ASN2GB(1)

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.

NCBI 2009-07-31 ASN2GB(1)