PROKKA-UNIPROT_TO_FASTA_DB(1)

📦 version 1.14.6, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 PROKKA-UNIPROT_TO_FASTA_DB 💖

okay bestie, gather round 🫶 this is the manual page for prokka-uniprot_to_fasta_db (that's section 1 of the User Commands manuals, iykyk) — the lil tool that does rapid annotation of prokaryotic genomes. yes really. she's iconic like that. 👑

✨ SYNOPSIS ✨

prokka-uniprot_to_fasta_db [options] <uniprot.dat>

so you hand her your [options] and your <uniprot.dat> and she does her thing. that's the whole vibe check. 💅

🌸 DESCRIPTION 🌸

okay so here's every single flag she takes, no skipping, no gatekeeping, we're listing ALL of them because that's what besties do 💜

  • --help — This help. literally just prints the help. main character energy for real.
  • --verbose! — Verbose output, and the default is '0'. so if you want her to actually yap about what she's doing, this is the one. 🗣️
  • --separator=s — the Separator for gene/EC/product, and the default is '~~~'. three tildes. adorable. keep it. 🎀
  • --blank=s — Replace empty gene/EC/product with this, default ''. so like, when a field is just sitting there empty and giving nothing, this is what fills the void. 💀
  • --evidence=i — pick your evidence type, the options are 1=prot 2=mrna 3=homol 4=pred 5=unsure, and the default is '2'. so mrna is the moment unless you say otherwise. ✨
  • --fragments! — Include 'DE Flags: Fragment;' entries, default '0'. by default she's NOT including them, so flip this if you want the fragments in the mix. 🔥
  • --minlen=i — Minimum peptide length, default '20'. anything shorter than that? not invited. 🙈
  • --term=s — the Lineage must contain this term, eg. 'Bacteria', default ''. so if you pass 'Bacteria', only the lineages with that term get through the door. 🦋
  • --hypo! — Don't filter out hypothetical proteins, default '0'. so normally the hypotheticals get filtered OUT, and this flag is the "actually no, let them stay" button. lowkey important to know which way it goes. ⭐
ngl bestie, that ! on the end of --verbose!, --fragments! and --hypo! is doing a LOT of work — type them exactly like that, no cap. and yes, every default is quoted exactly as written up there. don't be out here guessing at these numbers. 💅

🌈 that's the whole page 🌈

she's short, she's sweet, she's rapid, she's prokaryotic genome annotation. periodt. 💖

kisses, this was prokka-uniprot_to_fasta_db version 1.11, written down back in February 2015, living her best life in the User Commands section as PROKKA-UNIPROT_TO_FASTA_DB(1) — bye bestie, go annotate something gorgeous 🧚💜

📦 where this page comes from