BIOM(1)

✨ BIOM — Biological Observation Matrix (BIOM) format (Python 3) ✨

okay so bestie, welcome to biom(1), the User Commands era of your life 💅 this is the manual for the biom tool, and it's giving Biological Observation Matrix (BIOM) format, running on Python 3 🐍✨ lowkey iconic.

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🌸 SYNOPSIS 🌸

biom [OPTIONS] COMMAND [ARGS]...

that's the whole vibe: you pass some OPTIONS, then a COMMAND, then that command's ARGS. that's it, that's the girl 🫶

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🎀 OPTIONS 🎀

• --version — shows you the version and then dips. exit, stage left. 👋
• -h, --help — shows this message and bounces. your bestie when you're lost fr fr.

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🦋 Commands: 🦋

these are the little sub-commands that do the actual work, no cap:

• add-metadata — adds metadata to a BIOM table. giving it a lil personality ✨
• convert — converts to/from the BIOM table format. glow-up in both directions 💖
• export-metadata — exports metadata as TSV. plain, simple, slaying.
• from-uc — creates a BIOM table from a vsearch/uclust/usearch BIOM... 👀 (yes that's where the original description trails off, we don't gatekeep the ellipsis)
• head — dumps the first bit of a table. just a lil peek, not the whole story 🙈
• normalize-table — normalizes a BIOM table. therapy but for data 💆
• show-install-info — provides information about the biom-format installation. receipts! 🧾
• subset-table — subsets a BIOM table. choose your faves 🎀
• summarize-table — summarizes sample or observation data in a BIOM table. the TL;DR queen 👑
• table-ids — dumps IDs in a table. name them, bestie 💅
• validate-table — validates a BIOM-formatted file. vibe check, but make it rigorous ✅

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💜 AUTHOR 💜

this manpage was written by Nilesh Patra for the Debian distribution, and it can be used for any other usage of the program. absolute legend, we stan 🫶✨

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and that's the whole thing, bestie 🎀 this page is from biom version 2.1.8, dated July 2020 — old but still eating, fr fr. go forth and matrix those observations 💖🌈