module Bio.Data.Fastq
( Fastq(..)
, parseFastqC
, parseFastqUnsafeC
, fastqToByteString
, trimPolyA
) where
import Conduit
import Control.Monad (when)
import qualified Data.ByteString.Char8 as B
import qualified Data.ByteString as BS
import Data.Maybe (isJust)
-- | 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
, fastqSeqInfo :: B.ByteString
, fastqSeqQual :: B.ByteString
} deriving (Show, Eq)
parseFastqC :: Monad m => ConduitT B.ByteString Fastq m ()
parseFastqC = linesUnboundedAsciiC .| conduit
where
conduit = do
l1 <- await
l2 <- await
l3 <- await
l4 <- await
case mkFastqRecord <$> l1 <*> l2 <*> l3 <*> l4 of
Nothing -> when (isJust l1) $ error "file ends prematurely"
Just x -> yield x >> conduit
{-# INLINE parseFastqC #-}
parseFastqUnsafeC :: Monad m => ConduitT B.ByteString Fastq m ()
parseFastqUnsafeC = linesUnboundedAsciiC .| conduit
where
conduit = do
l1 <- await
l2 <- await
l3 <- await
l4 <- await
case mkFastqRecordUnsafe <$> l1 <*> l2 <*> l3 <*> l4 of
Nothing -> when (isJust l1) $ error "file ends prematurely"
Just x -> yield x >> conduit
{-# INLINE parseFastqUnsafeC #-}
fastqToByteString :: Fastq -> [B.ByteString]
fastqToByteString (Fastq a b c d) = ['@' `B.cons` a, b, '+' `B.cons` c, d]
{-# INLINE fastqToByteString #-}
-- | Make Fastq record from Bytestrings, without sanity check.
mkFastqRecordUnsafe :: B.ByteString -- ^ First line
-> B.ByteString -- ^ Second line
-> B.ByteString -- ^ Third line
-> B.ByteString -- ^ Fourth line
-> Fastq
mkFastqRecordUnsafe l1 l2 l3 l4 = Fastq (B.tail l1) l2 (B.tail l3) l4
{-# INLINE mkFastqRecordUnsafe #-}
mkFastqRecord :: B.ByteString -- ^ First line
-> B.ByteString -- ^ Second line
-> B.ByteString -- ^ Third line
-> B.ByteString -- ^ Fourth line
-> Fastq
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
{-# INLINE mkFastqRecord #-}
-- | Remove trailing 'A'
trimPolyA :: Int -> Fastq -> Fastq
trimPolyA n f@(Fastq a b c d)
| B.length trailing >= n = Fastq a b' c $ B.take (B.length b') d
| otherwise = f
where
(b', trailing) = B.spanEnd (=='A') b