asn2gb - Online in the Cloud

PROGRAM:

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

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