module Biobase.Infernal.TabularHit.Import where
import Data.ByteString.Char8 as BS
import Data.Iteratee as I
import Data.Iteratee.Iteratee as I
import Data.Iteratee.ListLike as I
import Data.Iteratee.Char as I
import Data.Either.Unwrap
import Data.Attoparsec as A hiding (takeTill)
import Data.Attoparsec.Char8 as A
import Control.Applicative
import Data.Iteratee.IO as I
import Biobase.Infernal.TabularHit
import Biobase.Infernal.Types
eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m a
eneeTabularHit = enumLinesBS ><> I.filter (\x -> not $ BS.null x || isPrefixOf "#" x) ><> mapStream f where
f = fromRight . parseOnly p
mkTH mName tName tStart tStop qStart qStop bScore eValue gc = TabularHit
(ModelIdentification tName)
(Scaffold tName)
tStart
tStop
qStart
qStop
(BitScore bScore)
eValue
gc
p = mkTH <$> pString
<*> pString
<*> pDecimal
<*> pDecimal
<*> pDecimal
<*> pDecimal
<*> pDouble
<*> pDouble
<*> pDecimal
pString = A.skipSpace *> A.takeTill A.isSpace
pDecimal = A.skipSpace *> A.decimal
pDouble = A.skipSpace *> A.double
fromFile :: FilePath -> IO [TabularHit]
fromFile fp = do
i <- enumFile 8192 fp . joinI $ eneeTabularHit stream2stream
run i