BiobaseFasta 0.0.0.1 → 0.0.0.2

raw patch · 2 files changed

+37/−12 lines, 2 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• Biobase/Fasta/Import.hs +36/−11
• BiobaseFasta.cabal +1/−1

@@ -30,7 +30,13 @@ -- convenience functions and replace the final conversion to a strict stream by -- your own conversion (or output) function. -type FastaFunction z = FastaHeader -> FastaData -> StartPos -> z+type FastaFunction z+  = FastaHeader     -- ^ the ">" header+  -> StartPos       -- ^ where in the original sequence to start+  -> WindowSize     -- ^ how many characters we are looking at+  -> PeekSize       -- ^ this many characters are from the next window (peeking into)+  -> FastaData      -- ^ the actual sequence data+  -> z              -- ^ and what we return as result  -- | Starting position in FASTA entry. @@ -44,8 +50,15 @@  type FastaData = ByteString +-- | Window +type WindowSize = Int +-- | How many characters to peek forward++type PeekSize = Int++ -- * conversion from FASTA to data of type 'z'.  -- | Takes a bytestring sequence, applies 'f' to each bytestring of windowsize@@ -53,9 +66,9 @@  rollingIter   :: (Monad m, Functor m, Nullable z, Monoid z)-  => (ByteString -> StartPos -> z)-  -> Int-  -> Int+  => (StartPos -> WindowSize -> PeekSize -> FastaData -> z)+  -> WindowSize+  -> PeekSize   -> Enumeratee ByteString z m a rollingIter f windowSize peekSize = unfoldConvStream go 0 where   go start = do@@ -63,26 +76,36 @@     case yss of       [ys] -> do let xs = BS.filter (/='\n') ys                  let l = BS.length xs-                 return $ (start + l, f xs start)+                 return $ (start + l, f start windowSize peekSize xs)       _ -> error "rollingIter: error"+{-# INLINE rollingIter #-}  -- | Outer enumeratee. See the two convenience functions for how to use it -- (just like any enumeratee, basically).+--+-- The fasta function 'f' manipulates small stretches of fasta data and has+-- arguments: fasta header, fasta data, start position (all filled by+-- eneeFasta).+--+-- Next we have the window size, how many characters to read at once,+--+-- followed by the the number of characters to read in addition.+--+-- The work is actually done by 'rollingIter'.  eneeFasta   :: (Monad m, Functor m, Nullable z, NullPoint z, Monoid z)-  => (ByteString -> ByteString -> StartPos -> z)-  -> Int-  -> Int+  => FastaFunction z+  -> WindowSize+  -> PeekSize   -> Enumeratee ByteString z m a eneeFasta f windowSize peekSize = unfoldConvStream go "" where   go hdr = do     hdr <- I.takeWhile (/=10) -- 10 == '\n'     is <- joinI-            $   I.takeUpTo 8192-            ><> I.breakE (==62)+            $   I.breakE (==62) -- 62 == '>'             ><> rollingIter (f hdr) windowSize peekSize-            $   stream2stream -- 62 == '>'+            $   stream2stream     return (hdr, is) {-# INLINE eneeFasta #-} @@ -99,6 +122,7 @@             . eneeFasta ff windowSize peekSize             $ stream2stream             )+{-# INLINE fromFile #-}  -- | From a gzip-compressed file. @@ -111,3 +135,4 @@             . eneeFasta ff windowSize peekSize             $ stream2stream             )+{-# INLINE fromFileZip #-}

@@ -1,5 +1,5 @@ name:           BiobaseFasta-version:        0.0.0.1+version:        0.0.0.2 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/