asn2gb1

Usage

Overview

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