GAEVAL(1)

📦 version 0.16.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ gaeval ✨

okay bestie, welcome to gaeval — the little tool that calculates coverage and integrity scores for gene models based on transcript alignments. that's the whole vibe. it looks at how well your gene models line up with your transcript alignments and hands you numbers. 💖

🌸 SYNOPSIS 🌸

gaeval [options] alignments.gff3 genes.gff3 [moregenes.gff3 ...]

so you pass it your alignments file first, then one or more gene files, and it does its thing. no cap. ✨

💅 DESCRIPTION 💅

here's everything it can do, section by section, because organization is self-care. 🎀

🫶 Basic options

  • -h, --help — prints this help message and then dips. exits right after, she's busy. 💅
  • -v, --version — prints the version number and exits. iconic behavior. ✨

⭐ Weights for calculating integrity score

okay so important: these weights must add up to 1.0. like, they literally have to. that's the rule. 🙈

  • -a, --alpha: DOUBLE — introns confirmed, or % expected CDS length for single-exon genes; default is 0.6. 💖
  • -b, --beta: DOUBLE — exon coverage; default is 0.3. 🦋
  • -g, --gamma: DOUBLE — % expected 5' UTR length; default is 0.05. 🌸
  • -e, --epsilon: DOUBLE — % expected 3' UTR length; default is 0.05. 🎀

👑 Expected feature lengths for calculating integrity score

these are your "what even counts as normal around here" numbers. 📏

  • -c, --exp-cds: INT — expected CDS length (in bp); default is 400. ⭐
  • -5, --exp-5putr: INT — expected 5' UTR length; default is 200. 🌈
  • -3, --exp-3putr: INT — expected 3' UTR length; default is 100. 💜
heads up bestie: the weights are the one place you cannot freestyle. -a, -b, -g and -e have to sum to exactly 1.0 or it's not gonna be your moment. 🫶

and that's the whole page, fr fr. this is gaeval version 0.15.1, dated January 2016 — a lil vintage, still slaying. thanks for reading my TED talk, mwah 💋

📦 where this page comes from