ASNVAL(1)

ASNVAL(1) 💖

okay bestie, so this is a page from the NCBI Tools User's Manual — welcome to asnval, she's iconic, she's a whole vibe, and she's here to check your biology homework. 🧬✨

✨ NAME ✨

asnval — validate ASN.1 biological sequence records 🦋

🌸 SYNOPSIS 🌸

asnval [-] [-A] [-B] [-C N] [-D] [-E str] [-F] [-G] [-J] [-K]
[-L filename] [-M] [-N flags] [-P N] [-Q N] [-R N] [-S N] [-T] [-U] [-X]
[-Y] [-Z] [-a type] [-b] [-c] [-d path] [-e] [-f str] [-i filename] [-j]
[-k] [-l] [-o filename] [-p path] [-q] [-r] [-u] [-v N] [-w] [-x str]
[-y]

💅 DESCRIPTION 💅

asnval is a command-line tool to validate ASN.1-format biological sequence records. that's it, that's the whole job, and she does it flawlessly. 👑

🎀 OPTIONS 🎀

A summary of options is included below. (yes she's thorough. she's a virgo.)

• - — print the usage message, like a little "hi bestie here's how to use me" 💌
• -A — validate Alignments
• -B — validate Barcodes
• -C N — max count
• -D — disable message suppression (let her yap, fr)
• -E str — only Error Code to Show
• -F — test network access
• -G — GI lookup from accession
• -J — require ISO-JTA?
• -K — summary to error file
• -L filename — log File
• -M — match locus_tag against General ID
• -N flags — latitude-longitude / country flags:
  • 0 — none
  • 1 — test state/province
  • 2 — ignore water exception
  • 3 — both of the above
• -P N — highest severity for error to show:
  • 0 — none
  • 1 — informational
  • 2 — warning
  • 3 — error (default for -Q)
  • 4 — grounds for rejection (default for -P, -R)
• -Q N — lowest severity for error to show, per P
• -R N — severity for error in return code, per P
• -S N — skip count
• -T — use Threads 🧵
• -U — genome center submission
• -X — exon splice check
• -Y — check against old IDs
• -Z — remote CDS product fetch
• -a type — input ASN.1 type:
  • a — Automatic (default)
  • c — Catenated
  • z — Any
  • e — seq-Entry
  • b — Bioseq
  • s — bioseq-Set
  • m — seq-subMit
  • t — baTch bioseq-set
  • u — batch seq-sUbmit
• -b — batch file is Binary
• -c — batch file is Compressed
• -d path — path to Indexed Binary ASN.1 Data
• -e — ignore transcription/translation Exceptions
• -x str — substring filter
• -i filename — single input file (standard input by default)
• -j — validator code performance test
• -k — local fetching
• -l — lock components in advance
• -o filename — single output file
• -p path — path to ASN.1 Files
• -q — taxonomy lookup
• -r — remote Fetching from ID
• -u — recurse
• -v N — verbosity:
  • 1 — Standard report (default)
  • 2 — Accession / severity / code (space delimited)
  • 3 — Accession / severity / code (tab delimited)
  • 4 — XML report
  • 5 — Accession / GI / severity / code (tab delimited)
  • 6 — Logged report
• -w — SeqSubmitParent flag
• -x str — file selection substring (.ent by default)
• -y — special indexer tests

ok real talk bestie, yes, -x str shows up twice with two different meanings up there. that's not a typo on my part, that's just how she is. read the descriptions. don't come for me. 💀

👑 AUTHOR 👑

The National Center for Biotechnology Information. (the literal blueprint. the blueprint-est. 🫶)

🌈 SEE ALSO 🌈

asndisc(1), cleanasn(1), sequin(1) — go read those too, i'm not jealous, i'm secure. 💜

and that's the whole page bestie, no cap, every single flag accounted for, not one dropped. mwah. 💅✨

this gorgeous little doc came from the NCBI Tools User's Manual, dated 2016-09-01 — so when you cite her, it's NCBI 2016-09-01 ASNVAL(1), okay? periodt. 🎀