CLEANASN(1)

💖 CLEANASN(1) 💖

okay bestie, so this is cleanasn from the NCBI Tools User's Manual, and it is literally the little goblin that tidies up your NCBI ASN.1 objects. no cap. she's giving ✨janitorial excellence✨ and honestly? obsessed.

🌸 NAME 🌸

cleanasn — clean up irregularities in NCBI ASN.1 objects

like. that's the whole job. she finds the weird little messes in your ASN.1 objects and she fixes them. iconic behavior.

🎀 SYNOPSIS 🎀

cleanasn [-] [-A filename] [-B str] [-C str] [-D str] [-F str] [-K str]
[-L filename] [-M filename] [-N str] [-O str] [-P str] [-Q str] [-R]
[-S str] [-T] [-U str] [-V str] [-X str] [-Z str] [-a str] [-b] [-c]
[-d str] [-f str] [-i filename] [-j filename] [-k filename] [-m str]
[-n path] [-o filename] [-p path] [-q path] [-r path] [-v path] [-x ext]

look at all those flags. she's highkey a whole alphabet. and every single one of them matters, so buckle up 🫶

🦋 DESCRIPTION 🦋

cleanasn is a utility program to clean up irregularities in NCBI ASN.1 objects.

that's it. that's the girl. she sees an irregularity, she cleans it. main character energy fr fr.

✨ OPTIONS ✨

a summary of options is included below. yes, all of them. no, we are not skipping any. periodt 💅

