Man page - asn2gb(1)
Packages contains this manual
- asn2ff(1)
- asn2gb(1)
- asntool(1)
- vecscreen(1)
- sortbyquote(1)
- trna2tbl(1)
- asn2xml(1)
- getpub(1)
- gil2bin(1)
- gene2xml(1)
- asn2all(1)
- checksub(1)
- subfuse(1)
- getmesh(1)
- taxblast(1)
- asn2asn(1)
- spidey(1)
- tbl2asn(1)
- asnval(1)
- asnmacro(1)
- idfetch(1)
- asndhuff(1)
- insdseqget(1)
- nps2gps(1)
- indexpub(1)
- findspl(1)
- asn2fsa(1)
- gbseqget(1)
- errhdr(1)
- asn2idx(1)
- trna2sap(1)
- cleanasn(1)
- asndisc(1)
- makeset(1)
- fa2htgs(1)
- debruijn(1)
apt-get install ncbi-tools-bin
Manual
ASN2GB
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO
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) |
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|
e |
seq-Entry |
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b |
Bioseq |
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s |
bioseq-Set |
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m |
seq-subMit |
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q |
Catenated |
[Release file; components individually processed and freed]
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t |
baTch bioseq-set |
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u |
batch seq-sUbmit |
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-b |
Input file is binary
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-c |
Batch file is compressed |
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|
-d |
Seq-loc minus strand |
-f format
Format:
|
b |
GenBank (default) |
bp or pb
GenBank and GenPept
|
e |
EMBL |
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p |
GenPept |
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|
q |
nucleotide GBSet (XML) |
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|
r |
protein GBSet (XML) |
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|
t |
Feature table only |
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|
x |
nucleotide INSDSet (XML) |
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|
y |
tiny seq (XML) |
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|
Y |
FASTA |
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|
z |
protein INSDSet (XML) |
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|
-g N |
Bit flags (all default to off):
|
1 |
HTML |
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|
2 |
XML |
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|
4 |
ContigFeats |
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|
8 |
ContigSrcs |
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|
16 |
FarTransl |
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|
-h N |
Lock/Lookup Flags (all default to off):
|
8 |
LockProd |
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|
16 |
LookupComp |
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|
64 |
LookupProd |
-i filename
Input file name (default = stdin)
|
-j N |
Start location (default is 0, beginning of sequence) |
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|
-k N |
End location (default is 0, end of sequence) |
-l filename
Log file
-m mode
Mode:
|
r |
Release |
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|
e |
Entrez |
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|
s |
Sequin (default) |
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|
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) |
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|
s |
Segment |
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|
m |
Master |
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|
c |
Contig |
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|
-t N |
Batch:
|
1 |
Report |
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|
2 |
Sequin/Release |
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|
3 |
asn2gb SSEC/nocleanup |
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4 |
asn2flat BSEC/nocleanup |
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|
5 |
asn2gb/asn2flat |
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|
6 |
asn2gb NEW dbxref/OLD dbxref |
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|
7 |
oldasn2gb/newasn2gb |
-u N Custom flags (all default to off):
|
4 |
Hide features |
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|
1792 |
Hide references |
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|
8192 |
Hide sources |
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|
262144 |
Hide translations |
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|
-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.