IDSEQ-BENCH-SCORE(1)

✨ IDSEQ-BENCH-SCORE(1) ✨

okay bestie, welcome to the User Commands section of the manual, where we're about to score some benchmark samples 💅 this one's called idseq-bench-score and she's here to grade your bench samples against the answer key, no cap.

🌸 NAME 🌸

idseq-bench-score — score benchmark samples based on answer key 🎀

🦋 SYNOPSIS 🦋

idseq-bench-score [-h] [-o OUTPUT_FILE] [-t [TRUTH_FILES [TRUTH_FILES
...]]] [-e ENV] [-p LOCAL_PATH] [--mono-aupr] project_id sample_id
pipeline_version

💖 DESCRIPTION 💖

So basically? This scores benchmark samples based on the answer key. The key can either be encoded in the fastq read IDs (that's the vibe for IDseq Bench samples) or you can hand over an answer key yourself. Either way, she's grading. ✨

👑 OPTIONS 👑

🧚 positional arguments:

• project_id — the ID of the project, bestie. you gotta tell her which project we're talking about 💜
• sample_id — the ID of the sample. yes, the actual sample. iconic that she needs it 🫶
• pipeline_version — the pipeline version to retrieve, written as <major>.<minor> ⭐

🍓 optional arguments:

• -h, --help — shows this help message and then dips. classic. 🙈
• -o OUTPUT_FILE, --output-file OUTPUT_FILE — path of the output file where the results get written. if you don't set this, the results go straight to stdout, which honestly? slay 🌈
• -t [TRUTH_FILES [TRUTH_FILES ...]], --truth_files [TRUTH_FILES [TRUTH_FILES ...]] — a space separated list of truth files. and what is a truth file, you ask? it's a TSV file with the fields <tax_id, absolute abundance, relative abundance, rank, tax_name>. periodt. 💅
• -e ENV, --env ENV — string name of the environment the sample lives in. the options are prod (which is the default, lowkey the main character) and staging 🎀
• -p LOCAL_PATH, --local-path LOCAL_PATH — root of the local path where IDseq files are stored. it must follow the same structure to store files as IDseq, so don't get creative with it bestie 😭
• --mono-aupr — computes adjusted AUPR by forcing the precision/recall curve to be monotonic decreasing. very demure, very monotonic 📉✨

💀 AUTHOR 💀

This manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. shoutout Andreas, we love a manpage author 🫶

okay so that's the whole thing, you're fully caught up 🦋 this was idseq-bench-score version 0.0~git202006..., dated July 2020, and yeah — go score those samples, bestie, you're gonna eat 💖✨👑