ASN2GB(1)

💖 ASN2GB 💖

okay bestie, so this is asn2gb(1), a page from the NCBI Tools User's Manual, and honestly? it's giving "glow-up era". it converts ASN.1 biological data into a GenBank-style flat format. we're so back.

✨ NAME ✨

asn2gb — convert ASN.1 biological data to a GenBank-style flat format 🧬✨

🌸 SYNOPSIS 🌸

asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format]
[-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode]
[-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N]
[-u N] [-y N]

🦋 DESCRIPTION 🦋

so asn2gb takes descriptions of biological sequences from NCBI's ASN.1 format and turns them into one of several flat-file formats. and it's literally the successor to asn2ff(1) — out with the old, in with the icon. 👑

🎀 OPTIONS 🎀

a summary of options is included below, and yes we're doing all of them, no skipping, that's the rule bestie.

• - — print the usage message 💬
• -A accession — the accession to fetch. it may take the form accession,complexity,flags — where complexity should normally be 0, and a flags value of -1 enables fetching of external features (same energy as the legacy -F option).
• -F — fetch remote annotations. this is equivalent to specifying -A accession,0,-1 ✈️
• -a asn-type — the ASN.1 Type:
  • [Single record]
    • a — Any (autodetected; default) 🔍
    • e — seq-Entry
    • b — Bioseq
    • s — bioseq-Set
    • m — seq-subMit
    • q — Catenated
  • [Release file; components individually processed and freed]
    • t — baTch bioseq-set
    • u — batch seq-sUbmit
• -b — input file is binary 🔢
• -c — batch file is compressed 🗜️
• -d — Seq-loc minus strand ⤵️
• -f format — the Format:
  • b — GenBank (default) 🌟
  • bp or pb — GenBank and GenPept
  • e — EMBL
  • p — GenPept
  • q — nucleotide GBSet (XML)
  • r — protein GBSet (XML)
  • t — Feature table only
  • x — nucleotide INSDSet (XML)
  • y — tiny seq (XML)
  • Y — FASTA
  • z — protein INSDSet (XML)
• -g N — Bit flags (they all default to off):
  • 1 — HTML
  • 2 — XML
  • 4 — ContigFeats
  • 8 — ContigSrcs
  • 16 — FarTransl
• -h N — Lock/Lookup Flags (all default to off):
  • 8 — LockProd
  • 16 — LookupComp
  • 64 — LookupProd
• -i filename — input file name (default = stdin) 📥
• -j N — start location (default is 0, beginning of sequence) 🏁
• -k N — end location (default is 0, end of sequence) 🏁
• -l filename — log file 📝
• -m mode — the Mode:
  • r — Release
  • e — Entrez
  • s — Sequin (default)
  • d — Dump
• -n filename — Asn2Flat Executable (default = asn2flat) ⚙️
• -o filename — output file name (default = stdout) 📤
• -p — propagate top descriptors 🔝
• -q filename — Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff) ⚙️
• -r — enable remote fetching 📡
• -s style — the Style:
  • n — Normal (default)
  • s — Segment
  • m — Master
  • c — Contig
• -t N — Batch:
  • 1 — Report
  • 2 — Sequin/Release
  • 3 — asn2gb SSEC/nocleanup
  • 4 — asn2flat BSEC/nocleanup
  • 5 — asn2gb/asn2flat
  • 6 — asn2gb NEW dbxref/OLD dbxref
  • 7 — oldasn2gb/newasn2gb
• -u N — Custom flags (all default to off):
  • 4 — Hide features
  • 1792 — Hide references
  • 8192 — Hide sources
  • 262144 — Hide translations
• -y N — Feature itemID 🏷️

💜 AUTHOR 💜

The National Center for Biotechnology Information. shoutout, genuinely iconic of them 💅

🌈 SEE ALSO 🌈

asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1), insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz.

and that's the whole page bestie, no cap. if you need me i'll be in the docs, being obsessed with flat files 🫶

NCBI · 2016-09-01 — yeah this one's from September 1, 2016, so it's lowkey vintage, but she still ate. mwah 💋✨