ASN2FF(1)

💖 ASN2FF(1) — the NCBI Tools User's Manual glow-up 💖

okay bestie, gather round, because we're talking about asn2ff — convert ASN.1 biological data to a flat format (old version). yes she's old, she's giving vintage, she's the blueprint, and we're gonna go through her whole vibe together. 🫶

✨ SYNOPSIS ✨

asn2ff [-] [-A X] [-B X] [-C] [-G] [-L F] [-M] [-R] [-V F] [-a filename]
[-b] [-d] [-e] [-f b/p/e/s/x/z] [-g] [-h F] [-k F] [-l filename]
[-m r/d/s/c/k/l/e/p] [-n F] [-o filename] [-p F] [-q] [-r filename] [-s]
[-t] [-v F] [-w] [-y] [-z]

like, look at her. so many little flags. so much main character energy. 👑

🌸 DESCRIPTION 🌸

so what does asn2ff actually do, you ask? she takes descriptions of biological sequences from NCBI's ASN.1 format and converts them into one of several flat-file formats. she's a translator. she's a multitasker. she's doing the most. 💅

but — and I need you to hear me on this — this program is built around a deprecated interface. deprecated. as in, she's still gorgeous but she's retired from the game. the manpage literally says please use asn2gb(1) instead. so like, use her if you must, but the glow-up successor exists and you should go support her. 💀

🎀 OPTIONS 🎀

a summary of options is included below. and bestie, we are going through every single one. no skips. no shortcuts. periodt. ✨

• - — prints the usage message. just a lil hello, a lil "here's how you work me." 🙈
• -A X — shows the region starting at X. the default is 0, so if you don't say anything, she starts from the very top. ⭐
• -B X — shows the region ending at X. the default is the last position, so she'll run it all the way to the end unless you tell her otherwise. 💜
• -C — shows Bankit comments. the tea is being served. 🍓
• -G — output is one top bioseq only, in genome view. just the one. she's being selective. 💅
• -L F — uses the old (pre-Genbank 127.0) LOCUS line format. yes, old old. vintage. retro. iconic. 🌈
• -M — output is map bioseqs only. maps only, bestie. 🦋
• -R — for GenBank Release. 🎀
• -V F — don't use VERSION. just… don't. 💀
• -a filename — filename for the ASN.1 input. the default is stdin, so if you're a "just pipe it in" kind of girl, she's got you. 🫶
• -b — input asnfile in binary mode. 🤖
• -d — use SeqMgr indexing. ✨
• -e — input is a Seq-entry. noted. 📝
• -f b/p/e/s/x/z — Output Format. the moment you've all been waiting for:
  • b — GenBank (this is the default, she's the standard, she's the moment)
  • p — GenPept
  • e — EMBL
  • s — PseudoEMBL
  • x — GenBankSelect
  • z — EMBLPEPT

so many formats. so many options. she's versatile. she contains multitudes. 🌸

• -g — show gi numbers. let the gi numbers breathe. 🔥
• -h F — hide sequence. she's shy. she's mysterious. 🙈
• -k F — don't use complex sets (phy-set, mut-set, pop-set). skip the drama, keep it simple. 💅
• -l filename — log errors to filename. so when things go wrong, they go wrong in a file. organized queen. 🎀
• -m r/d/s/c/k/l/e/p — Output mode. choose your fighter:
  • r — release (the default, she's the standard)
  • d — dump
  • s — Sequin
  • c — Chromoscope
  • k — dir-sub-debug
  • l — dir-sub
  • e — revise
  • p — partial report

eight whole modes. she woke up and chose range. ✨

• -n F — Strict gene_binding. no vibes-based gene binding today, we're being strict. 👑
• -o filename — Output Filename. the default is stdout, so she'll just yell it right into your terminal unless you redirect her. 📢
• -p F — omit new gene features. if you don't want the new ones, she'll leave them at home. 🦋
• -q — output is one top bioseq only. (yes, -G says something similar but that one's about genome view — this one's just the one bioseq, no extra qualifiers. keep them separate, bestie, they're different flags with different jobs. 💖)
• -r filename — output error logfile. the default is stderr, so errors come out screaming unless you send them somewhere quieter. 😭
• -s — input is a Seq-submit. 🌸
• -t — show verbose message text. she's giving detail. she's giving lore. she's giving paragraph. 📖
• -v F — suppress error messages. look away. nothing to see here. 🙈
• -w — use HTML output format. she's got a website now. 💅
• -y — print help format only. just the help. only the help. nothing but the help. ✨
• -z — new algorithm for orgnames. new algorithm, who dis. 🔥

🌟 AUTHOR 🌟

The National Center for Biotechnology Information. the icons themselves. the ones who built her. we stan. 👑

💜 SEE ALSO 💜

asn2all(1), asn2asn(1), asn2fsa(1), asn2gb(1), asn2xml(1), asndhuff(1).

(the whole friend group 💖 — and remember, asn2gb(1) is the one the manpage tells you to go hang out with instead. no cap.)

⚠️ real talk bestie: this program is built around a deprecated interface, and the manpage is not subtle about it. use asn2gb(1). this is not a drill. 🚨

and that's the whole page, bestie!! 🎀 this was ASN2FF(1) from the NCBI Tools User's Manual, source NCBI, dated 2005-05-16 — she's been slaying since 2005 and honestly? she still ate. bye babes!! 💖✨🦋🌸💅