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asnval - validate ASN.1 biological sequence records


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]


asnval is a command-line tool to validate ASN.1-format biological sequence records.


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)

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