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] [ -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

-P N

Highest severity for error to show:

-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:

-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:

-x str

File selection substring (.ent by default)

AUTHOR¶

The National Center for Biotechnology Information.

SEE ALSO¶

asndisc(1), cleanasn(1), sequin(1).