GO-SHO...TO-ROOT(1p)

📦
version 0.15 · 2 versions
, in debian trixie, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 NAME 💖

go-show-paths-to-root.pl — bestie, it shows you all possible paths from a term alllll the way to the top 🫶

✨ SYNOPSIS ✨

go-show-paths-to-root.pl -id GO:0008021 ontology/gene_ontology.obo
go-show-paths-to-root.pl -names -id GO:0008021 ontology/gene_ontology.obo

literally that's it. two vibes. pick your fighter 🎀

🌸 DESCRIPTION 🌸

okay so what it does: it traverses the DAG, showing you every single path — the terms and the intervening relationships — from where you are all the way up to the root. the whole journey. no skipping steps ✨

this script is purely file based tho. it has to parse the ontology every single time you run it. every time. no shortcuts, no stored memory, it's giving goldfish 🐠

good news tho: you can speed up the subsequent parses with the use_cache option. obsessed.

if you'd rather be using the GO MySQL db instead of files, go check out the script go-db-show-paths-to-root.pl over in the go-db-perl distribution. different girl, different vibe 💅

👑 ARGUMENTS 👑

  • -e ERRFILE — writes parse errors out as XML. defaults to STDERR. ngl there shouldn't be any parse errors if your files are well formed, so this is your safety net 🧚
  • -p FORMAT — tells it which parser to use. if you leave it unspecified it'll just take a guess based on the file suffix. see below for formats 👀

-use_cache ✨

if you specify this switch, caching mode is turned on. slay.

so here's how caching mode works: the first time you parse a file, an additional file gets exported in a special format that's fast to parse. this file has the same filename as the original file, except it gets the .cache suffix. cute right?

then the next time you parse that file, the program automatically checks whether the .cache file exists. if it does, and it's more recent than the file you specified, it parses that instead. if it does not exist, it gets rebuilt. periodt 💅

📚 DOCUMENTATION 📚

<http://www.godatabase.org/dev>

lowkey iconic that the docs are just one link and a dream. respect 🫡

okay bestie that's the whole page!! writing by perl v5.36.0, dated 2023-12-18 — go show some paths to the root, you got this 💖🦋💅

📦 where this page comes from