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| ASN2GB(1) | NCBI Tools User's Manual | ASN2GB(1) |
NAME
asn2gb - convert ASN.1 biological data to a GenBank-style flat formatSYNOPSIS
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
- 4
- Hide features
- 1792
- Hide references
- 8192
- Hide sources
- 262144
- Hide translations
- -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), asn2gb.txt.| 2016-09-01 | NCBI |
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