QIIME2LEFSE.PY(1)

✨ qiime2lefse.py — the manual page, but make it cute ✨

okay so bestie, gather round, because this little script is qiime2lefse.py from section 1 of the manual, and it's about to help you determine features of organisms, clades, taxonomic units, genes 💅 like. that's the whole NAME vibe. iconic behavior honestly.

🌸 DESCRIPTION 🌸

here's the usage, verbatim, no cap:

usage: qiime2lefse.py [-h] [--in [INPUT_FILE]] [--md [METADATA_FILE]]
                      [--out [OUTPUT_FILE]] [-c class attribute]
                      [-s subclass attribute] [-u subject attribute]

so what does it do? It converts a QIIME TSV BIOM table so you can use it with lefse 🦋

and listen — this part is IMPERATIVE, like genuinely non-negotiable, main-character-energy required: your table has to have taxa metadata associated with it named Consensus Lineage 🎀 if it doesn't, this whole thing is giving nothing.

luckily you can make that happen with, for example, the following biom convert script:

biom convert -i otu.biom -o otu.txt --to-tsv --header-key Taxonomy --outputmetadata-id 'Consensus Lineage'

slay. now your table has the metadata it needs 🫶

🎀 optional arguments 🎀

• -h, --help — shows this help message and dips. the classic. ✨
• --in [INPUT_FILE] — the Qiime OTU table file. if it's not present, you get stdin. 💜
• --md [METADATA_FILE] — the Qiime OTU table file; if it's not present you get only the OTU table without metadata. 🍓
• --out [OUTPUT_FILE] — the output file. if it's not present, it's stdout. 😌
• -c class attribute — the attribute to use as class. 👑
• -s subclass attribute — the attribute to use as subclass. 🧚
• -u subject attribute — the attribute to use as subject. 🌈

💖 AUTHOR 💖

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. ty bestie for your service 🫡💖

and that's the whole thing, babes! this was qiime2lefse.py version 1.1.2, dated September 2021 ⭐ go forth and convert those tables, you absolute icon 👑💅✨