asnval(1)
validate ASN.1 biological sequence records
Description
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.
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- |
Print usage message |
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-A |
Validate Alignments |
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-B |
Validate Barcodes |
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-C N |
Max count |
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-D |
Disable message suppression |
-E str
Only Error Code to Show
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-F |
Test network access |
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-G |
GI lookup from accession |
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-J |
Require ISO-JTA? |
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-K |
Summary to error file |
-L filename
Log File
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-M |
Match locus_tag against General ID |
-N flags
Latitude-longitude / country flags
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0 |
none |
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1 |
test state/province |
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2 |
ignore water exception |
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3 |
both of the above |
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-P N |
Highest severity for error to show:
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0 |
none |
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1 |
informational |
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2 |
warning |
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3 |
error (default for -Q) |
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4 |
grounds for rejection (default for -P, -R) |
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-Q N |
Lowest severity for error to show, per P
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-R N |
Severity for error in return code, per P |
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-S N |
Skip count |
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-T |
Use Threads |
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-U |
Genome center submission |
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-X |
Exon splice check |
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-Y |
Check against old IDs |
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-Z |
Remote CDS product fetch |
-a type
Input ASN.1 type:
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a |
Automatic (default) |
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c |
Catenated |
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z |
Any |
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e |
seq-Entry |
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b |
Bioseq |
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s |
bioseq-Set |
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m |
seq-subMit |
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t |
baTch bioseq-set |
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u |
batch seq-sUbmit |
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-b |
Batch file is Binary
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-c |
Batch file is Compressed |
-d path
Path to Indexed Binary ASN.1 Data
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-e |
Ignore transcription/translation Exceptions |
-x str
Substring filter
-i filename
Single input file (standard input by default)
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-j |
Validator code performance test |
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-k |
Local fetching |
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-l |
Lock components in advance |
-o filename
Single output file
-p path
Path to ASN.1 Files
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-q |
Taxonomy lookup |
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-r |
Remote Fetching from ID |
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-u |
Recurse |
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-v N |
Verbosity: |
1
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Standard report (default) |
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2 |
Accession / severity / code (space delimited) |
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3 |
Accession / severity / code (tab delimited) |
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4 |
XML report |
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5 |
Accession / GI / severity / code (tab delimited) |
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6 |
Logged report |
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-w |
SeqSubmitParent flag
-x str
File selection substring (.ent by default)
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-y |
Special indexer tests |
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
asndisc(1), cleanasn(1), sequin(1).