Bioinformatics.FASTA.hs

module Bioinformatics.FASTA (
  FASTAFormatLine(..),
  buildFASTALines,
  buildFASTALinesWith
) where

import qualified Bioinformatics.DNANucleotide as D
import qualified Data.List.Split as S

-- type FASTAFormatLine = (String, [D.DNANucleotide])
data FASTAFormatLine a = FASTAFormatLine {  name :: String,
                                            content :: [a]
                                         } deriving (Show)

stringToFASTAFormat :: String -> FASTAFormatLine D.DNANucleotide
stringToFASTAFormat [] = FASTAFormatLine { name = "", content = [] }
stringToFASTAFormat xs =
  let comps = lines xs
  in FASTAFormatLine { name = head comps, content = map D.charToDNANucleotide . concat $ tail comps }

buildFASTALines :: String -> [FASTAFormatLine D.DNANucleotide]
buildFASTALines = map stringToFASTAFormat . S.splitOn ">"

stringToFASTAFormatWith :: (Char -> a) -> String -> FASTAFormatLine a
stringToFASTAFormatWith _ [] = FASTAFormatLine {name = "", content = [] }
stringToFASTAFormatWith with xs =
  let comps = lines xs
  in FASTAFormatLine { name = head comps, content = map with . concat $ tail comps }

buildFASTALinesWith :: (Char -> a) -> String -> [FASTAFormatLine a]
buildFASTALinesWith with = map (stringToFASTAFormatWith with) . S.splitOn ">"