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| ASNVAL(1) | NCBI Tools User's Manual | ASNVAL(1) |
NAME
asnval - validate ASN.1 biological sequence recordsSYNOPSIS
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).| 2016-09-01 | NCBI |
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