read_kmers.hs

import System.Environment
import Data.List.Split
import Data.List
import qualified Data.Map.Strict as Map

main = do
  [f]      <- getArgs
  contents <- readFile f
  putStr . unlines . map unwords . map (kmers 6) . getSequences $ contents

getSequences :: String -> [String]
getSequences = map (\x -> x !! 1) . splitEvery 4 . lines

kmers :: Int -> String -> [String]
kmers k seq = (unfoldr f seq) ++ (unfoldr f $ map revcomp $ seq)
  where
    f xs
      | length xs >= k = Just ((take k xs), (tail xs))
      | otherwise      = Nothing
    revcomp 'A' = 'T'
    revcomp 'T' = 'A'
    revcomp 'G' = 'C'
    revcomp 'C' = 'G'
    revcomp  _  = 'N'