Man page - asnval(1)
Packages contains this manual
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apt-get install ncbi-tools-bin
Manual
ASNVAL
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO
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 |
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-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 |
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-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
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-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).