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ASNVAL

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).

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