Biobase.Taxonomy.Import

Functions for parsing, processing and visualization of taxonomy data.

Usage example:

• Read in taxonomy data

  eitherTaxtree <- readNamedTaxonomy "/path/to/NCBI_taxonomydump_directory"

• Process data

  let subtree = extractTaxonomySubTreebyLevel [562] (fromRight eitherTaxTree) (Just 4)

• Visualize result

  tput "pathto/dotdirectory" subtree

Datatypes

module Biobase.Taxonomy.Types

Parsing

readTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))

NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.

readNamedTaxonomy :: String -> IO (Either ParseError (Gr SimpleTaxon Double))

NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree with scientific names for each node is generated.

parseTaxonomy :: String -> Either ParseError (Gr SimpleTaxon Double)

NCBI taxonomy dump nodes and names in the input directory path are parsed and a SimpleTaxon tree is generated.

parseNCBITaxCitations :: String -> Either ParseError [TaxCitation]

parse NCBITaxCitations from input string

readNCBITaxCitations :: String -> IO (Either ParseError [TaxCitation])

parse NCBITaxCitations from input filePath

parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode]

parse NCBITaxDelNodes from input string

readNCBITaxDelNodes :: String -> IO (Either ParseError [TaxDelNode])

parse NCBITaxDelNodes from input filePath

parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision]

parse NCBITaxDivisons from input string

readNCBITaxDivisions :: String -> IO (Either ParseError [TaxDivision])

parse NCBITaxDivisons from input filePath

parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode]

parse NCBITaxGenCodes from input string

readNCBITaxGenCodes :: String -> IO (Either ParseError [TaxGenCode])

parse NCBITaxGenCodes from input filePath

parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode]

parse NCBITaxMergedNodes from input string

readNCBITaxMergedNodes :: String -> IO (Either ParseError [TaxMergedNode])

parse NCBITaxMergedNodes from input filePath

parseNCBITaxNames :: String -> Either ParseError [TaxName]

parse NCBITaxNames from input string

readNCBITaxNames :: String -> IO (Either ParseError [TaxName])

parse NCBITaxNames from input filePath

parseNCBITaxNodes :: String -> Either ParseError TaxNode

parse NCBITaxNames from input string

readNCBITaxNodes :: String -> IO (Either ParseError [TaxNode])

parse NCBITaxCitations from input filePath

parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon

parse NCBISimpleTaxNames from input string

readNCBISimpleTaxons :: String -> IO (Either ParseError [SimpleTaxon])

parse NCBITaxCitations from input filePath

readNCBITaxonomyDatabase :: String -> IO (Either [String] NCBITaxDump)

Parse the input as NCBITax datatype