SNAP(1)

📦 version 2013-11-29, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

🧬 SNAP(1) — User Commands 🧬

okay bestie, pull up a chair because we're about to talk about snap-hmm, which lives in section 1 of the manual (that's the User Commands girlies, iykyk). ✨

🌸 NAME 🌸

snap-hmm — Semi-HMM-based Nucleic Acid Parser

like... it parses nucleic acids. with a semi-HMM. the name literally ate and left no crumbs. 💅

✨ SYNOPSIS ✨

snap-hmm [options] <HMM file> <FASTA file> [options]

so you're gonna feed it an HMM file and a FASTA file, and yes, the options can go on either side of them, no cap. both positions are valid, that's just the vibe. 🦋

🎀 OPTIONS 🎀

okay here's the whole lineup, every single one, nobody's getting left out:

  • -help — report useful information. it's giving "just tell me what's going on" energy, and honestly? valid. 🫶
  • -lcmask — treat lowercase as N. lowercase letters get masked out like they're on read receipts. 🙈
  • -plus — predict on plus strand only. one strand, one main character. 👑
  • -minus — predict on minus strand only. the other strand gets its solo moment too. 💜
  • -gff — output annotation as GFF. it's giving structured, it's giving organized. ⭐
  • -ace — output annotation as ACED. a whole different format, and she's iconic for it. 💖
  • -quiet — do not send progress to STDERR. no yapping, just silence. shhh. 🤫
  • -aa <file> — create FASTA file of proteins. write those protein besties out to file. 🧚
  • -tx <file> — create FASTA file of transcripts. transcripts get their own file, as they should. 🌸
  • -xdef <file> — external definitions. pulling in definitions from file, because sometimes you need outside help and that's okay. 🌈
  • -name <string> — name for the gene [default snap]. if you don't name her, she's just snap, and honestly that's a pretty cute default. 🎀
lowkey reminder bestie: options can show up before or after the <HMM file> and <FASTA file> — the synopsis said so, so it's fr fr true. 🔥

and that's the whole page, periodt. this lil legend is snap, dated 2010-07-28, and the manual page itself is from October 2013. hope that helps you slay your nucleic acid parsing journey, ily, bye!! 💖✨🦋🎀

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