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] [−j] [−k] [−l] [−o filename] [−p path] [−q] [−r] [−u] [−v N] [−w] [−x str] [−y]
asnval is a command-line tool to validate ASN.1-format biological sequence records.
A summary of options is included below.
− |
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
−M |
Match locus_tag against General ID |
−N flags
Latitude-longitude / country flags
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:
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
−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:
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
−c |
Batch file is Compressed |
−d path
Path to Indexed Binary ASN.1 Data
−e |
Ignore transcription/translation Exceptions |
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−x str |
Substring filter |
−i filename
Single input file (standard input by default)
−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
−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
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 |
The National Center for Biotechnology Information.