GMOD_MA...ERMPATH(1p)

📦
version 1.31 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ GMOD_MA...ERMPATH(1p) ✨

okay bestie, welcome to the User Contributed Perl Documentation corner of the internet 💖 this one's called gmod_make_cvtermpath.pl and she is that girl. buckle up, grab a strawberry matcha, and let's get into it 🍓

🌸 NAME 🌸

gmod_make_cvtermpath.pl — she calculates the transitive closure</> on the ontology terms in the cvterm table. no cap, that's literally her whole job 💅

🦋 USAGE 🦋

so there's two ways to summon her, bestie:

perl gmod_make_cvtermpath.pl -H [dbhost] -D [dbname]  [-vt] -c cvname
perl gmod_make_cvtermpath.pl -g [GMODConf_profile] -c cvname

pick your fighter ✨

🎀 Parameters 🎀

  • -c — the name of the ontology (cv.name) you wanna compute the transitive closure on. this one is Required, like fr fr you cannot skip it 🙈
  • -v — verbose output. she'll yap (affectionately) about what she's doing 🗣️
  • -t — trial mode. does not perform any store operations at all. > heads up: this is Not implemented. so like, she's giving placeholder energy 💀
  • -o — outfile for writing errors and verbose messages. optional, but cute 🎀
  • -g — GMOD database profile name (can provide host and DB name). Default: 'default'
  • -D — Database name
  • -H — Hostname
  • -d — Database driver name (e.g. 'Pg' for postgres)
  • -u — [Optional- if default user is not used] Database user name
  • -p — [Optional- if you need a password to connect to your database] Password for your user to connect to the database
the way that… if you're not using a GMOD database profile (that's option -g), then you literally have to provide -D, -H, -d, and optionally -u and -p. no profile, no vibes, you're on your own 🫶

💜 DESCRIPTION 💜

okay so here's the tea ☕ this script calculates the transitive closure</> on the ontology terms in the cvterm table.

now listen — this is a computationally intensive operation, bestie. like, not a little bit. doing this on a large cv like the Gene Ontology can take several hours 😭 so go touch some grass, hydrate, maybe take a nap, she'll be there when you get back 🌈

want more info on what a transative closure even is? (yes we're spelling it exactly how the original did, no notes 💅) go read:

http://www.geneontology.org/GO.database.shtml#graphs

iykyk 🧚

👑 AUTHOR 👑

Naama Menda <nm249@cornell.edu> — icon behavior, we love her, no further questions 💖

⭐ VERSION AND DATE ⭐

Version 1.2, Feb. 2011.

and that's the whole page, bestie!! this was perl v5.30.0 doing her thing on 2019-12-05, filed under GMOD_MA...ERMPATH(1p). slay, ate, left no crumbs 💅✨🦋🎀

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