Taxonomy-2.2.0: Libary for parsing, processing and vizualization of taxonomy data
Safe HaskellNone
LanguageHaskell2010

Biobase.Taxonomy.Import

Description

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

Synopsis

Datatypes

Parsing

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

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)) Source #

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) Source #

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

parseNCBITaxCitations :: String -> Either ParseError [TaxCitation] Source #

parse NCBITaxCitations from input string

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

parse NCBITaxCitations from input filePath

parseNCBITaxDelNodes :: String -> Either ParseError [TaxDelNode] Source #

parse NCBITaxDelNodes from input string

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

parse NCBITaxDelNodes from input filePath

parseNCBITaxDivisions :: String -> Either ParseError [TaxDivision] Source #

parse NCBITaxDivisons from input string

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

parse NCBITaxDivisons from input filePath

parseNCBITaxGenCodes :: String -> Either ParseError [TaxGenCode] Source #

parse NCBITaxGenCodes from input string

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

parse NCBITaxGenCodes from input filePath

parseNCBITaxMergedNodes :: String -> Either ParseError [TaxMergedNode] Source #

parse NCBITaxMergedNodes from input string

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

parse NCBITaxMergedNodes from input filePath

parseNCBITaxNames :: String -> Either ParseError [TaxName] Source #

parse NCBITaxNames from input string

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

parse NCBITaxNames from input filePath

parseNCBITaxNodes :: String -> Either ParseError TaxNode Source #

parse NCBITaxNames from input string

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

parse NCBITaxCitations from input filePath

parseNCBISimpleTaxons :: String -> Either ParseError SimpleTaxon Source #

parse NCBISimpleTaxNames from input string

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

parse NCBITaxCitations from input filePath

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

Parse the input as NCBITax datatype