.TH ASN2GB 1 2011-09-02 NCBI "NCBI Tools User's Manual"
.SH NAME
asn2gb \- convert ASN.1 biological data to a GenBank-style flat format
.SH SYNOPSIS
.B asn2gb
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIaccession\fP\|]
[\|\fB\-F\fP\|]
[\|\fB\-a\fP\ \fIasn-type\fP\|]
[\|\fB\-b\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\|]
[\|\fB\-f\fP\ \fIformat\fP\|]
[\|\fB\-g\fP\ \fIN\fP\|]
[\|\fB\-h\fP\ \fIN\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-j\fP\ \fIN\fP\|]
[\|\fB\-k\fP\ \fIN\fP\|]
[\|\fB\-l\fP\ \fIfilename\fP\|]
[\|\fB\-m\fP\ \fImode\fP\|]
[\|\fB\-n\fP\ \fIfilename\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\|]
[\|\fB\-q\fP\ \fIfilename\fP\|]
[\|\fB\-r\fP\|]
[\|\fB\-s\fP\ \fIstyle\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-u\fP\ \fIN\fP\|]
.\" [\|\fB\-x\fP\ \fIacc\fP\|] \" disabled
[\|\fB\-y\fP\ \fIN\fP\|]
.SH DESCRIPTION
\fBasn2gb\fP converts descriptions of biological sequences from NCBI's
ASN.1 format to one of several flat-file formats, and is the successor
to \fBasn2ff\fP(1).
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP\ \fIaccession\fP
Accession to fetch; may take the form
.IB accession , complexity , flags
where \fIcomplexity\fP should normally be \fB0\fP and a \fIflags\fP
value of \fB-1\fP enables fetching of external features (as with the
legacy \fB-F\fP option)
.TP
\fB\-F\fP
Fetch remote annotations (equivalent to specifying
\fB-A\fP\ \fIaccession\fP\fB,0,-1\fP)
.TP
\fB\-a\fP\ \fIasn-type\fP
ASN.1 Type:
.RS
.PD 0
.IP "[Single record]"
.IP a
Any (autodetected; default)
.IP e
seq-Entry
.IP b
Bioseq
.IP s
bioseq-Set
.IP m
seq-subMit
.IP q
Catenated
.IP "[Release file; components individually processed and freed]"
.IP t
baTch bioseq-set
.IP u
batch seq-sUbmit
.PD
.RE
.TP
\fB\-b\fP
Input file is binary
.TP
\fB\-c\fP
Batch file is compressed
.TP
\fB\-d\fP
Seq-loc minus strand
.TP
\fB\-f\fP\ \fIformat\fP
Format:
.RS
.PD 0
.IP b
GenBank (default)
.IP "bp or pb"
GenBank and GenPept
.IP e
EMBL
.IP p
GenPept
.IP q
nucleotide GBSet (XML)
.IP r
protein GBSet (XML)
.IP t
Feature table only
.IP x
nucleotide INSDSet (XML)
.IP y
tiny seq (XML)
.IP Y
FASTA
.IP z
protein INSDSet (XML)
.PD
.RE
.TP
\fB\-g\fP\ \fIN\fP
Bit flags (all default to off):
.RS
.PD 0
.IP 1
HTML
.IP 2
XML
.IP 4
ContigFeats
.IP 8
ContigSrcs
.IP 16
FarTransl
.PD
.RE
.TP
\fB\-h\fP\ \fIN\fP
Lock/Lookup Flags (all default to off):
.RS
.PD 0
.IP 8
LockProd
.IP 16
LookupComp
.IP 64
LookupProd
.PD
.RE
.TP
\fB\-i\fP\ \fIfilename\fP
Input file name (default = stdin)
.TP
\fB\-j\fP\ \fIN\fP
Start location (default is 0, beginning of sequence)
.TP
\fB\-k\fP\ \fIN\fP
End location (default is 0, end of sequence)
.TP
\fB\-l\fP\ \fIfilename\fP
Log file
.TP
\fB\-m\fP\ \fImode\fP
Mode:
.RS
.PD 0
.IP r
Release
.IP e
Entrez
.IP s
Sequin (default)
.IP d
Dump
.PD
.RE
.TP
\fB\-n\fP\ \fIfilename\fP
Asn2Flat Executable (default = asn2flat)
.TP
\fB\-o\fP\ \fIfilename\fP
Output file name (default = stdout)
.TP
\fB\-p\fP
Propagate top descriptors
.TP
\fB\-q\fP\ \fIfilename\fP
Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff)
.TP
\fB\-r\fP
Enable remote fetching
.TP
\fB\-s\fP\ \fIstyle\fP
Style:
.RS
.PD 0
.IP n
Normal (default)
.IP s
Segment
.IP m
Master
.IP c
Contig
.PD
.RE
.TP
\fB\-t\fP\ \fIN\fP
Batch:
.RS
.PD 0
.IP 1
Report
.IP 2
Sequin/Release
.IP 3
asn2gb SSEC/nocleanup
.IP 4
asn2flat BSEC/nocleanup
.IP 5
asn2gb/asn2flat
.IP 6
asn2gb NEW dbxref/OLD dbxref
.IP 7
oldasn2gb/newasn2gb
.PD
.RE
\fB\-u\fP\ \fIN\fP
Custom flags (all default to off):
.RS
.PD 0
.IP 4
Hide features
.IP 1792
Hide references
.IP 8192
Hide sources
.IP 262144
Hide translations
.PD
.RE
.\" .TP
.\" \fB\-x\fP\ \fIacc\fP
.\" Accession to extract
.TP
\fB\-y\fP\ \fIN\fP
Feature itemID
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR asn2all (1),
.BR asn2asn (1),
.BR asn2ff (1),
.BR asn2fsa (1),
.BR asn2xml (1),
.BR asndhuff (1),
.BR insdseqget (1),
/usr/share/doc/libncbi6-dev/asn2gb.txt.gz.