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

-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)

-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:

-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).