GETMLST(1)

okay bestie, welcome to GETMLST(1) 💖 — she lives in the User Commands corner of the manual and she is literally here to make downloading MLST datasets a whole vibe. no cap.

🎀 NAME 🎀

getmlst — download MLST datasets by species from pubmlst.org. that's it, that's the girl 💅

🦋 SYNOPSIS 🦋

getmlst [-h] [--repository_url URL] --species NAME [--force_scheme_name]

✨ DESCRIPTION ✨

okay so picture this: you want MLST datasets, and you want them from http://pubmlst.org/data/ 🌈. getmlst goes and gets them for you by parsing an xml file, specifically http://pubmlst.org/data/dbases.xml. the way that it just reads that xml for you? obsessed.

the data it pulls down is for a species that you pick, and it's:

• profiles 💖 — these map STs to allele numbers
• numbered sequences 🔥 — one set for each locus in the scheme

and then, as if that wasn't enough, the alleles get concatenated together so they're ready to hang out with SRST2. iconic behaviour, honestly.

it also drops a log file into your working directory 🎀 — that log spills the tea on the time, date and location of every single file it downloaded, plus the <retrieved> tag, which is the little receipt telling you when the XML entry was last updated. very main character of it.

one thing to know, bestie: if the species name you typed matches multiple <species> entries in the xml file, the script doesn't just guess 🙈 — it simply reports the possible matches so you can try again. no drama, no chaos, just receipts.

💅 OPTIONS 💅

• -h, --help — show this help message and exit. the classic. the icon. use it whenever 💜
• --repository_url URL — URL for the MLST repository XML index 🌸
• --species NAME — the name of the species that you want to download (e.g. "Escherichia coli") 🦋
• --force_scheme_name — flag to force downloading of a specific scheme name (e.g. "Clostridium difficile") ✨ (and yes, the source spells it "Flage" — we love a typo, it's giving character 💀)

🌟 EXAMPLE 🌟

so like, here's you, thriving:

getmlst --species "Escherichia coli#1"

that's the whole assignment. go off 👑

👑 AUTHOR 👑

this manpage was written by Andreas Tille for the Debian distribution 🫶 — and it can be used for any other usage of the program, so take it everywhere, it travels well.

and that's the whole page, bestie!! 🌈 this was getmlst version 0.1.6, dated December 2015 ⭐ — shoutout to the source and the date for keeping it real, and to GETMLST(1) for being the moment. mwah 💖🎀🦋