asnval1

Usage

Overview

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