NAME
asnval - validate ASN.1 biological sequence records
SYNOPSIS
asnval [-] [-A] [-B] [-C N] [-E str] [-G] [-J] [-K] [-L filename] [-M]
[-N flags] [-P N] [-Q N] [-R N] [-S N] [-T] [-X] [-Y] [-Z] [-a type]
[-b] [-c] [-d path] [-e] [-i filename] [-k] [-l] [-o filename]
[-p path] [-r] [-u] [-v N] [-x str]
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
-E str Only Error Code to Show
-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
-X Exon splice check
-Y Check against old IDs
-Z Remote CDS product fetch
-a type
Input ASN.1 type:
a Automatic (default)
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
-i filename
Single input file (standard input by default)
-k Local fetching
-l Lock components in advance
-o filename
Single output file
-p path
Path to ASN.1 Files
-r Remote Fetching from ID
-u Recurse
-v N Verbosity, from 0 to 4 (1 by default)
-x str File selection substring (.ent by default)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
cleanasn(1), sequin(1).