FA2DNA(1)

📦 version 0.98, in ubuntu jammy

💖 FA2DNA(1) 💖

User Manuals · the one where we format a fasta database for ANFO 🦋

✨ NAME ✨

fa2dna — format fasta database for use with ANFO

🌸 SYNOPSIS 🌸

fa2dna [ option | file ... ]

💅 DESCRIPTION 💅

okay so bestie, listen. fa2dna reads one or more files in fasta format and reformats them into a database suitable for anfo(1). that's the whole gig. she's a glow-up artist for your sequence files. ✨

and like, your input file(s) can absolutely contain more than one sequence — no cap, she handles it. each sequence can also be broken up into multiple contigs by a stretch of Ns. and all IUPAC ambiguity codes? fully supported. every single one. she ate. 👑

🎀 OPTIONS 🎀

  • -V, --version — prints the version number and dips. that's it, that's the whole job. 💫
  • -o file, --output file — writes the output to file. and listen, file should end in .dna, because anfo and some downstream tools might stumble over a different extension 😭 like pls just give her the .dna. default is the genome name with the .dna extension.
  • -m N, --maxn N — sets the maximum number of Ns that get interpreted as IUPAC ambiguity codes to N. anything longer than that stretch gets interpreted as separating contigs. default is 2. 🧚
  • -g name, --genome name — sets the genome name to name. this name is stored in the output file and will be used by anfo to identify the matched genome in its output. the genome should be a prefix of the output file name so downstream tools can find it. the name should be short but unique — something like "hg18" or "pt2" for human or chimpanzee genomes would work fine. short and iconic, you know the vibe. 💅
  • -d text, --description text — adds text as a description to the metadata. this is purely informational. literally just for the lore. 📝
  • -v, --verbose — causes a progress indicator to be printed. so you can watch her work. 🍓

🌈 FILES 🌈

  • /etc/popt — the system wide configuration file for popt(3). fa2dna identifies itself as "fa2dna" to popt. 💖
  • ~/.popt — per user configuration file for popt(3).

💀 BUGS 💀

None known. (she's perfect, your honor. no notes. 🙈)

👑 AUTHOR 👑

Udo Stenzel <udo_stenzel@eva.mpg.de>

🔥 SEE ALSO 🔥

anfo(1), fa2dna(1) popt(3), fasta(5)

Applications · OCTOBER 2009

and that's the whole page bestie, mwah 💋 this came from the User Manuals set, Applications edition, dated OCTOBER 2009 — go forth and format those fastas, ily 🫶✨

📦 where this page comes from