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

Synopsis

Documentation

data Genbank Source

Genbank type representing the content of a genbank record

Constructors

Genbank

Fields

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

Instances

Eq Genbank
Show Genbank

data Feature Source

Genbank Feature - e.g gene, repeat region

Constructors

Feature
Fields featureType :: ByteString featureCoordinates :: CoordinateSet attributes :: [Attribute] subFeatures :: [SubFeature]

Instances

Eq Feature
Show Feature

data Attribute Source

Genbank attribute of feature or subfeature, either a flag field or a GO attribute

Constructors

Flag
Fields flagType :: ByteString
Field
Fields fieldType :: ByteString fieldValue :: ByteString
GOattribute
Fields gotype :: ByteString goid :: ByteString goname :: ByteString

Instances

Eq Attribute
Show Attribute

data SubFeature Source

Genbank subfeature, e.g. CDS, MiscFeature, NcRNA, Mobile Element, STS rRNA, tRNA, tmRNA, reporigin

Constructors

SubFeature
Fields subFeatureType :: ByteString subFeatureCoordinates :: CoordinateSet subFeatureAttributes :: [Attribute] subFeatureTranslation :: Maybe SeqData

Instances

Eq SubFeature
Show SubFeature

data Reference Source

Genbank reference associating record with publication

Constructors

Reference
Fields index :: Int baseFrom :: Maybe Int baseTo :: Maybe Int authors :: String title :: String journal :: String pubmedId :: Maybe String remark :: Maybe String

Instances

Eq Reference
Show Reference

data Coordinates Source

Coordinate pair for a nucleotide sequence

Constructors

Coordinates
Fields coordinatesFrom :: Int coordinateFromEqualitySymbol :: Maybe Char coordinatesTo :: Int coordinateToEqualitySymbol :: Maybe Char complement :: Bool

Instances

Eq Coordinates
Show Coordinates

data DbXRef Source

Constructors

DbXRef
Fields db :: ByteString ref :: ByteString

Instances

Eq DbXRef
Show DbXRef

data CoordinateSet Source

Set of coordinates, with type order, join

Constructors

CoordinateSet
Fields setCoordinates :: [Coordinates] setType :: Maybe String

Instances

Eq CoordinateSet
Show CoordinateSet

data OriginSlice Source

Slices of the nucleotide sequence contained in the Genbank record

Constructors

OriginSlice
Fields originIndex :: Int originSequence :: String

Instances

Eq OriginSlice
Show OriginSlice

data GOterm Source

Gene Onthology term

Constructors

GOterm
Fields goType :: String goId :: String goName :: String

Instances

Eq GOterm
Show GOterm