Taxonomy.hs

{-# LANGUAGE PatternGuards #-}

-- | Infernal contains a taxonomy database. This is a simple module reflecting
-- said database.

module Biobase.Infernal.Taxonomy where

import qualified Data.ByteString.Char8 as BS
import Data.Char (toLower)

import Biobase.Infernal.Types



-- | For each species, we store the name and a classification list from most
-- general (head) to most specific (last). The database comes with the NCBI
-- taxon identifier (taxid).

data SpeciesTaxonomy = SpeciesTaxonomy
  { stAccession      :: !SpeciesAccession
  , stName           :: !SpeciesName
  , stClassification :: ![Classification]
  } deriving (Show)

-- | Given a name such as "Drosophila Melanogaster", returns "d.melanogaster".

shortenName :: SpeciesName -> SpeciesName
shortenName (SpeciesName xs)
  | null ws   = SpeciesName xs
  | [w] <- ws = SpeciesName w
  | otherwise = SpeciesName . BS.map toLower $ BS.take 1 (ws!!0) `BS.append` (BS.cons '.' $ ws!!1)
  where ws = BS.words xs