--- name: "cleanasn" section: "1" platform: "linux" package: "ncbi-tools-bin" version: "6.1.20170106+dfsg2-6" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/cleanasn" --- # cleanasn(1) clean up irregularities in NCBI ASN.1 objects ## NAME cleanasn - clean up irregularities in NCBI ASN.1 objects ## SYNOPSIS **cleanasn** \[**-**\] \[**-A** *filename*\] \[**-B** *str*\] \[**-C** *str*\] \[**-D** *str*\] \[**-F** *str*\] \[**-K** *str*\] \[**-L** *filename*\] \[**-M** *filename*\] \[**-N** *str*\] \[**-O** *str*\] \[**-P** *str*\] \[**-Q** *str*\] \[**-R**\] \[**-S** *str*\] \[**-T**\] \[**-U** *str*\] \[**-V** *str*\] \[**-X** *str*\] \[**-Z** *str*\] \[**-a** *str*\] \[**-b**\] \[**-c**\] \[**-d** *str*\] \[**-f** *str*\] \[**-i** *filename*\] \[**-j** *filename*\] \[**-k** *filename*\] \[**-m** *str*\] \[**-n** *path*\] \[**-o** *filename*\] \[**-p** *path*\] \[**-q** *path*\] \[**-r** *path*\] \[**-v** *path*\] \[**-x** *ext*\] ## DESCRIPTION **cleanasn** is a utility program to clean up irregularities in NCBI ASN.1 objects. ## OPTIONS A summary of options is included below. - **-** Print usage message - **-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**) ## AUTHOR The National Center for Biotechnology Information. ## SEE ALSO [**asndisc**(1)](/asndisc/1.md), [**asnval**(1)](/asnval/1.md), [**sequin**(1)](/sequin/1.md).