• - — Print usage message. that's it, bestie, just a lonely little dash and she tells you how to use her.
• -A filename — Accession list file.
• -B str — Branch, per the flags in str:
  • c — Has coding regions
  • d — No coding regions
  • p — Passes validation
  • q — Validator errors or rejects
  • r — Only pop/phy/mut/eco/WGS sets
  • s — Exclude pop/phy/mut/eco/WGS sets
  • t — Only nuc-prot sets
  • u — Exclude nuc-prot sets
  • v — Only segmented sequences
  • w — Exclude segmented sequences
  • x — Only segmented proteins
  • y — Exclude segmented proteins
• -C str — Sequence operations, per the flags in str:
  • c — Compress
  • d — Decompress
  • l — Recalculated segmented sequence length
  • v — Virtual gaps inside segmented sequence
  • s — Convert segmented set to delta sequence
  • t — Non-NucProt segmented set to delta sequence
  • u — Improved non-NucProt segmented set to delta sequence
  • g — Raw to delta by assembly gap
  • m — Merge assembly gap features
• -D str — Clean up descriptors, per the flags in str:
  • t — Remove Title
  • c — Remove Comment
  • n — Remove Nuc-Prot Set title
  • e — Remove Pop/Phy/Mut/Eco Set title
  • m — Remove mRNA title
  • p — Remove Protein title
  • a — Title to name
  • b — AutoDef title or name
  • x — Prefix title with organism name
• -F str — Clean up features, per the flags in str:
  • u — Remove User-objects
  • d — Remove db_xrefs
  • e — Remove /evidence and /inference
  • g — Fuse multi-interval genes
  • i — Fuse adjacent-interval imported features
  • r — Remove redundant gene xrefs
  • f — Fuse duplicate features
  • s — Package features on referenced Bioseq
  • k — Package coding-region or parts features
  • z — Delete or update EC numbers
  • b — Set Best coding-region reading frame
  • x — Retranslate coding regions
  • a — Adjust for missing stop codon
• -K str — Perform a general cleanup, per the flags in str:
  • b — BasicSeqEntryCleanup
  • p — C++ BasicCleanup (via an external utility)
  • v — AdvancedSeqEntryCleanup
  • s — SeriousSeqEntryCleanup
  • x — ExtendedSeqEntryCleanup
  • g — GpipeSeqEntryCleanup
  • n — Normalize descriptor order
  • u — Remove NcbiCleanup User Objects
  • c — Synchronize genetic Codes
  • f — CDS partial from translation
  • e — Impose CDS partials
  • d — Resynchronize CDS partials
  • m — Resynchronize mRNA partials
  • t — Resynchronize Peptide partials
  • a — Adjust consensus splice
  • i — Promote to "worst" Seq-ID
  • r — Reassign local IDs
  • l — Remove locus
• -L filename — Log file.
• -M filename — Macro file.
• -N str — Clean up links, per the flags in str:
  • o — Link CDS mRNA by Overlap
  • p — Link CDS mRNA by Product
  • l — Link CDS mRNA by Label and Location
  • r — Reassign feature IDs
  • m — Merge colliding feature IDs
  • f — Fix missing reciprocal feature IDs
  • c — Clear feature IDs
• -O str — Missing prot-ref name.
• -P str — Publication options:
  • a — Remove All publications
  • s — Remove Serial number
  • f — Remove Figure, numbering, and name
  • r — Remove Remark
  • u — Update PMID-only publication
  • j — Lookup ISO Journal title abbreviation
  • m — Merge identical publication features
  • # — Replace unpublished with PMID
• -Q str — Report:
  • c — Record count
  • r — ASN.1 BSEC report
  • s — ASN.1 SSEC report
  • n — NORM vs. SSEC report
  • e — PopPhyMutEco AutoDef report
  • o — Overlap report
  • l — Latitude-longitude country diff
  • d — Log SSEC differences
  • g — GenBank SSEC diff
  • f — asn2gb/asn2flat diff
  • h — Seg-to-delta GenBank diff
  • v — Validator SSEC diff
  • m — Modernize Gene/RNA/PCR
  • u — Unpublished Pub lookup
  • p — Published Pub lookup
  • j — Unindexed Journal report
  • t — tRNA anticodon report
  • w — Component offset report
  • x — Custom scan
• -R — Remote fetching from ID (NCBI sequence databases).
• -S str — Selective difference filter (capital letters skip):
  • s — SSEC
  • b — BSEC
  • A — Author
  • p — Publication
  • l — Location
  • r — RNA
  • q — Qualifier sort order
  • g — Genbank block
  • k — Package CdRegion or parts features
  • m — Move publication
  • o — Leave duplicate Bioseq publication
  • d — Automatic definition line
  • e — Pop/Phy/Mut/Eco Set definition line
• -T — Taxonomy Lookup.
• -U str — Modernize, per the flags in str:
  • g — Genes
  • r — RNA
  • p — PCR Primers
• -V str — Remove features by validator severity:
  • r — Reject
  • e — Error
  • w — Warning
  • i — Info
• -X str — Miscellaneous options, per str:
  • d — Automatic definition line
  • s — Automatic definition line with Source qualifiers
  • e — Pop/Phy/Mut/Eco Set definition line
  • n — Instantiate NC title
  • m — Instantiate NM titles
  • x — Special XM titles
  • p — Instantiate Protein titles
  • g — GPipe instantiate titles
  • c — Create mRNAs for coding sequences
  • f — Fix reciprocal protein_id/transcript_id
  • v — Revert preRNA or ncRNA transcript_id
  • t — Parse anticodon from Sequence
  • b — Batch cleanup of multireader output
  • z — Wrap SegSet with NucProt set
  • w — GFF/WGS genome cleanup
• -Z str — Remove indicated User-object.
• -a str — ASN.1 type:
  • a — Any (default)
  • e — Seq-entry
  • b — Bioseq
  • s — Bioseq-set
  • m — Seq-submit
  • t — Batch Bioseq-set
  • u — Batch Seq-submit
• -b — Input ASN.1 is Binary.
• -c — Input ASN.1 is Compressed.
• -d str — Source database:
  • a — Any (default)
  • g — GenBank
  • e — EMBL
  • d — DDBJ
  • b — EMBL or DDBJ
  • i — INSD
  • r — RefSeq
  • n — NCBI
  • x — Exclude EMBL/DDBJ
  • y — Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts
• -f str — Substring filter.
• -i filename — Single input file (defaults to stdin).
• -j filename — First filename.
• -k filename — Last filename.
• -m str — Flatfile mode:
  • r — Release
  • e — Entrez
  • s — Sequin
  • d — Dump
• -n path — asn2flat executable (default is /netopt/ncbi_tools/bin/asn2flat).
• -o filename — Single output file (defaults to stdout).
• -p path — Process all matching files in path.
• -q path — ffdiff executable (default is /netopt/genbank/subtool/bin/ffdiff).
• -r path — Path for results.
• -v path — asnval executable (default is /netopt/ncbi_tools/bin/asnval).
• -x ext — File selection suffix for use with -p (defaults to .ent).

🫶 quick reminder bestie: -i defaults to stdin, -o defaults to stdout, and -n, -q, and -v all have hardcoded default paths up there, so don't come for me when your tool lives somewhere else. check your paths. 💀

👑 AUTHOR 👑

The National Center for Biotechnology Information.

(they did that. they made her. respect. 🎀)

🌈 SEE ALSO 🌈

asndisc(1), asnval(1), sequin(1).

go read those too, bestie, they're all in the same friend group ✨

and that's the whole page, no notes, no skips, every single flag accounted for 💖

this was the NCBI Tools User's Manual, dated 2017-01-09, and cleanasn came to you from the lovely people at NCBI. mwah. bye bestie! 🦋