ASN2ALL(1)

✨ ASN2ALL(1) — the NCBI Tools User's Manual glow-up ✨

okay so bestie, gather round, because we're talking about asn2all — a little NCBI icon that turns ASN.1 biological data into literally every report format you could want. she contains multitudes 💅

🎀 NAME 🎀

asn2all — generate reports from ASN.1 biological data

🌸 SYNOPSIS 🌸

asn2all [-] [-A acc] [-F filename] [-G] [-J n] [-K n] [-M] [-T] [-X]
[-a type] [-b] [-c] [-d path] [-f format] [-h] [-i filename] [-k] [-l]
[-n policy] [-o filename] [-p path] [-r] [-s db] [-v filename] [-x ext]

🦋 DESCRIPTION 🦋

so asn2all is primarily intended for making reports out of the binary ASN.1 Bioseq-set release files you download from the NCBI ftp site (that's the ncbi-asn1 directory, iykyk). and she's flexible fr — she can produce:

• GenBank and GenPept flatfiles
• FASTA sequence files
• INSDSet structured XML
• TinySeq XML
• Sequin-style 5-column feature tables

the release files have the extension .aso.gz, and bestie you must uncompress them with gunzip(1) first, which gives you files with the extension .aso. like, for example, gbpri1.aso is the first file in the primate division, and this command:

gunzip gbpri1.aso.gz

will result in gbpri1.aso being created. and heads up — the original gbpri1.aso.gz file gets removed after successful decompression, so don't come crying to me 🙈

in asn2all, you tell her which file to process with the -i command line argument. use -a t to say "hey this is a release file" and -b to say "hey this is binary ASN.1". if you've got a text ASN.1 file from Entrez instead, just use -a a instead of -a t -b. easy 💖

nucleotide and protein records can be processed simultaneously — no cap, at the same time. use -o to point at the nucleotide output file, and -v for the protein output file. two files, one run, main character energy 👑

the -f argument decides which format gets generated, and it's documented in more detail (along with other options) in the next section. keep scrolling babe ⬇️

💅 OPTIONS 💅

a summary of options is included below. yes, all of them. we're not skipping a single one, periodt.

• - — Print usage message
• -A accession — Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1 enables fetching of external features
• -F filename — Accession Filter file
• -G — Relaxed Genome Mapping
• -J n — Seq-loc from
• -K n — Seq-loc to
• -M — Seq-loc Minus strand
• -T — Use Threads
• -X — EXtended qualifier output
• -a type — Input ASN.1 type:
  • a — Automatic (default)
  • c — Catenated
  • p — Piped
  • z — Any
  • e — Seq-entry
  • b — Bioseq
  • s — Bioseq-set
  • m — Seq-submit
  • t — Batch Bioseq-set
  • u — Batch Seq-submit
• -b — Bioseq-set is Binary
• -c — Bioseq-set is Compressed
• -d path — Path to indexed binary ASN.1 Data
• -f format — Output Format:
  • g — GenBank/GenPept (default)
  • m — GenBank Master Style
  • f — FASTA
  • d — CDS FASTA
  • e — Gene FASTA
  • r — Regenerated Defline
  • t — Sequin-style 5-column feature table
  • y — TinySet XML (akin to FASTA)
  • s — INSDSet XML (akin to GenBank/GenPept)
  • a — structurally equivalent text ASN.1
  • x — structurally equivalent XML
  • c — cache components
• -h — Display extra Help message
• -i filename — Input file name (standard input by default)
• -k — Enable local fetching
• -l — Lock components in advance
• -n policy — Near FASTA policy:
  • a — All
  • n — Near only (default)
  • f — Far only
• -o filename — Nucleotide Output file name
• -p path — Path to files
• -r — Enable Remote fetching
• -s db — Source database:
  • a — Any (default)
  • w — Exclude segmented sequences
• -v filename — Protein output file name
• -x ext — File selection suffix when working with entire directories. (default is .aso)

🔥 EXAMPLES 🔥

this command right here:

asn2all -i gbpri1.aso -a t -b -f g -o gbpri1.nuc -v gbpri1.prt

will generate GenBank and GenPept reports from gbpri1.aso. iconic, honestly. ate and left no crumbs 🍓

🫶 AUTHOR 🫶

The National Center for Biotechnology Information.

⭐ SEE ALSO ⭐

asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asn2idx(1), asn2xml(1), asndhuff(1), gene2xml(1), gunzip(1).

and that's the whole vibe bestie 💜 this page came from NCBI, dated 2016-09-01, and it's ASN2ALL(1) — go forth and generate some reports, you've got this 🌈✨