ARDEN-ANALYZE(1)

📦 version 1.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

✨ arden-analyze ✨ — the manual page, bestie edition 💅

okay so this is the man page for arden-analyze, which lives in section 1 (User Commands) of the manual, and honestly? it's a lil cutie with a big job. let's get into it 🫶

🦋 NAME 🦋

arden-analyze — analyze the results of the artificial reference genome mapping

like. that's the whole vibe. it analyzes the results of the artificial reference genome mapping. iconic behavior, no notes 💖

🌸 SYNOPSIS 🌸

arden-analyze [options] [INPUT FILE] [OUTPUTFOLDER] ...

yes bestie, options first, then your input file, then your output folder(s), and the ... is there because the universe (and this script) said "you may have more than one" 💫

🎀 DESCRIPTION 🎀

so basically: this is a script that analyzes the results of the artificial reference genome mapping. that's its whole main character moment.

what it actually does for you: it identifies the putative TPs / FPs on a specific data set (reads). true positives, false positives, the whole dramatic saga. it's giving detective energy 🔍✨

💅 OPTIONS 💅

here's the menu, bestie. every single one, no gatekeeping:

  • OUTPUTFOLDER — the path to your output destination folder. where the good stuff goes to live 💖
  • INPUT FILE — the ppath to your ini file (yes, "ppath", that's literally what it says, we don't question the ancestors 🙈). to get the required format, have a look at the example files — they're your blueprint, fr fr.
  • --version — show the program's version number and exit. quick lil peek and then it dips 👋
  • -h, --help — show this help message and exit. the "help me help you" option 🫶
  • -p PHRED, --phred=PHRED — specify the PHRED encoding of the input reads, i.e. Illumina 1.3+ = -p 33. default is 33 ✨
  • -r RANK, --internalrank=RANK — use internal ranking for reads. this one is needed if the read names cannot be lexicographically sorted in the same way in python and your OS by sam tools. so like, if python and your OS are beefing over sort order, this is the peace treaty 🕊️ default is 1.
ngl, that -r one is the sneaky important one. if your read names are chaotic and python + your OS + samtools all disagree on the alphabet, you're gonna want internal ranking on. lowkey a lifesaver 🧚

🌈 that's the whole page 🌈

that's it, that's the man page. short, sweet, and fully committed to the bit.

<cute sign-off> this page is for arden-analyze version 2013-04-25, and the manual itself is dated February 2014 — so yeah, it's a vintage baddie, and it still slays 💜 bye bestie, go map some genomes ✨

📦 where this page comes from