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.