asn2gb(1)
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.