| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.GenbankData
Description
This module contains data structures for genbank format For more information on genbank consult: http://www.ncbi.nlm.nih.gov/genbank/ Genbank record sample: http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
- data Genbank = Genbank {
- locus :: ByteString
- genbankLength :: Int
- moleculeType :: ByteString
- circular :: ByteString
- division :: ByteString
- creationDate :: ByteString
- definition :: ByteString
- accession :: ByteString
- version :: ByteString
- geneIdentifier :: ByteString
- dblink :: ByteString
- keywords :: ByteString
- source :: ByteString
- organism :: ByteString
- references :: [Reference]
- comment :: ByteString
- features :: [Feature]
- contig :: Maybe String
- origin :: SeqData
- data Feature = Feature {}
- data Attribute
- = Flag { }
- | Field { }
- | GOattribute {
- gotype :: ByteString
- goid :: ByteString
- goname :: ByteString
- data SubFeature = SubFeature {}
- data Reference = Reference {}
- data Coordinates = Coordinates {}
- data DbXRef = DbXRef {
- db :: ByteString
- ref :: ByteString
- data CoordinateSet = CoordinateSet {
- setCoordinates :: [Coordinates]
- setType :: Maybe String
- data OriginSlice = OriginSlice {}
- data GOterm = GOterm {}
Documentation
Genbank type representing the content of a genbank record
Constructors
| Genbank | |
Fields
| |
Genbank Feature - e.g gene, repeat region
Constructors
| Feature | |
Fields
| |
Genbank attribute of feature or subfeature, either a flag field or a GO attribute
Constructors
| Flag | |
Fields | |
| Field | |
Fields | |
| GOattribute | |
Fields
| |
data SubFeature Source
Genbank subfeature, e.g. CDS, MiscFeature, NcRNA, Mobile Element, STS rRNA, tRNA, tmRNA, reporigin
Constructors
| SubFeature | |
Instances
Genbank reference associating record with publication
Constructors
| Reference | |
data Coordinates Source
Coordinate pair for a nucleotide sequence
Constructors
| Coordinates | |
Fields | |
Instances
Constructors
| DbXRef | |
Fields
| |
data CoordinateSet Source
Set of coordinates, with type order, join
Constructors
| CoordinateSet | |
Fields
| |
Instances
data OriginSlice Source
Slices of the nucleotide sequence contained in the Genbank record
Constructors
| OriginSlice | |
Fields
| |
Instances