NAME

       asnval - validate ASN.1 biological sequence records

SYNOPSIS

       asnval [-] [-A] [-B] [-C N] [-D] [-E str] [-F] [-G] [-J] [-K] [-L filename] [-M] [-N flags] [-P N] [-Q N]
       [-R N]  [-S N]  [-T]  [-U]  [-X] [-Y] [-Z] [-a type] [-b] [-c] [-d path] [-e] [-f str] [-i filename] [-j]
       [-k] [-l] [-o filename] [-p path] [-q] [-r] [-u] [-v N] [-w] [-x str] [-y]

DESCRIPTION

       asnval is a command-line tool to validate ASN.1-format biological sequence records.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A     Validate Alignments

       -B     Validate Barcodes

       -C N   Max count

       -D     Disable message suppression

       -E str Only Error Code to Show

       -F     Test network access

       -G     GI lookup from accession

       -J     Require ISO-JTA?

       -K     Summary to error file

       -L filename
              Log File

       -M     Match locus_tag against General ID

       -N flags
              Latitude-longitude / country flags
              0      none
              1      test state/province
              2      ignore water exception
              3      both of the above

       -P N   Highest severity for error to show:
              0      none
              1      informational
              2      warning
              3      error (default for -Q)
              4      grounds for rejection (default for -P, -R)

       -Q N   Lowest severity for error to show, per P

       -R N   Severity for error in return code, per P

       -S N   Skip count

       -T     Use Threads

       -U     Genome center submission

       -X     Exon splice check

       -Y     Check against old IDs

       -Z     Remote CDS product fetch

       -a type
              Input ASN.1 type:
              a      Automatic (default)
              c      Catenated
              z      Any
              e      seq-Entry
              b      Bioseq
              s      bioseq-Set
              m      seq-subMit
              t      baTch bioseq-set
              u      batch seq-sUbmit

       -b     Batch file is Binary

       -c     Batch file is Compressed

       -d path
              Path to Indexed Binary ASN.1 Data

       -e     Ignore transcription/translation Exceptions

       -x str Substring filter

       -i filename
              Single input file (standard input by default)

       -j     Validator code performance test

       -k     Local fetching

       -l     Lock components in advance

       -o filename
              Single output file

       -p path
              Path to ASN.1 Files

       -q     Taxonomy lookup

       -r     Remote Fetching from ID

       -u     Recurse

       -v N   Verbosity:
              1      Standard report (default)
              2      Accession / severity / code (space delimited)
              3      Accession / severity / code (tab delimited)
              4      XML report
              5      Accession / GI / severity / code (tab delimited)
              6      Logged report

       -w     SeqSubmitParent flag

       -x str File selection substring (.ent by default)

       -y     Special indexer tests

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asndisc(1), cleanasn(1), sequin(1).

NCBI                                               2016-09-01                                          ASNVAL(1)