GO::Me...Panther(3pm)

💖 GO::Metadata::Panther — the Perl doc, but make it a group chat 💖

okay so bestie, this is GO::Me...Panther(3pm), aka GO::Metadata::Panther, and she's part of the User Contributed Perl Documentation, section 3pm. she's giving very niche, very useful, lowkey iconic. let's get into it 🫶

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✨ NAME ✨

GO::Metadata::Panther — literally all the species info for the data that Panther Clusters use. that's the whole job. she's the species plug 💅

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🌸 SYNOPSIS 🌸

like, the vibe in code:

use GO::Metadata::Panther;
my $s = GO::Metadata::Panther->code('YEAST');

that's it, that's the entrance. go off 🦋

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💜 DESCRIPTION 💜

first things first: she inherits functions from GO::Metadata::UniProt::Species. so a lot of the family tree energy is coming from up there.

what she actually does is access information related to species inside the Panther seq2pthr.gz file. yep, that one.

and where do you get that file, you ask? you can fetch it from:

ftp://ftp.pantherdb.org/genome/pthr7.0/

bookmark her. maybe. i don't make the rules ✨

🎀 Exportable Subroutines

• panther_codes() — hands you back the list of UniProt species codes that get used in Panther clusters. the whole roster. the squad list. periodt.
• GO::Metadata::Panther->panther_all() — returns a list of "GO::Metadata::Panther" objects that are used in Panther clusters. so like, all the objects. all of them. the full collection 💖
• valid_codes(...) — returns a true value if every argument is a UniProt species code used in Panther clusters. otherwise? false. that's it. one wrong code and she's like "no <3". one hater in the group chat ruins the vibe check, yk?

🧚 OO Function

• GO::Metadata::Panther->new(...); — this basically just hands things off to GO::Metadata::UniProt::Species's new function. then she populates that with all the other Panther/GO specific information, and does a lil error correction while she's at it. multitasking queen 👑
• $s->ncbi_taxa_ids() — returns the list of NCBI taxa identifiers associated with the UniProt species code. and listen: in a perfect world this would only ever return one single value. in reality you might get more than one, so heads up. in any case, the first value is gonna be the actual numeric identifier that's associated. so like, first one is the real one, ok? 😭
• $s->prefers() — returns a list of id types (these generally get populated in "dbxref.xref_dbname") and the order they're in is the order of preference for use. and if you get a null list? that means we have literally never encountered a conflict that needed resolving. no drama, no notes, no cap 🫶

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👑 SEE ALSO 👑

GO::Metadata::UniProt::Species — her origin story, basically. go read it, iykyk 💅

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🌈 AUTHOR 🌈

Sven Heinicke <sven@genomics.princeton.edu></gt>

(yeah the tag is a lil broken bestie, we don't talk about it 🙈)

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and that's the whole page!! mwah 💋

this manual page came to you via perl v5.36.0, dated 2023-12-18, serving pure GO::Me...Panther(3pm) energy — stay hydrated, back up your stuff, and remember: the first NCBI taxa value is the real one 🎀✨