asnval - validate ASN.1 biological sequence records
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]
asnval is a command-line tool to validate ASN.1-format biological
sequence records.
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
The National Center for Biotechnology Information.
asndisc(1),
cleanasn(1),
sequin(1).