CNVKIT_IMPORT-SEG(1)

📦
version 0.9.13 · 3 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ CNVKIT_IMPORT-SEG ✨

okay so bestie, welcome to cnvkit_import-seg 💖 — the little tool that takes your SEG file and turns it into CNVkit .cns files. it's giving glow-up for your data. no cap.

🌸 SYNOPSIS 🌸

cnvkit.py import-seg [-h] [-c CHROMOSOMES] [-p PREFIX]
[--from-log10]

[-d DIRECTORY]
       segfile

💅 DESCRIPTION 💅

so here's the whole vibe: you got a SEG file, you want a .cns file, and this is literally the converter for that. that's it. that's the function. periodt.

🎀 positional arguments 🎀

  • segfile — your input file, in SEG format. heads up: it may contain multiple samples, so it's not just a one-sample kinda situation. she's versatile. 💁♀️

🦋 options 🦋

  • -h, --help — shows this help message and then dips. exit stage left. 👋
  • -c CHROMOSOMES, --chromosomes CHROMOSOMES — this one maps chromosome indexes to names, like a little name tag situation. the syntax is literally:
"from1:to1,from2:to2"

orrrr you can just use "human" for the preset, which is:

"23:X,24:Y,25:M"

iconic preset, honestly. 🧬

  • -p PREFIX, --prefix PREFIX — adds a prefix to your chromosome names. the example given is 'chr', which renames '8' in the SEG file to 'chr8' in the output. it's giving ✨accessorizing✨.
  • --from-log10 — converts base-10 logarithm values in the input into base-2 logs. math but make it fashion. 📐
  • -d DIRECTORY, --output-dir DIRECTORY — the output directory name. that's where your stuff lands. put it somewhere cute. 🎀
💀 real talk: that's the entire option list. no hidden flags, no secret menu. we keep it simple here.

sign-off bestie 🌈 — this whole thing is cnvkit.py import-seg version 0.9.10, dated July 2023. go forth and convert your SEG files, queen. 🫶👑

📦 where this page comes from