Provided by: ncbi-tools-bin_6.1.20170106-6_amd64 bug


       cleanasn - clean up irregularities in NCBI ASN.1 objects


       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]


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


       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)


       The National Center for Biotechnology Information.


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