Safe Haskell | None |
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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 :: Maybe ByteString
- division :: ByteString
- creationDate :: ByteString
- definition :: ByteString
- accession :: ByteString
- version :: ByteString
- geneIdentifier :: ByteString
- dblink :: Maybe ByteString
- keywords :: ByteString
- source :: ByteString
- organism :: ByteString
- references :: [Reference]
- comment :: Maybe ByteString
- features :: [Feature]
- contig :: Maybe String
- origin :: SeqData
- data Feature = Feature {
- featureType :: ByteString
- featureCoordinates :: CoordinateSet
- attributes :: [Attribute]
- subFeatures :: [SubFeature]
- data Attribute
- = Flag {
- flagType :: ByteString
- | Field {
- fieldType :: ByteString
- fieldValue :: ByteString
- | GOattribute { }
- = Flag {
- data SubFeature = SubFeature {
- subFeatureType :: ByteString
- subFeatureCoordinates :: CoordinateSet
- subFeatureAttributes :: [Attribute]
- subFeatureTranslation :: Maybe SeqData
- data Reference = Reference {}
- data Coordinates = Coordinates {
- coordinatesFrom :: Int
- coordinateFromEqualitySymbol :: Maybe Char
- coordinatesTo :: Int
- coordinateToEqualitySymbol :: Maybe Char
- complement :: Bool
- data DbXRef = DbXRef {}
- data CoordinateSet = CoordinateSet {
- setCoordinates :: [Coordinates]
- setType :: Maybe String
- data OriginSlice = OriginSlice {
- originIndex :: Int
- originSequence :: String
- data GOterm = GOterm {}
Documentation
Genbank type representing the content of a genbank record
Genbank | |
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Genbank Feature - e.g gene, repeat region
Feature | |
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Genbank attribute of feature or subfeature, either a flag field or a GO attribute
Flag | |
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Field | |
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GOattribute | |
data SubFeature Source
Genbank subfeature, e.g. CDS, MiscFeature, NcRNA, Mobile Element, STS rRNA, tRNA, tmRNA, reporigin
SubFeature | |
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Eq SubFeature | |
Show SubFeature |
Genbank reference associating record with publication
data Coordinates Source
Coordinate pair for a nucleotide sequence
Coordinates | |
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Eq Coordinates | |
Show Coordinates |
data CoordinateSet Source
Set of coordinates, with type order, join
CoordinateSet | |
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Eq CoordinateSet | |
Show CoordinateSet |
data OriginSlice Source
Slices of the nucleotide sequence contained in the Genbank record
OriginSlice | |
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Eq OriginSlice | |
Show OriginSlice |