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.