module Biobase.Infernal.VerboseHit.Import
( eneeVerboseHit
, fromFile
) where
import Control.Applicative
import Control.Monad as M
import Data.Attoparsec as A
import Data.Attoparsec.Char8 as A8
import Data.Attoparsec.Iteratee as EAP
import Data.ByteString.Char8 as BS
import Data.Either.Unwrap
import Data.Iteratee as I
import Data.Iteratee.Char as I
import Data.Iteratee.IO as I
import Data.Iteratee.Iteratee as I
import Data.Iteratee.ListLike as I
import Data.Tuple.Select
import Prelude as P
import Biobase.Infernal.VerboseHit
import Biobase.Infernal.VerboseHit.Internal
eneeVerboseHit :: (Functor m, Monad m) => Enumeratee BS.ByteString [VerboseHit] m a
eneeVerboseHit = enumLinesBS ><> I.filter (not . BS.null) ><> unfoldConvStream f (AliGo BS.empty BS.empty '?') where
f acc = do
h' <- tryHead
case h' of
Nothing -> return (acc, [])
(Just h)
| "CM: " `BS.isInfixOf` h -> return (acc{aliCM = BS.copy $ BS.drop 4 h}, [])
| ">" `BS.isInfixOf` h -> return (acc{aliScaffold = BS.copy $ BS.drop 1 h}, [])
| " Plus" `BS.isInfixOf` h -> return (acc{aliStrand = '+'}, [])
| " Minus" `BS.isInfixOf` h -> return (acc{aliStrand = '-'}, [])
| " Query" `BS.isInfixOf` h -> do
x <- qs h (aliCM acc) (aliScaffold acc) (aliStrand acc)
return (acc,x)
| otherwise -> return (acc,[])
qs :: Monad m => BS.ByteString -> BS.ByteString -> BS.ByteString -> Char -> Iteratee [BS.ByteString] m [VerboseHit]
qs query cm scaf pm = do
let q = fromRight . parseOnly qt $ query
s <- I.head >>= return . fromRight . parseOnly sepg
l <- fourLines $ sel4 q
return . pure $ VerboseHit
{ vhScaffold = scaf
, vhCM = cm
, vhStrand = pm
, vhQuery = (sel1 q, sel2 q)
, vhTarget = (sel3 q, sel4 q)
, vhScore = sel1 s
, vhEvalue = sel2 s
, vhPvalue = sel3 s
, vhGC = sel4 s
, vhWuss = cpy $ l!!0
, vhConsensus = cpy $ l!!1
, vhScoring = cpy $ l!!2
, vhSequence = cpy $ l!!3
}
where
cpy = BS.copy . BS.concat
qt = (,,,) <$ A.string " Query = " <*> A8.decimal <* A.string " - " <*> A8.decimal
<* A.string ", Target = " <*> A8.decimal <* A.string " - " <*> A8.decimal
<?> "qt"
sepg = (,,,) <$ A.string " Score = " <*> A8.double
<* A.string ", E = " <*> A8.double
<* A.string ", P = " <*> A8.double
<* A.string ", GC = " <* A8.skipSpace <*> A8.decimal
<?> "sepg"
fourLinesOld to = do
I.dropWhile BS.null
ls <- joinI $ I.take 4 stream2stream
let ws = BS.length . BS.takeWhile isSpace . P.head $ ls
let cs = BS.length . BS.dropWhile isSpace . P.head $ ls
let xs = P.map (BS.take cs . BS.drop ws) ls
if (P.length ls /= 4) ||
("-" == (P.last . BS.words . P.last $ ls)) ||
(to == (read . BS.unpack . P.last . BS.words . P.last $ ls))
then return . P.map (:[]) $ xs
else fourLines to >>= return . (P.zipWith (:) xs)
fourLines to = do
I.dropWhile BS.null
mp <- I.peek
case mp of
Nothing -> return $ P.replicate 4 []
Just p
| "//" `isInfixOf` p
|| "CM" `isInfixOf` p
|| "Query" `isInfixOf` p
|| ">" `isPrefixOf` p
|| "strand" `isInfixOf` p
|| "#" `isPrefixOf` p
-> return $ P.replicate 4 []
| otherwise
-> do ls <- joinI $ I.take 4 stream2stream
let ws = BS.length . BS.takeWhile isSpace . P.head $ ls
let cs = BS.length . BS.dropWhile isSpace . P.head $ ls
let xs = P.map (BS.take cs . BS.drop ws) ls
fourLines to >>= return . (P.zipWith (:) xs)
fromFile :: FilePath -> IO [VerboseHit]
fromFile fp = do
i <- enumFile 8192 fp . joinI $ eneeVerboseHit stream2list
run i
test = do
i <- enumFile 8192 "test.vh" $ joinI $ eneeVerboseHit stream2list
xs <- run i
P.mapM_ (\x -> print x >> P.putStrLn "\n\n\n") xs
print $ P.length xs