man asn2gb (Commandes) - convert ASN.1 biological data to a GenBank-style flat format

NAME

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

SYNOPSIS

asn2gb [-] [-A accession] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode] [-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
-a asn-type
ASN.1 Type:
a
Any (default)
e
Seq-entry
b
Bioseq
s
Bioseq-set
m
Seq-submit
t
Bioseq-set batch
u
Seq-submit batch
-b
Bioseq-set is binary
-c
Bioseq-set 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
-o filename
Output file name (default = stdout)
-p
Propagate top descriptors
-q filename
Gbdjoin Executable (default = /netopt/genbank/subtool/bin/gbdjoin)
-r
Enable remote fetching
-s style
Style:
n
Normal (default)
s
Segment
m
Master
c
Contig
-t N
Batch:
1
Report
2
Sequin/Release -u N Custom flags (all default to off):
2
Hide most imported features
4
Hide SNP features
-y N
Feature itemID

AUTHOR

The National Center for Biotechnology Information.

SEE ALSO