CLEANASN(1)						     NCBI Tools User's Manual						       CLEANASN(1)

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).

NCBI
								    2012-06-24							       CLEANASN(1)