Man pages sections > man1 > asnval

asnval - validate ASN.1 biological sequence records

ASNVAL(1) NCBI Tools User's Manual ASNVAL(1)

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).
2016-09-01 NCBI