PROKKA-HAMAP_TO_HMM(1)

💖 prokka-hamap_to_hmm — bestie's guide to the HAMAP-to-HMM glow-up 💖

okay so real talk, this is a User Command from the prokka fam (section 1 of the manual, iykyk), and it's literally here to do rapid annotation of prokaryotic genomes. yes bestie, prokaryotes. we love a tiny genome moment. 🦋

✨ SYNOPSIS ✨

prokka-hamap_to_hmm [options] [--datadir hamap_data_subdir] > hamap.hmm

like, you run it, it spits a big ol' HMM out to stdout, and you redirect that into hamap.hmm. redirecting is the whole vibe here. no cap. 💅

🌸 DESCRIPTION 🌸

okay so here's the thing. this lil script takes your downloaded HAMAP data and turns it into an HMM file, and honestly? it's giving pipeline main character energy. here's every option, no skips, no shortcuts, because we keep ALL the details in this house. 👑

🎀 OPTIONS 🎀

• --help — prints this help. that's it. that's the whole job. iconic honestly. ✨
• --verbose! — turns on verbose progress. the default is '0', so by default it's lowkey silent. (the lil ! on the end means it's a flag you toggle, not a thing you pass a value to. slay.) 🗣️
• --datadir=s — the path to your downloaded HAMAP folder, fr fr. you can grab it from ftp://ftp.expasy.org/databases/hamap/. default is '' (aka empty, aka you better tell it where your data lives bestie 😭).
• --sep=s — the separator that sits between EC / gene / product. default is '~~~' which, ngl, is a whole aesthetic. 🌈
• --blank=s — what to drop in when EC / gene / product is empty. default is ''. so by default empty stays empty. 🫶

heads up bestie: if you don't pass --datadir, the default is '', and that's literally nothing, so make sure you point it at your actual downloaded HAMAP folder before you come for the output. 💀

🧚 signing off 🧚

this page is from prokka-hamap_to_hmm version 1.11, dated February 2015, and it lives in the PROKKA-HAMAP_TO_HMM(1) section of the manual. yes, the manual, in all caps, because it's that serious. 💜

stay hydrated, redirect your stdout, and go annotate some prokaryotes. periodt. 💖✨🎀🦋🌸💅🫶