GT-FEATUREINDEX(1)

📦
version 1.6.6 · 5 versions
, in ubuntu resolute, ubuntu stonking

💖 gt-featureindex 💖

okay so bestie, this is the GenomeTools manual page for gt-featureindex, and honestly? it's giving annotation retrieval realness. Let me put you on.

✨ NAME ✨

gt-featureindex — Retrieve annotations from a persistent feature index as GFF3 output.

Like. It goes and gets your annotations back out of a persistent feature index, and hands them to you as GFF3. That's the whole vibe. 👑

🌸 SYNOPSIS 🌸

gt featureindex [option ...] indexfilename

So you call gt featureindex, throw whatever options you want in there, and then give it an indexfilename. That's the one argument you don't skip, fr fr. 🫶

🦋 DESCRIPTION 🦋

Okay so here's the whole menu of options, no gatekeeping, every single one:

  • -range [start end] — range constraint for index query (default: undefined). You pass it a start and an end, and it constrains the query to that range. Don't pass it? Then it's undefined, bestie, no range for you. 💅
  • -seqid [string] — sequence region (default: undefined). You hand it a string and that's your sequence region. Leave it out and, yep, undefined. 🎀
  • -retain [yes|no] — retain attributes (default: yes). The default here is yes, so attributes are retained unless you say otherwise. Iconic default behavior, honestly.
  • -backend [...] — database backend to use choose from [sqlite] (default: sqlite). So your choices are... sqlite. That's the list. sqlite is also the default. The math is mathing. 😭
  • -filename [string] — filename for feature database (sqlite backend only) (default: undefined). Heads up: this one is sqlite backend only, so don't come at it with a different backend and expect magic. Default is undefined.
  • -v [yes|no] — be verbose (default: no). Want it chatty? Say yes. Default is a chill no. 🙈
  • -help — display help and exit. Exactly what it says. It shows help and then it leaves. Respect the exit. 🚪✨
  • -version — display version information and exit. Shows you the version info, then dips. Periodt.

🍓 REPORTING BUGS 🍓

Found a bug? First of all, oof. Second of all, don't suffer in silence — report it here:

https://github.com/genometools/genometools/issues

That's the spot. Go tell them. They wanna know. 💜

lowkey a whole feature index just sitting there, waiting to hand you annotations as GFF3. main character energy, no cap. 🔥

GenomeTools 1.6.6 — 11/09/2025 — and that's the whole page bestie, slay, go query something 💅✨🦋🎀

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