{-# LANGUAGE LambdaCase #-}
{-# LANGUAGE OverloadedStrings #-}
module Bio.Data.Fastq
( Fastq(..)
, parseFastqC
, fastqToByteString
, qualitySummary
, trimPolyA
) where
import Conduit
import Control.Monad (when)
import qualified Data.ByteString.Char8 as B
import qualified Data.ByteString.Lazy as BL
import qualified Data.ByteString as BS
import Data.Maybe (isJust)
import Data.Attoparsec.ByteString
import Data.Conduit.Attoparsec
-- | A FASTQ file normally uses four lines per sequence.
--
-- * Line 1 begins with a '@' character and is followed by a sequence
-- identifier and an optional description (like a FASTA title line).
--
-- * Line 2 is the raw sequence letters.
--
-- * Line 3 begins with a '+' character and is optionally followed by the
-- same sequence identifier (and any description) again.
--
-- * Line 4 encodes the quality values for the sequence in Line 2, and must
-- contain the same number of symbols as letters in the sequence.
data Fastq = Fastq
{ fastqSeqId :: B.ByteString
, fastqSeq :: B.ByteString
, fastqSeqQual :: B.ByteString
} deriving (Show, Eq)
parseFastqC :: MonadThrow m => ConduitT B.ByteString Fastq m ()
parseFastqC = conduitParser fastqParser .| mapC snd
{-# INLINE parseFastqC #-}
fastqParser :: Parser Fastq
fastqParser = do
ident <- word8 64 *> takeTill (==10)
sequence <- BS.filter (/=10) <$> takeTill (==43)
skip (/=10)
score <- BS.filter (/=10) <$> takeTill (==64)
return $ Fastq ident sequence score
{-# INLINE fastqParser #-}
fastqToByteString :: Fastq -> B.ByteString
fastqToByteString (Fastq a b c) = "@" <> a <> "\n" <> b <> "\n+\n" <> c
{-# INLINE fastqToByteString #-}
-- | Get the mean and variance of quality scores at every position.
qualitySummary :: Monad m => ConduitT Fastq o m [(Double, Double)]
qualitySummary = mapC (map fromIntegral . decodeQualSc) .| meanVarianceC
meanVarianceC :: Monad m => ConduitT [Double] o m [(Double, Double)]
meanVarianceC = peekC >>= \case
Nothing -> error "Empty input"
Just x -> fst <$> foldlC f (replicate (length x) (0,0), 0)
where
f (acc, n) xs = let acc' = zipWith g acc xs in (acc', n')
where
n' = n + 1
g (m, s) x = (m', s')
where
m' = m + d / fromIntegral n'
s' = s + d * (x - m')
d = x - m
{-# INLINE meanVarianceC #-}
decodeQualSc :: Fastq -> [Int]
decodeQualSc = map (fromIntegral . (\x -> x - 33)) . BS.unpack .fastqSeqQual
{-# INLINE decodeQualSc #-}
pError :: Int -> Double
pError x = 10 ** (negate (fromIntegral x) / 10)
{-# INLINE pError #-}
{-
mkFastqRecord l1 l2 l3 l4 = Fastq (parseLine1 l1) (parseLine2 l2)
(parseLine3 l3) (parseLine4 l4)
where
parseLine1 x | B.head x == '@' = B.tail x
| otherwise = error $ "Parse line 1 failed: " ++ B.unpack x
parseLine2 x | B.all f x = x
| otherwise = error $ "Parse line 2 failed: " ++ B.unpack x
where
f 'C' = True
f 'G' = True
f 'T' = True
f 'A' = True
f 'N' = True
f _ = False
parseLine3 x | B.head x == '+' = B.tail x
| otherwise = error $ "Parse line 3 failed: " ++ B.unpack x
parseLine4 x | BS.all f x = x
| otherwise = error $ "Parse line 4 failed: " ++ B.unpack x
where
f b = let b' = fromIntegral b :: Int
in b' >= 33 && b' <= 126
-}
-- | Remove trailing 'A'
trimPolyA :: Int -> Fastq -> Fastq
trimPolyA n f@(Fastq a b c)
| B.length trailing >= n = Fastq a b' $ B.take (B.length b') c
| otherwise = f
where
(b', trailing) = B.spanEnd (=='A') b