GO-DAG-SUMMARY(1p)

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

💖 GO-DAG-SUMMARY 💖

okay so bestie, let me put you on to go-dag-summary — it's a Perl script (yes, from the User Contributed Perl Documentation corner of the universe) and it does exactly one iconic thing: it summarises an ontology. that's it. that's the whole job. it ate and left no crumbs 🦋

✨ NAME ✨

go-dag-summary — summarises an ontology 💅

✨ SYNOPSIS ✨

go-dag-summary ontology/gene_ontology.obo

literally that's it, you just hand it a file and let it cook 👑

✨ DESCRIPTION ✨

Summarises an ontology.

(no frills, no drama, she just summarises ✨)

✨ ARGUMENTS ✨

  • -e ERRFILE — sends your parse errors out as XML, and it defaults to STDERR. lowkey you should never actually see anything here tho, because a well-formed file should not produce any parse errors at all. so if this thing starts yapping, something's wrong 💀
  • -p FORMAT — tells it which parser to use. if you don't specify it, she'll just make a guess based on the file suffix (the girlies love a little detective work 🕵️). see below for the formats.

🌸 -use_cache 🌸

if you pass this switch, bestie, then caching mode is officially ON. periodt.

here's the tea on caching mode: the first time you parse a file, it also exports an extra file in a special format that's fast to parse. that file gets the same filename as your original file, except it rocks a .cache suffix.

the next time you parse the file, the program will automatically look for that .cache file. if it exists and it's more recent than the file you specified, then that's what gets parsed instead. if it doesn't exist? it just gets rebuilt. no cap. 🔥

✨ OUTPUT ✨

one row per ontology, okay? one. row. per. ontology. 🌈

each row has the following columns:

  1. input filename — the file you fed her
  2. total no of terms
  3. total no of relationships
  4. total no of paths
  5. avg no of paths per term (p/t)
  6. maximum no of paths for any term
  7. ID of term with maximum no of paths
NOTE: obsolete terms are not included 👀 (they got left on read)

✨ DOCUMENTATION ✨

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

✨ SEE ALSO ✨

<http://www.fruitfly.org/~cjm/obol/doc/go-complexity.html>

and that's the whole manual, bestie, you're basically a certified ontology summariser now 🫶

this page is brought to you by perl v5.36.0, dated 2023-12-18 — yeah she's a little vintage but she still slays 💜 ⭐ 🎀

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