asnval(1) 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] [-k] [-l] [-o filename] [-p path] [-q] [-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
-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)
-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)
-x str
File selection substring (.ent by default)

AUTHOR

The National Center for Biotechnology Information.