PROKKA-BIOCYC_TO_FASTA_DB(1)

🌸 PROKKA-BIOCYC_TO_FASTA_DB 🌸

okay bestie, this is a page from the User Commands manual (yes that's the manual name, slay) and it's about prokka-biocyc_to_fasta_db, which is part of the whole "rapid annotation of prokaryotic genomes" moment. sit down, grab a boba, we're doing this 💖

✨ NAME ✨

prokka-biocyc_to_fasta_db — rapid annotation of prokaryotic genomes

✨ SYNOPSIS ✨

prokka-biocyc_to_fasta_db [options] [--datadir biocyc_data_subdir] > proteins.faa

like. it prints to stdout and you funnel it straight into a file. classic. redirect that output or it just yells into your terminal, no cap 🫶

✨ DESCRIPTION ✨

here's the whole rundown of the flags, and ngl every single one of them matters, so read all of them, don't skip, i will know 🌸

• --help — prints this help. the moment you're lost, just ask for help, we love a self-aware queen 👑
• --verbose! — verbose progress. default is '0', so it's off unless you say otherwise. turn it on if you want to watch everything happen in real time, main character energy ✨
• --datadir=s — path to the data/ folder inside your BioCyc organism directory. default is '' (empty, so it's on you to tell it where to look, bestie) 🎀
• --sep=s — the separator that goes between EC/gene/product. default is '~~~' which is genuinely iconic of it 💅
• --blank=s — what to swap in when EC/gene/product is empty. default is '' (nothing at all, so it just stays blank unless you fill it) 🦋
• --pseudo! — include /pseudo genes. default '0', so no by default. flip it on if you want them in there 🔥
• --hypo! — include 'hypothetical protein' genes. default '0', also off unless you ask. sometimes you want the mystery proteins, sometimes you don't 🙈
• --minlen=i — minimum peptide length. default '0', meaning nothing gets filtered out by length unless you raise it ⭐

lowkey important: those defaults are defaults, so if a thing isn't showing up or IS showing up when you didn't want it, check which of these you actually set. the vibes are configurable, the behaviour follows the config 😭

that's literally it, go forth and annotate 🧚

prokka-biocyc_to_fasta_db 1.11, February 2015 — stay iconic, stay annotated, mwah 💖✨