NAME
asn2gb - convert ASN.1 biological data to a GenBank-style flat format
SYNOPSIS
asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format]
[-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode]
[-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N]
[-u N] [-y N]
DESCRIPTION
asn2gb converts descriptions of biological sequences from NCBI’s ASN.1
format to one of several flat-file formats, and is the successor to
asn2ff(1).
OPTIONS
A summary of options is included below.
- Print usage message
-A accession
Accession to fetch
-F Fetch remote annotations
-a asn-type
ASN.1 Type:
[Single record]
a Any (autodetected; default)
e seq-Entry
b Bioseq
s bioseq-Set
m seq-subMit
q Catenated
[Release file; components individually processed and freed]
t baTch bioseq-set
u batch seq-sUbmit
-b Input file is binary
-c Batch file is compressed
-d Seq-loc minus strand
-f format
Format:
b GenBank (default)
bp or pb
GenBank and GenPept
e EMBL
p GenPept
q nucleotide GBSet (XML)
r protein GBSet (XML)
t Feature table only
x nucleotide INSDSet (XML)
y tiny seq (XML)
Y FASTA
z protein INSDSet (XML)
-g N Bit flags (all default to off):
1 HTML
2 XML
4 ContigFeats
8 ContigSrcs
16 FarTransl
-h N Lock/Lookup Flags (all default to off):
8 LockProd
16 LookupComp
64 LookupProd
-i filename
Input file name (default = stdin)
-j N Start location (default is 0, beginning of sequence)
-k N End location (default is 0, end of sequence)
-l filename
Log file
-m mode
Mode:
r Release
e Entrez
s Sequin (default)
d Dump
-n filename
Asn2Flat Executable (default = asn2flat)
-o filename
Output file name (default = stdout)
-p Propagate top descriptors
-q filename
Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff)
-r Enable remote fetching
-s style
Style:
n Normal (default)
s Segment
m Master
c Contig
-t N Batch:
1 Report
2 Sequin/Release
3 asn2gb SSEC/nocleanup
4 asn2flat BSEC/nocleanup
5 asn2gb/asn2flat
6 asn2gb NEW dbxref/OLD dbxref
7 oldasn2gb/newasn2gb
-u N Custom flags (all default to off):
4 Hide features
1792 Hide references
8192 Hide sources
262144 Hide translations
-y N Feature itemID
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1),
insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz.