.TH ASNVAL 1 2012-06-24 NCBI "NCBI Tools User's Manual"
.SH NAME
asnval \- validate ASN.1 biological sequence records
.SH SYNOPSIS
.B asnval
[\|\fB\-\fP\|]
[\|\fB\-A\fP\|]
[\|\fB\-B\fP\|]
[\|\fB\-C\fP\ \fIN\fP\|]
[\|\fB\-D\fP\|]
[\|\fB\-E\fP\ \fIstr\fP\|]
[\|\fB\-F\fP\|]
[\|\fB\-G\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-K\fP\|]
[\|\fB\-L\fP\ \fIfilename\fP\|]
[\|\fB\-M\fP\|]
[\|\fB\-N\fP\ \fIflags\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-Q\fP\ \fIN\fP\|]
[\|\fB\-R\fP\ \fIN\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-X\fP\|]
[\|\fB\-Y\fP\|]
[\|\fB\-Z\fP\|]
[\|\fB\-a\fP\ \fItype\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\ \fIpath\fP\|]
[\|\fB\-e\fP\|]
[\|\fB\-f\fP\ \fIstr\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-k\fP\|]
[\|\fB\-l\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIpath\fP\|]
[\|\fB\-q\fP\|]
[\|\fB\-r\fP\|]
[\|\fB\-u\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-x\fP\ \fIstr\fP\|]
.SH DESCRIPTION
\fBasnval\fP is a command-line tool to validate ASN.1-format
biological sequence records.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP
Validate Alignments
.TP
\fB\-B\fP
Validate Barcodes
.TP
\fB\-C\fP\ \fIN\fP
Max count
.TP
\fB\-D\fP
Disable message suppression
.TP
\fB\-E\fP\ \fIstr\fP
Only Error Code to Show
.TP
\fB\-F\fP
Test network access
.TP
\fB\-G\fP
GI lookup from accession
.TP
\fB\-J\fP
Require ISO-JTA?
.TP
\fB\-K\fP
Summary to error file
.TP
\fB\-L\fP\ \fIfilename\fP
Log File
.TP
\fB\-M\fP
Match locus_tag against General ID
.TP
\fB\-N\fP\ \fIflags\fP
Latitude-longitude / country flags
.RS
.PD 0
.IP 0
none
.IP 1
test state/province
.IP 2
ignore water exception
.IP 3
both of the above
.PD
.RE
.TP
\fB\-P\fP\ \fIN\fP
Highest severity for error to show:
.RS
.PD 0
.IP 0
none
.IP 1
informational
.IP 2
warning
.IP 3
error (default for \fB\-Q\fP)
.IP 4
grounds for rejection (default for \fB\-P\fP, \fB\-R\fP)
.PD
.RE
.TP
\fB\-Q\fP\ \fIN\fP
Lowest severity for error to show, per \fBP\fP
.TP
\fB\-R\fP\ \fIN\fP
Severity for error in return code, per \fBP\fP
.TP
\fB\-S\fP\ \fIN\fP
Skip count
.TP
\fB\-T\fP
Use Threads
.TP
\fB\-U\fP
Genome center submission
.TP
\fB\-X\fP
Exon splice check
.TP
\fB\-Y\fP
Check against old IDs
.TP
\fB\-Z\fP
Remote CDS product fetch
.TP
\fB\-a\fP\ \fItype\fP
Input ASN.1 type:
.RS
.PD 0
.IP a
Automatic (default)
.IP c
Catenated
.IP z
Any
.IP e
seq-Entry
.IP b
Bioseq
.IP s
bioseq-Set
.IP m
seq-subMit
.IP t
baTch bioseq-set
.IP u
batch seq-sUbmit
.PD
.RE
.TP
\fB\-b\fP
Batch file is Binary
.TP
\fB\-c\fP
Batch file is Compressed
.TP
\fB\-d\fP\ \fIpath\fP
Path to Indexed Binary ASN.1 Data
.TP
\fB\-e\fP
Ignore transcription/translation Exceptions
.TP
\fB\-x\fP\ \fIstr\fP
Substring filter
.TP
\fB\-i\fP\ \fIfilename\fP
Single input file (standard input by default)
.TP
\fB\-k\fP
Local fetching
.TP
\fB\-l\fP
Lock components in advance
.TP
\fB\-o\fP\ \fIfilename\fP
Single output file
.TP
\fB\-p\fP\ \fIpath\fP
Path to ASN.1 Files
.TP
\fB\-q\fP
Taxonomy lookup
.TP
\fB\-r\fP
Remote Fetching from ID
.TP
\fB\-u\fP
Recurse
.TP
\fB\-v\fP\ \fIN\fP
Verbosity:
.RS
.PD 0
.IP 1
Standard report (default)
.IP 2
Accession / severity / code (space delimited)
.IP 3
Accession / severity / code (tab delimited)
.IP 4
XML report
.IP 5
Accession / GI / severity / code (tab delimited)
.PD
.RE
.TP
\fB\-x\fP\ \fIstr\fP
File selection substring (\fB.ent\fP by default)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR asndisc (1),
.BR cleanasn (1),
.BR sequin (1).