MASON_METHYLATION(1)

📦
version 2.5.2 · 2 versions
, in ubuntu stonking

👑 NAME 👑

mason_methylation — Methylation Level Simulation. That's it, that's the whole vibe. She simulates, she methylates, she serves.

🌸 SYNOPSIS 🌸

mason_methylation [OPTIONS] -i IN.fa -o OUT.fa

✨ DESCRIPTION ✨

okay so bestie, here's the tea: mason_methylation simulates methylation levels for IN.fa and writes them straight into OUT.fa. In, out, done. Iconic behavior tbh. 💖

💅 OPTIONS 💅

  • -h, --help — shows you the help message. your lil safety net fr.
  • --version — spills the version info.
  • -q, --quiet — low verbosity. she's being chill, not chatty.
  • -v, --verbose — higher verbosity. she's talking more now.
  • -vv, --very-verbose — highest verbosity. she is telling you EVERYTHING and honestly? we love that for her.
  • --seed UINT64 — the seed for the RNG. Default: 0.
  • -i, --in INPUT_FILE — input FASTA file with genome. valid filetypes are literally: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where the * can be any of these extensions: gz, bz2, and bgzf — that's for transparent (de)compression, so she unzips without you even asking. 💅
  • -o, --out INPUT_FILE — input FASTA file with genome. valid filetypes are: .sam[.*], .raw[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .fas[.*], .faa[.*], .fa[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
not me noticing the page says "input FASTA file" for --out too 👀 but that's exactly what it says, so that's exactly what I'm telling you. no cap.

🧬 Methylation Level Simulation 🧬

  • --methylation-levels — enables the methylation level simulation. the main character switch fr fr.
  • --meth-cg-mu DOUBLE — median of the beta distribution for the methylation level of CpG loci. in range [0..1]. Default: 0.6.
  • --meth-cg-sigma DOUBLE — standard deviation of the beta distribution for the methylation level of CpG loci. in range [0..1]. Default: 0.03.
  • --meth-chg-mu DOUBLE — median of the beta distribution for the methylation level of CHG loci. in range [0..1]. Default: 0.08.
  • --meth-chg-sigma DOUBLE — standard deviation of the beta distribution for the methylation level of CHG loci. in range [0..1]. Default: 0.008.
  • --meth-chh-mu DOUBLE — median of the beta distribution for the methylation level of CHH loci. in range [0..1]. Default: 0.05.
  • --meth-chh-sigma DOUBLE — standard deviation of the beta distribution for the methylation level of CHH loci. in range [0..1]. Default: 0.005.
🎀 three flavors of loci — CpG, CHG, CHH — each with a mu and a sigma, all living in [0..1]. know your defaults, bestie. 🦋

and that's the whole page, periodt. this lil masterpiece is mason_methylation version 2.0.13 from the [tarball] build, and you're reading the MASON_METHYLATION(1) manual. mwah. 💖✨🌈

📦 where this page comes from