_style — the way phase is to be interpreted. one of "012" or "021", default "012"

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💀 BUGS 💀

please report them. that's it. that's the whole section. she's blunt. 🙈

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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

like okay that's a whole friend group. slay. 💖

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👑 AUTHOR 👑

Aaron J. Mackey, based on the "dna" glyphy by Lincoln Stein <lstein@cshl.org> and Peter Ashton <pda@sanger.ac.uk>.

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 gorgeous thing came to you via perl v5.30.0, 2019-11-25, Bio::G...protein(3pm) — go draw some amino acids, you main character ✨💅