GO::IO::Blast(3pm)

🌸 GO::IO::Blast 💥

okay bestie, buckle up, because this is GO::IO::Blast — the Gene Ontology Blast Reports module, and yes, DEPRECATED is literally right there in the name, iykyk. She's an icon but she's retired. 👑

This one lives in the User Contributed Perl Documentation corner of the perl man pages, section 3pm. Come sit with me.

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✨ SYNOPSIS ✨

...yeah. There is genuinely nothing here. The synopsis is empty. Not me hyping up a section that has no content 🙈. Moving on fr fr.

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💅 DESCRIPTION 💅

So what does she actually do? She parses a blast report. And not just any blast report — it has to be a blast that was performed on a seqdb whose headers can be mapped to GO terms via the go database. No random fasta, bestie, we have standards. 🎀

She takes the blast hits, and she finds the corresponding GO terms for them. Heads up: right now it requires the fasta to have "genename:" in the header — but the original author literally says we should make it configurable. So it's giving "we know, we know, it's on the list."

Then, using those GO terms, a GO::Model::Graph gets built, with the blast hits attached according to product<->term links. Cute. Structural. Obsessed. 🌈

Here's the ✨main character✨ concept: any blast hit H that corresponds to a term T implicitly corresponds to all the terms above T in the DAG. Like, if you hit a G-protein coupled receptor, you also implicitly hit a transmembrane receptor. The vibes propagate upward, no cap. 🦋

At every node, all the scores get combined — including those implicit scores from hits further down. And right now they're "playing with" this as the scoring scheme:

log2( 2 ** score1 + 2 ** score2 +.... 2** scoreN)

Important: hits are only counted once at each node. No double dipping, periodt. 💀

And now, the TODO list — the "we'll get to it" board of dreams:

• TODO — use bioperl to parse full report if required (currently parses summary)
• TODO — configurable ways to go from fasta header to GO terms
• TODO — different scoring schemes
• TODO — result object

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🔥 PUBLIC METHODS - Blast 🔥

Bestie... that's it. That's the whole section. <pink>PUBLIC METHODS - Blast</pink> is listed as a heading and then there is absolutely nothing under it. She said "public methods" and then ghosted us. 👻 Not a single method documented. Iconic behaviour, honestly.

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🫶 FEEDBACK 🫶

Got thoughts? Feelings? Bug reports? Hit up:

Email: cjm@fruitfly.berkeley.edu

And the license tea: this library is free software — you can redistribute it and/or modify it under the same terms as Perl itself. So go off, bestie, legally. 💜

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okay that's the whole page!! No more sections. You made it. 🎉

cute little sign-off for you: this lovely was served up by perl v5.36.0 and stamped 2023-12-18. Basically vintage. A classic. 💖✨