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)
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-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 |
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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)
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-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.