| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.TaxonomyData
Description
This module contains data structures for taxonomy data
- data SimpleTaxon = SimpleTaxon {}
- data CompareTaxon = CompareTaxon {
- compareScientificName :: ByteString
- compareRank :: Rank
- inTree :: [Int]
- data Taxon = Taxon {}
- data TaxonName = TaxonName {}
- data LineageTaxon = LineageTaxon {}
- data NCBITaxDump = NCBITaxDump {
- taxCitations :: [TaxCitation]
- taxDelNodes :: [TaxDelNode]
- taxDivisions :: [TaxDivision]
- taxGenCodes :: [TaxGenCode]
- taxMergedNodes :: [TaxMergedNode]
- taxNames :: [TaxName]
- taxNodes :: [TaxNode]
- data TaxCitation = TaxCitation {}
- data TaxDelNode = TaxDelNode {}
- data TaxDivision = TaxDivision {}
- data TaxGenCode = TaxGenCode {
- geneticCodeId :: Int
- abbreviation :: Maybe String
- geneCodeName :: String
- cde :: String
- starts :: String
- data TaxMergedNode = TaxMergedNode {}
- data TaxName = TaxName {}
- data Rank
- = Norank
- | Form
- | Variety
- | Infraspecies
- | Subspecies
- | Speciessubgroup
- | Species
- | Speciesgroup
- | Superspecies
- | Series
- | Section
- | Subgenus
- | Genus
- | Subtribe
- | Tribe
- | Supertribe
- | Subfamily
- | Family
- | Superfamily
- | Parvorder
- | Infraorder
- | Suborder
- | Order
- | Superorder
- | Magnorder
- | Cohort
- | Legion
- | Parvclass
- | Infraclass
- | Subclass
- | Class
- | Superclass
- | Microphylum
- | Infraphylum
- | Subphylum
- | Phylum
- | Superphylum
- | Infrakingdom
- | Subkingdom
- | Kingdom
- | Superkingdom
- | Domain
- readsRank :: String -> [(Rank, String)]
- data TaxNode = TaxNode {
- taxId :: Int
- parentTaxId :: Int
- rank :: Rank
- emblCode :: Maybe String
- nodeDivisionId :: String
- inheritedDivFlag :: Bool
- nodeGeneticCodeId :: String
- inheritedGCFlag :: Bool
- mitochondrialGeneticCodeId :: String
- inheritedMGCFlag :: Bool
- genBankHiddenFlag :: Bool
- hiddenSubtreeRootFlag :: Bool
- nodeComments :: Maybe String
- data SimpleGene2Accession = SimpleGene2Accession {}
- data Gene2Accession = Gene2Accession {
- taxIdEntry :: Int
- geneID :: Int
- status :: String
- rnaNucleotideAccessionVersion :: String
- rnaNucleotideGi :: String
- proteinAccessionVersion :: String
- proteinGi :: String
- genomicNucleotideAccessionVersion :: String
- genomicNucleotideGi :: String
- startPositionOnTheGenomicAccession :: String
- endPositionOnTheGenomicAccession :: String
- orientation :: String
- assembly :: String
- maturePeptideAccessionVersion :: String
- maturePeptideGi :: String
- simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value
Documentation
data SimpleTaxon Source
SimpleTaxon only contains the most relevant fields of a taxonomy entry. For all annotaded fields use the Taxon datatype and its associated functions
Constructors
| SimpleTaxon | |
Fields | |
Instances
data CompareTaxon Source
Datastructure for tree comparisons
Constructors
| CompareTaxon | |
Fields
| |
Instances
Data structure for Entrez taxonomy fetch result
Constructors
| Taxon | |
Fields
| |
data LineageTaxon Source
Lineage Taxons denote all parent Taxonomy nodes of a node retrieved by Entrez fetch
Constructors
| LineageTaxon | |
Fields
| |
Instances
data NCBITaxDump Source
NCBI Taxonomy database dump hierachichal data structure as defined in ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump_readme.txt
Constructors
| NCBITaxDump | |
Fields
| |
Instances
data TaxCitation Source
Datastructure for entries of Taxonomy database dump citations file
Constructors
| TaxCitation | |
Instances
data TaxDelNode Source
Datastructure for entries of Taxonomy database dump deleted nodes file
Constructors
| TaxDelNode | |
Instances
data TaxDivision Source
Datastructure for entries of Taxonomy database dump division file
Constructors
| TaxDivision | |
Fields
| |
Instances
data TaxGenCode Source
Datastructure for entries of Taxonomy database dump gencode file
Constructors
| TaxGenCode | |
Fields
| |
Instances
data TaxMergedNode Source
Datastructure for entries of Taxonomy database dump mergednodes file
Constructors
| TaxMergedNode | |
Instances
Datastructure for entries of Taxonomy database dump names file
Constructors
| TaxName | |
Fields
| |
Taxonomic ranks: NCBI uses the uncommon Speciessubgroup
Constructors
Datastructure for entries of Taxonomy database dump nodes file
Constructors
| TaxNode | |
Fields
| |
data Gene2Accession Source
Datastructure for Gene2Accession table
Constructors
Instances
simpleTaxonJSONValue :: Gr SimpleTaxon Double -> Node -> Value Source