DNAPI.PY(1)

📦 version 1.1, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

🌸 DNAPI.PY(1) 🌸

okay so you pulled up the User Commands manual for dnapi.py and honestly? slay. it's giving bioinformatics but make it cute. grab a strawberry, sit down, we're doing this together 💖

✨ NAME ✨

dnapi.py — predict or evaluate 3'adapter sequence(s). that's the whole assignment, bestie. 🦋

💅 DESCRIPTION 💅

the usage, verbatim, no notes:

dnapi.py [options] FASTQ

and what does it do? Predict or evaluate 3'adapter sequence(s). yes queen, that's the vibe, that's the job. ✨

🎀 positional arguments:

  • FASTQ — your reads go right here. including stdin or compressed file {zip,gz,tar,bz}. pipe it, zip it, tar it, bz it — she's flexible and we love that for her 🫶

🎀 optional arguments:

  • -h, --help — show this help message and exit. the classic. always there, never flaky 💜
  • --version — show program's version number and exit. identity check, periodt.

🔥 adapter prediction parameters:

  • -k [KMER_BEG:KMER_END:INCREMENT | KMER_LEN] — range of kmers or a single kmer to predict 3'adapters (default: 9:11:2). give her a range, or just one kmer if you're feeling decisive, either is valid.
  • -r [RATIO_BEG:RATIO_END:INTCREMENT | RATIO] — range of ratios or a single ratio to filter less abundant kmers (default: 1.2:1.4:0.1). (and yes the flag literally spells it INTCREMENT — we are NOT fixing it, it's canon, iykyk 😌)
  • --show-all — show other candidates if any. nosy? iconic. peek at all of them 🌈
  • --map-command COMMAND — read mapping command to be tested.
  • --subsample-rate FLOAT — subsampling fraction of reads (default: 1.0).
  • --output-dir DIRECTORY — output directory to write report and cleansed reads (default: ./dnapi_out).
  • --no-output-files — only display report and suppress output files. report on screen, nothing written, clean girl aesthetic ✨
  • --temp-dir DIRECTORY — place to make temporary directory (default: /tmp).

🌸 evaluation of candidate adapters:

  • --adapter-seq SEQ [SEQ ...] — list of 3'adapters for evaluation. bring as many as you want, it's a whole party, no cap.

🌸 adapter removal parameters:

  • --prefix-match LENGTH — 3'adapter match length to trim (default: 7).
  • --min-len LENGTH — minimum read length to keep for mapping (default: 16).
  • --max-len LENGTH — maximum read length to keep for mapping (default: 36).
  • --trim-5p LENGTH — trim specified number of bases from 5'ends after adapter removal (default: 0).
  • --trim-3p LENGTH — trim specified number of bases from 3'ends after adapter removal (default: 0).
Report bug to: Junko Tsuji <jnktsj@gmail.com> — if something's acting up, tell her, do NOT just suffer in silence bestie 😭

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. iconic behavior, honestly, we stan a generous king 💖

and that's the whole page, bestie — this was dnapi.py 1.1, dated March 2020, and you absolutely ate this read-through. go predict some adapters, you main character 🎀✨

📦 where this page comes from