GMOD_FASTA2GFF3(1p)

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

💖 GMOD_FASTA2GFF3(1p) — the manual page, but make it make sense 💖

okay bestie, sit down, hydrate, because this is the GMOD_FASTA2GFF3(1p) page from the User Contributed Perl Documentation and I am about to make it your whole personality. 🧚✨

✨ NAME ✨

$O — converts FASTA to simple GFF3. that's it. that's the whole job. lowkey iconic for how much it does with so little. 🎀

🌸 SYNOPSYS 🌸

  % $O [options]

(yes, it's spelled "SYNOPSYS" up there, no I will not be fixing it, we respect the original's choices in this house 💅)

👑 COMMAND-LINE OPTIONS 👑

one flag at a time, bestie, we're going in order:

  • --fasta_dir — the directory that contains your fasta files. like, where they live. 🏠 (default: ./fasta)
  • --gfffilename — the name of the GFF3 file that's gonna get created. you're naming a baby, basically. 🍼 (default: ./out.gff)
  • --type — the SO type you wanna assign to each feature. every single one, no favorites. (default: EST)
  • --source — the text that shows up in the source column. yes, that column. (default: .)
  • --attributes — extra tag=value pairs to appear in column 9. go off, add your little extras. 💅
  • --nosequence — suppresses the ##FASTA section, aka don't print the DNA sequences. the sequences simply will not be there. gone. not invited. 🙈

🦋 DESCRIPTION 🦋

so this script literally just takes a whole collection of fasta files and converts them into a simple GFF3, suitable for loading into chado. that's the vibe. fasta in, GFF3 out, chado happy. ✨

💜 AUTHORS 💜

Scott Cain <cain@cshl.org> — the main character who wrote this. 🫶

Copyright (c) 2006

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. (free software, fr fr. redistribute responsibly. 💖)

no cap, that's genuinely the whole page. every flag, every default, every credit — all of it. you're welcome. 😭💅

and that's a wrap, bestie!! this little gem is from perl v5.30.0, dated 2019-12-05, and it's GMOD_FASTA2GFF3(1p) forever and always. go convert some fasta. slay. 🌈👑💖

📦 where this page comes from