ASNVAL(1) NCBI Tools User's Manual ASNVAL(1)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] [-k] [-l] [-o filename] [-p path] [-q] [-r] [-u] [-v N] [-x str]
DESCRIPTION
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)
-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)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asndisc(1), cleanasn(1), sequin(1).
NCBI 2012-06-24 ASNVAL(1)
Check Out this Related Man Page
CLEANASN(1) NCBI Tools User's Manual CLEANASN(1)NAME
cleanasn - clean up irregularities in NCBI ASN.1 objects
SYNOPSIS
cleanasn [-] [-A filename] [-C str] [-D str] [-F str] [-K str] [-L filename] [-M filename] [-N str] [-P str] [-Q str] [-R] [-S str] [-T]
[-U str] [-V str] [-X str] [-Z str] [-a str] [-b] [-c] [-d str] [-f str] [-i filename] [-j filename] [-k filename] [-m str] [-n path]
[-o filename] [-p path] [-q path] [-r path] [-v path] [-x ext]
DESCRIPTION
cleanasn is a utility program to clean up irregularities in NCBI ASN.1 objects.
OPTIONS
A summary of options is included below.
- Print usage message
-A filename
Accession list file
-C str Sequence operations, per the flags in str:
c Compress
d Decompress
v Virtual gaps inside segmented sequence
s Convert segmented set to delta sequence
-D str Clean up descriptors, per the flags in str:
t Remove Title
c Remove Comment
n Remove Nuc-Prot Set title
e Remove Pop/Phy/Mut/Eco Set title
m Remove mRNA title
p Remove Protein title
-F str Clean up features, per the flags in str:
u Remove User-objects
d Remove db_xrefs
e Remove /evidence and /inference
r Remove redundant gene xrefs
f Fuse duplicate features
k Package coding-region or parts features
z Delete or update EC numbers
-K str Perform a general cleanup, per the flags in str:
b BasicSeqEntryCleanup
p C++ BasicCleanup (via an external utility)
s SeriousSeqEntryCleanup
g GpipeSeqEntryCleanup
n Normalize descriptor order
u Remove NcbiCleanup User Objects
c Synchronize genetic Codes
d Resynchronize CDS partials
m Resynchronize mRNA partials
t Resynchronize Peptide partials
a Adjust consensus splice
i Promote to "worst" Seq-ID
-L filename
Log file
-M filename
Macro file
-N str Clean up links, per the flags in str:
o Link CDS mRNA by Overlap
p Link CDS mRNA by Product
r Reassign feature IDs
f Fix missing reciprocal feature IDs
c Clear feature IDs
-P Publication options:
a Remove All publications
s Remove Serial number
f Remove Figure, numbering, and name
r Remove Remark
u Update PMID-only publication
# Replace unpublished with PMID
-Q str Report:
c Record count
r ASN.1 BSEC report
s ASN.1 SSEC report
n NORM vs. SSEC report
e PopPhyMutEco AutoDef report
o Overlap report
l Latitude-longitude country diff
d Log SSEC differences
g GenBank SSEC diff
f asn2gb/asn2flat diff
h Seg-to-delta GenBank diff
v Validator SSEC diff
m Modernize Gene/RNA/PCR
u Unpublished Pub lookup
p Published Pub lookup
j Unindexed Journal report
x Custom scan
-R Remote fetching from ID (NCBI sequence databases)
-S str Selective difference filter (capital letters skip)
s SSEC
b BSEC
A Author
p Publication
l Location
r RNA
q Qualifier sort order
g Genbank block
k Package CdRegion or parts features
m Move publication
o Leave duplicate Bioseq publication
d Automatic definition line
e Pop/Phy/Mut/Eco Set definition line
-T Taxonomy Lookup
-U str Modernize, per the flags in str:
g Genes
r RNA
p PCR Primers
-V str Remove features by validator severity:
r Reject
e Error
w Warning
i Info
-X str Miscellaneous options, per str:
d Automatic definition line
e Pop/Phy/Mut/Eco Set definition line
n Instantiate NC title
m Instantiate NM titles
x Special XM titles
p Instantiate Protein titles
c Create mRNAs for coding sequences
f Fix reciprocal protein_id/transcript_id
-Z str Remove indicated User-object
-a str ASN.1 type
a Any (default)
e Seq-entry
b Bioseq
s Bioseq-set
m Seq-submit
t Batch Processing [String]
-b Input ASN.1 is Binary
-c Input ASN.1 is Compressed
-d str Source database
a Any (default)
g GenBank
e EMBL
d DDBJ
b EMBL or DDBJ
r RefSeq
n NCBI
v Only segmented sequences
w Exclude segmented sequences
x Exclude EMBL/DDBJ
y Exclude gbcon, gbest, gbgss, gbhtg, gbpat, gbsts
-f str Substring filter
-i filename
Single input file (defaults to stdin)
-j filename
First filename
-k filename
Last filename
-m str Flatfile mode:
r Release
e Entrez
s Sequin
d Dump
-n path
asn2flat executable (default is /netopt/ncbi_tools/bin/asn2flat)
-o filename
Single output file (defaults to stdout)
-p path
Process all matching files in path
-q path
ffdiff executable (default is /netopt/genbank/subtool/bin/ffdiff)
-r path
Path for results
-v path
asnval executable (default is /netopt/ncbi_tools/bin/asnval)
-x ext File selection suffix for use with -p (defaults to .ent)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asndisc(1), asnval(1), sequin(1).
NCBI 2012-06-24 CLEANASN(1)