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CLEANASN(1) NCBI Tools User's Manual CLEANASN(1) 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 ob- jects. 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 -C str Sequence operations, per the flags in str: c Compress d Decompress 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), asnval(1), sequin(1). NCBI 2016-09-01 CLEANASN(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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