NAME

       cleanasn - clean up irregularities in NCBI ASN.1 objects

SYNOPSIS

       cleanasn [-] [-A filename] [-C str] [-D str] [-F str] [-K str] [-L filename] [-M filename]
       [-N 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

       -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

       -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

       -F str Clean up features, per the flags in str:
              u      Remove User-objects
              d      Remove db_xrefs
              e      Remove /evidence and /inference
              r      Remove redundant gene xrefs
              f      Fuse duplicate features
              k      Package coding-region or parts features
              z      Delete or update EC numbers

       -K str Perform a general cleanup, per the flags in str:
              b      BasicSeqEntryCleanup
              p      C++ BasicCleanup (via an external utility)
              s      SeriousSeqEntryCleanup
              g      GpipeSeqEntryCleanup
              n      Normalize descriptor order
              u      Remove NcbiCleanup User Objects
              c      Synchronize genetic Codes
              d      Resynchronize CDS partials
              m      Resynchronize mRNA partials
              t      Resynchronize Peptide partials
              a      Adjust consensus splice
              i      Promote to "worst" Seq-ID

       -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
              r      Reassign feature IDs
              f      Fix missing reciprocal feature IDs
              c      Clear feature IDs

       -P     Publication options:
              a      Remove All publications
              s      Remove Serial number
              f      Remove Figure, numbering, and name
              r      Remove Remark
              u      Update PMID-only publication
              #      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
              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
              e      Pop/Phy/Mut/Eco Set definition line
              n      Instantiate NC title
              m      Instantiate NM titles
              x      Special XM titles
              p      Instantiate Protein titles
              c      Create mRNAs for coding sequences
              f      Fix reciprocal protein_id/transcript_id

       -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 Processing [String]

       -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
              r      RefSeq
              n      NCBI
              v      Only segmented sequences
              w      Exclude segmented sequences
              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).