PYENSEMBL(1)

📦 version 2.6.9, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu stonking

✨ NAME ✨

pyensembl — installs data from the Ensembl genome database 💖

🌸 DESCRIPTION 🌸

okay so bestie, here's the vibe: this thing lets you manipulate pyensembl's local cache. that's the whole job. it's giving cache-wrangler energy and honestly? iconic.

The general shape of it is:

pyensembl {install, delete, delete-sequence-cache} [--release XXX --species human...]

so you pick an action, and then you can point at a --release and a --species and it does the thing. no cap. 💅

🧚 To install particular Ensembl human release(s):

pyensembl install --release 75 77

🦋 To install particular Ensembl mouse release(s):

pyensembl install --release 75 77 --species mouse

💀 To delete all downloaded and cached data for a particular Ensembl release:

pyensembl delete-all-files --release 75 --species human
be so serious when you run this one, bestie — it is not playing around, it takes all the downloaded and cached data for that release. gone. periodt. 😭
pyensembl delete-index-files --release 75

(see how it's only the transcript and protein sequence cache? surgical. we love a targeted delete. 🔥)

👑 To list all installed genomes:

pyensembl list

just. the receipts. what's actually on your machine. chef's kiss.

🌈 To install a genome from source files:

pyensembl install --reference-name "GRCh38"  --gtf URL_OR_PATH  --transcript-fasta URL_OR_PATH  --protein-fasta URL_OR_PATH

you're handing it a reference name plus paths (or URLs!) for the --gtf, --transcript-fasta and --protein-fasta files, and it builds the genome from those. DIY but make it slay. ✨

and if you forget to tell it what to actually do? yeah. it will simply say:

pyensembl: error: the following arguments are required: action

the audacity, honestly. but also fair. it needs an action, bestie. it's not a mind reader. 🙈

🫶 AUTHOR 🫶

This manpage was written by Nilesh Patra for the Debian distribution and can be used for any other usage of the program.

okay that's the whole page, ily, go install some genomes 🌸 — this lil manual is from pyensembl 1.9.1+ds, dated May 2021. main character documentation energy, fr fr. 💖✨🎀

📦 where this page comes from