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asn2gb - convert ASN.1 biological data to a GenBank-style flat format

ASN2GB(1) NCBI Tools User's Manual 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; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1 enables fetching of external features (as with the legacy -F option)
-F
Fetch remote annotations (equivalent to specifying -A  accession,0,-1)
-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.
2016-09-01 NCBI