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       cleanasn - clean up irregularities in NCBI ASN.1 objects


       cleanasn  [-]  [-D str]  [-F str]  [-K str] [-L filename] [-M filename]
       [-N str] [-P] [-Q str] [-R] [-T] [-U str] [-X str] [-a str]  [-b]  [-c]
       [-f str]   [-i filename]  [-m str]  [-o filename]  [-p path]  [-q path]
       [-r path] [-x ext]


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


       A summary of options is included below.

       -      Print usage message

       -D str Clean up descriptors, per the flags in str:
              t      Remove Title

       -F str Clean up features, per the flags in str:
              u      Remove User-objects
              d      Remove db_xrefs
              r      Remove redundant gene xrefs

       -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

       -L filename
              Log file

       -M filename
              Macro file

       -N str Clean up links, per the flags in str:
              o      LinkCDSmRNAbyOverlap
              p      LinkCDSmRNAbyProduct
              r      ReassignFeatureIDs
              c      ClearFeatureIDs

       -P     Publication Lookup

       -Q str Report:
              r      ASN.1 BSEC/SSEC Report
              g      GenBank SSEC Diff
              m      Modernization

       -R     Remote fetching from ID (NCBI sequence databases)

       -T     Taxonomy Lookup

       -U str Modernize, per the flags in str:
              g      Genes
              r      RNA
              p      PCR Primers

       -X str Miscellaneous options, per str:
              d      Automatic definition line

       -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

       -f str Substring filter

       -i filename
              Single input file (defaults to stdin)

       -m str Flatfile mode:
              r      Release
              e      Entrez
              s      Sequin
              d      Dump

       -o filename
              Single output file (defaults to stdout)

       -p path
              Process all matching files in path

       -q path
              Ffdiff             executable             (default            is

       -r path
              Path for results

       -x ext File selection suffix for use with -p (defaults to .ent)


       The National Center for Biotechnology Information.


       asnval (1), sequin (1).