diff --git a/Biobase/Primary/AA.hs b/Biobase/Primary/AA.hs --- a/Biobase/Primary/AA.hs +++ b/Biobase/Primary/AA.hs @@ -1,7 +1,11 @@ --- | This module has the translation tables for the genetic code. We do --- have a symbol 'Undef' for undefined amino acids (say because of @N@s in --- the nucleotide code). +-- | This module has the translation tables for the genetic code. +-- +-- In addition, @Any@ is included to denote that any amino acid is ok, and +-- @Unknown@ to denote unknown data. We do have a symbol 'Undef' for undefined +-- amino acids, which denotes error condition. +-- +-- TODO this nomenclature might change! module Biobase.Primary.AA where @@ -14,7 +18,6 @@ import Data.Tuple (swap) import Data.Vector.Unboxed.Deriving import GHC.Base (remInt,quotInt) -import qualified GHC.Exts as GHC import GHC.Generics (Generic) import qualified Data.Bijection.HashMap as B import qualified Data.ByteString.Char8 as BS @@ -25,77 +28,87 @@ import qualified Data.Vector.Generic as VG import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU +import qualified GHC.Exts as GHC +import Biobase.Types.BioSequence +import Data.Info + import Biobase.Primary.Letter --- | Amino acid phantom type. - -data AA - -pattern Stop = Letter 0 :: Letter AA -pattern A = Letter 1 :: Letter AA -pattern B = Letter 2 :: Letter AA -pattern C = Letter 3 :: Letter AA -pattern D = Letter 4 :: Letter AA -pattern E = Letter 5 :: Letter AA -pattern F = Letter 6 :: Letter AA -pattern G = Letter 7 :: Letter AA -pattern H = Letter 8 :: Letter AA -pattern I = Letter 9 :: Letter AA -pattern K = Letter 10 :: Letter AA -pattern L = Letter 11 :: Letter AA -pattern M = Letter 12 :: Letter AA -pattern N = Letter 13 :: Letter AA -pattern P = Letter 14 :: Letter AA -pattern Q = Letter 15 :: Letter AA -pattern R = Letter 16 :: Letter AA -pattern S = Letter 17 :: Letter AA -pattern T = Letter 18 :: Letter AA -pattern V = Letter 19 :: Letter AA -pattern W = Letter 20 :: Letter AA -pattern X = Letter 21 :: Letter AA -pattern Y = Letter 22 :: Letter AA -pattern Z = Letter 23 :: Letter AA -pattern Undef = Letter 24 :: Letter AA - +pattern Stop = Letter 0 :: Letter AA n +pattern A = Letter 1 :: Letter AA n +pattern B = Letter 2 :: Letter AA n +pattern C = Letter 3 :: Letter AA n +pattern D = Letter 4 :: Letter AA n +pattern E = Letter 5 :: Letter AA n +pattern F = Letter 6 :: Letter AA n +pattern G = Letter 7 :: Letter AA n +pattern H = Letter 8 :: Letter AA n +pattern I = Letter 9 :: Letter AA n +pattern K = Letter 10 :: Letter AA n +pattern L = Letter 11 :: Letter AA n +pattern M = Letter 12 :: Letter AA n +pattern N = Letter 13 :: Letter AA n +pattern P = Letter 14 :: Letter AA n +pattern Q = Letter 15 :: Letter AA n +pattern R = Letter 16 :: Letter AA n +pattern S = Letter 17 :: Letter AA n +pattern T = Letter 18 :: Letter AA n +pattern V = Letter 19 :: Letter AA n +pattern W = Letter 20 :: Letter AA n +pattern X = Letter 21 :: Letter AA n +pattern Y = Letter 22 :: Letter AA n +pattern Z = Letter 23 :: Letter AA n +pattern Any = Letter 24 :: Letter AA n -- TODO @Any == X@ supposedly! +pattern Unknown = Letter 25 :: Letter AA n +pattern Undef = Letter 26 :: Letter AA n -- * Creating functions and aa data. -aa :: Int -> Letter AA +aa :: Int -> Letter AA n aa = Letter +{-# Inline aa #-} -aaRange = [Stop .. pred Undef] +aaRange = VU.fromList [Stop .. pred Undef] +{-# NoInline aaRange #-} -instance LetterChar AA where +instance Bounded (Letter AA n) where + minBound = Stop + maxBound = Undef + +instance LetterChar AA n where letterChar = aaChar charLetter = charAA -instance ToJSON (Letter AA) where +instance ToJSON (Letter AA n) where toJSON = toJSON . letterChar -instance FromJSON (Letter AA) where +instance FromJSON (Letter AA n) where parseJSON = fmap charLetter . parseJSON +instance Info (Letter AA n) where + info = (:[]) . aaChar + --instance (GHC.IsString f) => ToJSON (Pretty f (Letter AA)) where -- toJSON = toJSON . T.pack . map letterChar . GHC.toList . getPretty -- | Translate 'Char' amino acid representation into efficient 'AA' newtype. -charAA :: Char -> Letter AA +charAA :: Char -> Letter AA n charAA = B.findWithDefaultL Undef charBaa {-# INLINE charAA #-} -- | 'Char' representation of an 'AA'. -aaChar :: Letter AA -> Char +aaChar :: Letter AA n -> Char aaChar = B.findWithDefaultR '?' charBaa {-# INLINE aaChar #-} -- * lookup tables -charBaa :: B.Bimap (B.HashMap Char (Letter AA)) (B.HashMap (Letter AA) Char) +charBaa :: B.Bimap (B.HashMap Char (Letter AA n)) (B.HashMap (Letter AA n) Char) charBaa = B.fromList [ ('*',Stop) , ('A',A) @@ -121,25 +134,30 @@ , ('X',X) , ('Y',Y) , ('Z',Z) - , ('?',Undef) + , ('?',Unknown) ] {-# NOINLINE charBaa #-} +-- | List of the twenty "default" amino acids. Used, for example, by HMMer. +twentyAA :: VU.Vector (Letter AA n) +twentyAA = VU.fromList [ A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y ] +{-# NoInline twentyAA #-} + -- * instances -instance Show (Letter AA) where +instance Show (Letter AA n) where show n = [aaChar n] -instance Read (Letter AA) where +instance Read (Letter AA n) where readsPrec p [] = [] readsPrec p (x:xs) | x==' ' = readsPrec p xs | aa <- charAA x = [(aa,xs)] | otherwise = [] -instance Enum (Letter AA) where +instance Enum (Letter AA n) where succ Undef = error "succ/Undef:AA" succ (Letter x) = Letter $ x+1 pred Stop = error "pred/Stop:AA" @@ -148,6 +166,6 @@ toEnum k = error $ "toEnum/Letter RNA " ++ show k fromEnum (Letter k) = k -instance MkPrimary (VU.Vector Char) AA where +instance MkPrimary (VU.Vector Char) AA n where primary = VU.map charAA diff --git a/Biobase/Primary/Hashed.hs b/Biobase/Primary/Hashed.hs --- a/Biobase/Primary/Hashed.hs +++ b/Biobase/Primary/Hashed.hs @@ -19,26 +19,26 @@ -- | The hash of a primary sequence. -newtype HashedPrimary t = HashedPrimary { unHashedPrimary :: Int } +newtype HashedPrimary t n = HashedPrimary { unHashedPrimary :: Int } deriving (Eq,Ord,Ix,Read,Show,Enum,Bounded) derivingUnbox "HashedPrimary" - [t| forall a . HashedPrimary a -> Int |] [| unHashedPrimary |] [| HashedPrimary |] + [t| forall t n . HashedPrimary t n -> Int |] [| unHashedPrimary |] [| HashedPrimary |] -- | Given a piece of primary sequence information, reduce it to an index. -- The empty input produces an index of 0. -mkHashedPrimary :: forall t . (VU.Unbox (Letter t), Bounded (Letter t), Enum (Letter t)) => Primary t -> HashedPrimary t +mkHashedPrimary :: forall t n . (VU.Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => Primary t n -> HashedPrimary t n mkHashedPrimary = HashedPrimary . fst . VU.foldl' f (0, 1) where - f (z, c) n = (z + c * (fromEnum n +1), c * (fromEnum (maxBound :: Letter t) + 1)) + f (z, c) n = (z + c * (fromEnum n +1), c * (fromEnum (maxBound :: Letter t n) + 1)) {-# INLINE mkHashedPrimary #-} -- | Turn a hash back into a sequence. Will fail if the resulting sequence -- has more than 100 elements. -hash2primary :: forall t . (VU.Unbox (Letter t), Bounded (Letter t), Enum (Letter t)) => HashedPrimary t -> Primary t +hash2primary :: forall t n . (VU.Unbox (Letter t n), Bounded (Letter t n), Enum (Letter t n)) => HashedPrimary t n -> Primary t n hash2primary (HashedPrimary h) = VU.unfoldrN l f h where - m = fromEnum (maxBound :: Letter t) +1 + m = fromEnum (maxBound :: Letter t n) +1 l = VU.length . VU.takeWhile (>0) . VU.iterateN 100 (`div` m) $ h f k = if k>0 then Just (toEnum $ ((k-1) `mod` m) , (k-1) `div` m) else Nothing diff --git a/Biobase/Primary/IUPAC.hs b/Biobase/Primary/IUPAC.hs --- a/Biobase/Primary/IUPAC.hs +++ b/Biobase/Primary/IUPAC.hs @@ -11,13 +11,15 @@ import Control.Arrow ((***)) import Data.ByteString.Char8 (ByteString,unpack) import Data.Char (toUpper) -import Data.FileEmbed (embedFile) +import Data.FileEmbed (makeRelativeToProject, embedFile) import Data.List (nub,sort) import Data.String import Data.Tuple (swap) import qualified Data.Vector.Unboxed as VU import Control.Category ((>>>)) +import Biobase.Types.BioSequence + import Biobase.Primary.Letter import Biobase.Primary.Nuc import qualified Biobase.Primary.Nuc.RNA as R @@ -27,28 +29,28 @@ data DEG -pattern A = Letter 0 :: Letter DEG -pattern C = Letter 1 :: Letter DEG -pattern G = Letter 2 :: Letter DEG -pattern T = Letter 3 :: Letter DEG -pattern U = Letter 4 :: Letter DEG -pattern W = Letter 5 :: Letter DEG -pattern S = Letter 6 :: Letter DEG -pattern M = Letter 7 :: Letter DEG -pattern K = Letter 8 :: Letter DEG -pattern R = Letter 9 :: Letter DEG -pattern Y = Letter 10 :: Letter DEG -pattern B = Letter 11 :: Letter DEG -pattern D = Letter 12 :: Letter DEG -pattern H = Letter 13 :: Letter DEG -pattern V = Letter 14 :: Letter DEG -pattern N = Letter 15 :: Letter DEG +pattern A = Letter 0 :: Letter DEG n +pattern C = Letter 1 :: Letter DEG n +pattern G = Letter 2 :: Letter DEG n +pattern T = Letter 3 :: Letter DEG n +pattern U = Letter 4 :: Letter DEG n +pattern W = Letter 5 :: Letter DEG n +pattern S = Letter 6 :: Letter DEG n +pattern M = Letter 7 :: Letter DEG n +pattern K = Letter 8 :: Letter DEG n +pattern R = Letter 9 :: Letter DEG n +pattern Y = Letter 10 :: Letter DEG n +pattern B = Letter 11 :: Letter DEG n +pattern D = Letter 12 :: Letter DEG n +pattern H = Letter 13 :: Letter DEG n +pattern V = Letter 14 :: Letter DEG n +pattern N = Letter 15 :: Letter DEG n -instance Bounded (Letter DEG) where +instance Bounded (Letter DEG n) where minBound = A maxBound = N -instance Enum (Letter DEG) where +instance Enum (Letter DEG n) where succ N = error "succ/N:DEG" succ (Letter x) = Letter $ x+1 pred A = error "pred/A:DEG" @@ -95,16 +97,16 @@ N -> 'N' {-# INLINE degChar #-} -instance Show (Letter DEG) where +instance Show (Letter DEG n) where show c = [degChar c] -degSeq :: MkPrimary n DEG => n -> Primary DEG +degSeq :: MkPrimary p DEG n => p -> Primary DEG n degSeq = primary -instance MkPrimary (VU.Vector Char) DEG where +instance MkPrimary (VU.Vector Char) DEG n where primary = VU.map charDEG -instance IsString [Letter DEG] where +instance IsString [Letter DEG n] where fromString = map charDEG @@ -119,18 +121,18 @@ fromDegenerate = maybe [] id . flip lookup iupacXDNAchars toDegenerate = flip lookup (map swap iupacXDNAchars) . nub . sort -instance Degenerate (Letter RNA) where +instance Degenerate (Letter RNA n) where fromDegenerate 'T' = [] fromDegenerate x = map dnaTrna $ fromDegenerate x toDegenerate xs | xs == [R.U] = Just 'U' | otherwise = toDegenerate $ map rnaTdna xs -instance Degenerate (Letter DNA) where +instance Degenerate (Letter DNA n) where fromDegenerate 'U' = [] fromDegenerate x = map charDNA $ fromDegenerate x toDegenerate = toDegenerate . map dnaChar -instance Degenerate (Letter XNA) where +instance Degenerate (Letter XNA n) where fromDegenerate = map charXNA . fromDegenerate toDegenerate = toDegenerate . map xnaChar @@ -149,5 +151,5 @@ -- | Raw iupac data, embedded into the library. iupacNucleotides :: ByteString -iupacNucleotides = $(embedFile "sources/iupac-nucleotides") +iupacNucleotides = $(makeRelativeToProject "sources/iupac-nucleotides" >>= embedFile) diff --git a/Biobase/Primary/Letter.hs b/Biobase/Primary/Letter.hs --- a/Biobase/Primary/Letter.hs +++ b/Biobase/Primary/Letter.hs @@ -1,18 +1,21 @@ --- | A newtype with an attached phenotype which allows us to encode --- nucleotides and amino acids. Actual seqence-specific functions can be --- founds in the appropriate modules @AA@ and @Nuc@. +-- | A newtype with an attached phantom type which allows us to encode +-- nucleotides and amino acids. Actual seqence-specific functions can be founds +-- in the appropriate modules @AA@ and @Nuc@. module Biobase.Primary.Letter where import Control.DeepSeq (NFData) import Data.Aeson import Data.Binary +import Data.Coerce +import Data.Data import Data.Hashable (Hashable) import Data.Ix (Ix(..)) import Data.Serialize (Serialize(..)) import Data.String (IsString(..)) -import Data.Vector.Fusion.Stream.Monadic (map,Step(..)) +import Data.Typeable +import Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import Data.Vector.Unboxed.Deriving import GHC.Base (remInt,quotInt) import GHC.Generics (Generic) @@ -24,51 +27,75 @@ import qualified Data.Vector.Unboxed as VU import Data.PrimitiveArray hiding (map) +import Data.Info --- | A 'Letter' together with its phantom type @t@ encodes bio-sequences. +-- | A 'Letter' together with its phantom type @seqTy@ encodes bio-sequences, +-- while @nameTy@ allows to specify a type-level name for a letter. -newtype Letter t = Letter { getLetter :: Int } - deriving (Eq,Ord,Generic,Ix) +newtype Letter (seqTy :: *) (nameTy :: k) = Letter { getLetter :: Int } + deriving (Eq,Ord,Generic,Ix,Typeable) -instance Binary (Letter t) -instance Serialize (Letter t) +-- | While @coerce@ will always work, this way restricts the change to just the +-- @nameTy@. -instance NFData (Letter t) +changeNameTy :: Letter seqTy nameTy -> Letter seqTy newNameTy +{-# Inline changeNameTy #-} +changeNameTy = coerce -type Primary t = VU.Vector (Letter t) +-- | Manual @Data@ instance because @Letter@ should not show its +-- implementation. This also allows for better use of generic programming +-- downstream. +instance (Typeable t, Typeable (Letter t n)) => Data (Letter t n) where + toConstr = mkIntegralConstr letterDataType . getLetter + gunfold _ z c = case constrRep c of + (IntConstr x) -> z (Letter $ fromIntegral x) + _ -> errorWithoutStackTrace $ "Biobase.Primary.Letter.gunfold: Constructor " + ++ show c + ++ " is not of type Letter (using Int-rep)" + dataTypeOf _ = letterDataType +letterDataType = mkDataType "Biobase.Primary.Letter" [letterConstr] +letterConstr = mkConstr letterDataType "Letter" [] Prefix + +instance Binary (Letter t n) +instance Serialize (Letter t n) + +instance NFData (Letter t n) + +type Primary t n = VU.Vector (Letter t n) + -- | Convert 'Letter' types into character forms. @DNA@, @RNA@, and @amino -- acid@ sequences can make use of this. Other @Letter@ types only if they -- have single-char representations. -class LetterChar t where - letterChar :: Letter t -> Char - charLetter :: Char -> Letter t +class LetterChar t n where + letterChar :: Letter t n -> Char + charLetter :: Char -> Letter t n -- | Conversion from a large number of sequence-like inputs to primary -- sequences. -class MkPrimary n t where - primary :: n -> Primary t +class MkPrimary c t n where + primary :: c -> Primary t n -instance (MkPrimary (VU.Vector Char) t) => MkPrimary String t where +instance MkPrimary (VU.Vector Char) t n => MkPrimary String t n where primary = primary . VU.fromList -instance MkPrimary (VU.Vector Char) t => MkPrimary T.Text t where +instance MkPrimary (VU.Vector Char) t n => MkPrimary T.Text t n where primary = primary . VU.fromList . T.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary TL.Text t where +instance MkPrimary (VU.Vector Char) t n => MkPrimary TL.Text t n where primary = primary . VU.fromList . TL.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary BS.ByteString t where +instance MkPrimary (VU.Vector Char) t n => MkPrimary BS.ByteString t n where primary = primary . VU.fromList . BS.unpack -instance MkPrimary (VU.Vector Char) t => MkPrimary BSL.ByteString t where +instance MkPrimary (VU.Vector Char) t n => MkPrimary BSL.ByteString t n where primary = primary . VU.fromList . BSL.unpack -instance (VU.Unbox (Letter t), IsString [Letter t]) => IsString (VU.Vector (Letter t)) where +instance (VU.Unbox (Letter t n), IsString [Letter t n]) => IsString (VU.Vector (Letter t n)) where fromString = VU.fromList . fromString @@ -76,45 +103,62 @@ -- *** Instances for 'Letter'. derivingUnbox "Letter" - [t| forall a . Letter a -> Int |] [| getLetter |] [| Letter |] + [t| forall t n . Letter t n -> Int |] [| getLetter |] [| Letter |] -instance Hashable (Letter t) +instance Hashable (Letter t n) -instance Index (Letter l) where - linearIndex _ _ (Letter i) = i +-- | +-- +-- TODO replace @LtLetter Int@ with more specific limits? Maybe some constants? + +instance Index (Letter l n) where + newtype LimitType (Letter l n) = LtLetter (Letter l n) + linearIndex _ (Letter i) = i {-# Inline linearIndex #-} - smallestLinearIndex _ = error "still needed?" - {-# Inline smallestLinearIndex #-} - largestLinearIndex (Letter h) = h - {-# Inline largestLinearIndex #-} - size _ (Letter h) = h+1 + fromLinearIndex _ k = Letter k + {-# Inline fromLinearIndex #-} + size (LtLetter (Letter h)) = h+1 {-# Inline size #-} - inBounds (Letter l) (Letter h) (Letter i) = l <= i && i <= h + inBounds (LtLetter h) i = zeroBound <= i && i <= h {-# Inline inBounds #-} + zeroBound = Letter 0 + {-# Inline zeroBound #-} + zeroBound' = LtLetter zeroBound + {-# Inline zeroBound' #-} + totalSize (LtLetter (Letter k)) = [ fromIntegral k + 1 ] + {-# Inline totalSize #-} + showBound (LtLetter (Letter k)) = [ show k ] + showIndex (Letter k) = [ show k ] -instance IndexStream z => IndexStream (z:.Letter l) where - streamUp (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamUp ls hs +deriving instance (Bounded (Letter l n)) => Bounded (LimitType (Letter l n)) +deriving instance Eq (LimitType (Letter l n)) +deriving instance Generic (LimitType (Letter l n)) +deriving instance (Read (Letter l n)) => Read (LimitType (Letter l n)) +deriving instance (Show (Letter l n)) => Show (LimitType (Letter l n)) +deriving instance Typeable (LimitType (Letter l n)) +deriving instance Data (Letter l n) => Data (LimitType (Letter l n)) + +instance IndexStream z => IndexStream (z:.Letter l n) where + streamUp (ls:..LtLetter l) (hs:..LtLetter h) = flatten mk step $ streamUp ls hs where mk z = return (z,l) step (z,k) | k > h = return $ Done - | otherwise = return $ Yield (z:.Letter k) (z,k+1) + | otherwise = return $ Yield (z:.k) (z,Letter $ getLetter k +1) {-# Inline [0] mk #-} {-# Inline [0] step #-} {-# Inline streamUp #-} - streamDown (ls:.Letter l) (hs:.Letter h) = flatten mk step $ streamDown ls hs + streamDown (ls:..LtLetter l) (hs:..LtLetter h) = flatten mk step $ streamDown ls hs where mk z = return (z,h) step (z,k) | k < l = return $ Done - | otherwise = return $ Yield (z:.Letter k) (z,k-1) + | otherwise = return $ Yield (z:.k) (z,Letter $ getLetter k -1) {-# Inline [0] mk #-} {-# Inline [0] step #-} {-# Inline streamDown #-} --- TODO temporary, because defaults dont inline - -instance IndexStream (Letter l) where - streamUp l h = map (\(Z:.k) -> k) $ streamUp (Z:.l) (Z:.h) +instance IndexStream (Letter l n) where + streamUp l h = map (\(Z:.k) -> k) $ streamUp (ZZ:..l) (ZZ:..h) + streamDown l h = map (\(Z:.k) -> k) $ streamDown (ZZ:..l) (ZZ:..h) {-# Inline streamUp #-} - streamDown l h = map (\(Z:.k) -> k) $ streamDown (Z:.l) (Z:.h) {-# Inline streamDown #-} diff --git a/Biobase/Primary/Nuc/Conversion.hs b/Biobase/Primary/Nuc/Conversion.hs --- a/Biobase/Primary/Nuc/Conversion.hs +++ b/Biobase/Primary/Nuc/Conversion.hs @@ -1,9 +1,9 @@ -{-# Language CPP #-} - -#if __GLASGOW_HASKELL__ < 710 -{-# LANGUAGE OverlappingInstances #-} -#endif +-- {-# Language CPP #-} +-- +-- #if __GLASGOW_HASKELL__ < 710 +-- {-# LANGUAGE OverlappingInstances #-} +-- #endif -- | Convert between different nucleotide representations @@ -12,7 +12,7 @@ import Control.Lens (iso, from) import qualified Data.Vector.Unboxed as VU -import Biobase.Types.Sequence (Transcribe(..)) +import Biobase.Types.BioSequence (Transcribe(..),RNA,DNA) import Biobase.Primary.Letter (Letter(..), Primary) import qualified Biobase.Primary.Nuc.DNA as D @@ -90,23 +90,23 @@ -- ** Transcription between RNA and DNA. Both on the individual sequence level, -- and on the level of primary sequence data. -instance Transcribe (Letter R.RNA) where - type TranscribeTo (Letter R.RNA) = Letter D.DNA +instance Transcribe (Letter RNA n) where + type TranscribeTo (Letter RNA n) = Letter DNA n transcribe = iso rnaTdna dnaTrna {-# Inline transcribe #-} -instance Transcribe (Letter D.DNA) where - type TranscribeTo (Letter D.DNA) = Letter R.RNA +instance Transcribe (Letter DNA n) where + type TranscribeTo (Letter DNA n) = Letter RNA n transcribe = from transcribe {-# Inline transcribe #-} -instance Transcribe (Primary R.RNA) where - type TranscribeTo (Primary R.RNA) = Primary D.DNA +instance Transcribe (Primary RNA n) where + type TranscribeTo (Primary RNA n) = Primary DNA n transcribe = iso (VU.map rnaTdna) (VU.map dnaTrna) {-# Inline transcribe #-} -instance Transcribe (Primary D.DNA) where - type TranscribeTo (Primary D.DNA) = Primary R.RNA +instance Transcribe (Primary DNA n) where + type TranscribeTo (Primary DNA n) = Primary RNA n transcribe = iso (VU.map dnaTrna) (VU.map rnaTdna) {-# Inline transcribe #-} diff --git a/Biobase/Primary/Nuc/DNA.hs b/Biobase/Primary/Nuc/DNA.hs --- a/Biobase/Primary/Nuc/DNA.hs +++ b/Biobase/Primary/Nuc/DNA.hs @@ -17,24 +17,22 @@ import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU +import Biobase.Types.BioSequence (DNA) + import Biobase.Primary.Bounds import Biobase.Primary.Letter --- | DNA nucleotides. - -data DNA - -- Single-character names for nucleotides. -pattern A = Letter 0 :: Letter DNA -pattern C = Letter 1 :: Letter DNA -pattern G = Letter 2 :: Letter DNA -pattern T = Letter 3 :: Letter DNA -pattern N = Letter 4 :: Letter DNA +pattern A = Letter 0 :: Letter DNA n +pattern C = Letter 1 :: Letter DNA n +pattern G = Letter 2 :: Letter DNA n +pattern T = Letter 3 :: Letter DNA n +pattern N = Letter 4 :: Letter DNA n -instance Enum (Letter DNA) where +instance Enum (Letter DNA n) where succ N = error "succ/N:DNA" succ (Letter x) = Letter $ x+1 pred A = error "pred/A:DNA" @@ -43,7 +41,7 @@ toEnum k = error $ "toEnum/Letter DNA " ++ show k fromEnum (Letter k) = k -instance LetterChar DNA where +instance LetterChar DNA n where letterChar = dnaChar charLetter = charDNA @@ -53,7 +51,7 @@ --instance (MkPrimary (VU.Vector Char) DNA) => FromJSON (Primary DNA) where -- parseJSON = fmap (primary :: String -> Primary DNA) . parseJSON -acgt :: [Letter DNA] +acgt :: [Letter DNA n] acgt = [A .. T] charDNA = toUpper >>> \case @@ -76,28 +74,28 @@ -- underlying @Char@s actually represent a DNA sequence. This allows typesafe -- modification of DNA sequences since only @[A,C,G,T,N]@ are allowed. -cdna ∷ Iso' Char (Letter DNA) +cdna ∷ Iso' Char (Letter DNA n) cdna = iso charDNA dnaChar -instance Show (Letter DNA) where +instance Show (Letter DNA n) where show c = [dnaChar c] -instance Read (Letter DNA) where +instance Read (Letter DNA n) where readsPrec p [] = [] readsPrec p (x:xs) | x==' ' = readsPrec p xs | otherwise = [(charDNA x, xs)] -dnaSeq :: MkPrimary n DNA => n -> Primary DNA +dnaSeq :: MkPrimary p DNA n => p -> Primary DNA n dnaSeq = primary -instance Bounded (Letter DNA) where +instance Bounded (Letter DNA n) where minBound = A maxBound = N -instance MkPrimary (VU.Vector Char) DNA where +instance MkPrimary (VU.Vector Char) DNA n where primary = VU.map charDNA -instance IsString [Letter DNA] where +instance IsString [Letter DNA n] where fromString = map charDNA diff --git a/Biobase/Primary/Nuc/RNA.hs b/Biobase/Primary/Nuc/RNA.hs --- a/Biobase/Primary/Nuc/RNA.hs +++ b/Biobase/Primary/Nuc/RNA.hs @@ -5,10 +5,12 @@ import Control.Lens (Iso', iso) import Data.Aeson import Data.Char (toUpper) +import Data.Data import Data.Ix (Ix(..)) import Data.Primitive.Types import Data.String import Data.Tuple (swap) +import Data.Typeable import qualified Data.ByteString.Builder as BB import qualified Data.ByteString.Char8 as BS import qualified Data.ByteString.Lazy.Char8 as BSL @@ -18,26 +20,24 @@ import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU +import Biobase.Types.BioSequence (RNA) + import Biobase.Primary.Bounds import Biobase.Primary.Letter --- | RNA nucleotides. - -data RNA - -pattern A = Letter 0 :: Letter RNA -pattern C = Letter 1 :: Letter RNA -pattern G = Letter 2 :: Letter RNA -pattern U = Letter 3 :: Letter RNA -pattern N = Letter 4 :: Letter RNA +pattern A = Letter 0 ∷ Letter RNA n +pattern C = Letter 1 ∷ Letter RNA n +pattern G = Letter 2 ∷ Letter RNA n +pattern U = Letter 3 ∷ Letter RNA n +pattern N = Letter 4 ∷ Letter RNA n -instance Bounded (Letter RNA) where +instance Bounded (Letter RNA n) where minBound = A maxBound = N -instance Enum (Letter RNA) where +instance Enum (Letter RNA n) where succ N = error "succ/N:RNA" succ (Letter x) = Letter $ x+1 pred A = error "pred/A:RNA" @@ -46,14 +46,14 @@ toEnum k = error $ "toEnum/Letter RNA " ++ show k fromEnum (Letter k) = k -instance LetterChar RNA where +instance LetterChar RNA n where letterChar = rnaChar charLetter = charRNA -instance ToJSON (Letter RNA) where +instance ToJSON (Letter RNA n) where toJSON = toJSON . letterChar -instance FromJSON (Letter RNA) where +instance FromJSON (Letter RNA n) where parseJSON = fmap charLetter . parseJSON -- We encode 'Primary RNA' directly as a string. @@ -64,10 +64,10 @@ -- toJSON = toJSON . VU.toList . VU.map letterChar -- --instance FromJSON (Primary RNA) where --- parseJSON = fmap (primary :: String -> Primary RNA) . parseJSON +-- parseJSON = fmap (primary ∷ String → Primary RNA) . parseJSON -acgu :: [Letter RNA] +acgu ∷ [Letter RNA n] acgu = [A .. U] charRNA = toUpper >>> \case @@ -84,30 +84,35 @@ G -> 'G' U -> 'U' N -> 'N' + _ -> '\9888' {-# INLINE rnaChar #-} -- | An isomorphism from 'Char' to 'Letter RNA'. This assumes that the -- underlying @Char@s actually represent an RNA sequence. This allows typesafe -- modification of RNA sequences since only @[A,C,G,U,N]@ are allowed. -crna ∷ Iso' Char (Letter RNA) +crna ∷ Iso' Char (Letter RNA n) crna = iso charRNA rnaChar -instance Show (Letter RNA) where +instance Show (Letter RNA n) where show c = [rnaChar c] -instance Read (Letter RNA) where +instance Read (Letter RNA n) where readsPrec p [] = [] readsPrec p (x:xs) | x==' ' = readsPrec p xs | otherwise = [(charRNA x, xs)] -rnaSeq :: MkPrimary n RNA => n -> Primary RNA +rnaSeq ∷ MkPrimary p RNA n ⇒ p → Primary RNA n rnaSeq = primary -instance MkPrimary (VU.Vector Char) RNA where +instance MkPrimary (VU.Vector Char) RNA n where primary = VU.map charRNA -instance IsString [Letter RNA] where +instance IsString [Letter RNA n] where fromString = map charRNA + +viennaPairs = [ (C,G), (G,C), (G,U), (U,G), (A,U), (U,A) ] +viennaPairsNN = viennaPairs ++ [ (N,N) ] + diff --git a/Biobase/Primary/Nuc/XNA.hs b/Biobase/Primary/Nuc/XNA.hs --- a/Biobase/Primary/Nuc/XNA.hs +++ b/Biobase/Primary/Nuc/XNA.hs @@ -16,6 +16,8 @@ import qualified Data.Vector.Unboxed as VU import Control.Category ((>>>)) +import Biobase.Types.BioSequence + import Biobase.Primary.Bounds import Biobase.Primary.Letter @@ -23,20 +25,18 @@ -- | Combine both, RNA and DNA. -data XNA - -pattern A = Letter 0 :: Letter XNA -pattern C = Letter 1 :: Letter XNA -pattern G = Letter 2 :: Letter XNA -pattern T = Letter 3 :: Letter XNA -pattern U = Letter 4 :: Letter XNA -pattern N = Letter 5 :: Letter XNA +pattern A = Letter 0 :: Letter XNA n +pattern C = Letter 1 :: Letter XNA n +pattern G = Letter 2 :: Letter XNA n +pattern T = Letter 3 :: Letter XNA n +pattern U = Letter 4 :: Letter XNA n +pattern N = Letter 5 :: Letter XNA n -instance Bounded (Letter XNA) where +instance Bounded (Letter XNA n) where minBound = A maxBound = N -instance Enum (Letter XNA) where +instance Enum (Letter XNA n) where succ N = error "succ/N:XNA" succ (Letter x) = Letter $ x+1 pred A = error "pred/A:XNA" @@ -45,7 +45,7 @@ toEnum k = error $ "toEnum/Letter XNA " ++ show k fromEnum (Letter k) = k -instance LetterChar XNA where +instance LetterChar XNA n where letterChar = xnaChar charLetter = charXNA @@ -73,21 +73,21 @@ N -> 'N' {-# INLINE xnaChar #-} -instance Show (Letter XNA) where +instance Show (Letter XNA n) where show c = [xnaChar c] -instance Read (Letter XNA) where +instance Read (Letter XNA n) where readsPrec p [] = [] readsPrec p (x:xs) | x==' ' = readsPrec p xs | otherwise = [(charXNA x, xs)] -xnaSeq :: MkPrimary n XNA => n -> Primary XNA +xnaSeq :: MkPrimary p XNA n => p -> Primary XNA n xnaSeq = primary -instance MkPrimary (VU.Vector Char) XNA where +instance MkPrimary (VU.Vector Char) XNA n where primary = VU.map charXNA -instance IsString [Letter XNA] where +instance IsString [Letter XNA n] where fromString = map charXNA diff --git a/Biobase/Primary/Pretty.hs b/Biobase/Primary/Pretty.hs --- a/Biobase/Primary/Pretty.hs +++ b/Biobase/Primary/Pretty.hs @@ -16,15 +16,15 @@ newtype Pretty f a = Pretty { getPretty :: f a } -instance (LetterChar x) => ToJSON (Pretty VU.Vector (Letter x)) where +instance (LetterChar x n) => ToJSON (Pretty VU.Vector (Letter x n)) where toJSON = String . T.pack . map letterChar . VU.toList . getPretty -instance (LetterChar x) => ToJSON (Pretty V.Vector (Letter x)) where +instance (LetterChar x n) => ToJSON (Pretty V.Vector (Letter x n)) where toJSON = String . T.pack . map letterChar . V.toList . getPretty -instance (LetterChar x, VS.Storable (Letter x)) => ToJSON (Pretty VS.Vector (Letter x)) where +instance (LetterChar x n, VS.Storable (Letter x n)) => ToJSON (Pretty VS.Vector (Letter x n)) where toJSON = String . T.pack . map letterChar . VS.toList . getPretty -instance (LetterChar x) => ToJSON (Pretty [] (Letter x)) where +instance (LetterChar x n) => ToJSON (Pretty [] (Letter x n)) where toJSON = String . T.pack . map letterChar . getPretty diff --git a/Biobase/Primary/Trans.hs b/Biobase/Primary/Trans.hs --- a/Biobase/Primary/Trans.hs +++ b/Biobase/Primary/Trans.hs @@ -15,62 +15,65 @@ module Biobase.Primary.Trans where +import Control.Lens import Control.Arrow ((***)) import Data.ByteString.Char8 (ByteString,unpack) -import Data.FileEmbed (embedFile) import Data.Map.Strict (Map) import Data.Tuple (swap) import qualified Data.Map.Strict as M import qualified Data.Vector.Unboxed as VU +import Biobase.Types.BioSequence +import Biobase.Types.Codon + import Biobase.Primary.AA import Biobase.Primary.Nuc import Biobase.Primary.Letter +import Biobase.GeneticCodes.Translation +import Biobase.GeneticCodes.Types --- | Using the codon table, create an amino acid sequence from a @DNA@ --- sequence (encoded as 'Primary DNA'). Suffixed @seq@ as we deal with --- sequences, not letters. - -dnaAAseq :: Primary DNA -> Primary AA -dnaAAseq = VU.fromList . go where - go (VU.length -> 0) = [] - go (VU.splitAt 3 -> (hs,ts)) = case M.lookup hs dnaAAmap of - Just aa -> aa : go ts - _ -> error $ "dnaAAseq: " ++ show (hs,ts) - --- | Transform an amino acid sequence back into DNA. --- --- WARNING: This is lossy! - -aaDNAseq :: Primary AA -> Primary DNA -aaDNAseq = VU.concatMap go where - go aa = case M.lookup aa aaDNAmap of - Just codon -> codon - Nothing -> error $ "aaDNAseq" ++ show aa - - --- * Embedded codon data - --- | Lossy backtransformation. - -aaDNAmap :: M.Map (Letter AA) (Primary DNA) -aaDNAmap = M.fromList . map swap . M.assocs $ dnaAAmap -{-# NOINLINE aaDNAmap #-} - -dnaAAmap :: Map (Primary DNA) (Letter AA) -dnaAAmap = M.fromList . map (primary *** charAA) . M.assocs $ codonTable where -{-# NOINLINE dnaAAmap #-} +-- | Transform translation tables into the @Letter DNA/Letter AA@ format. -codonTable :: Map String Char -codonTable = M.fromList . map (go . words) . lines . unpack $ codonListEmbedded where - go [cs,[c]] = (cs,c) - go e = error $ "codonTable:" ++ show e -{-# NOINLINE codonTable #-} +letterTranslationTable :: TranslationTable Char Char -> TranslationTable (Letter DNA n) (Letter AA n) +letterTranslationTable tbl = TranslationTable + { _codonToAminoAcid = M.fromList . map (ftriplet *** felement) . M.toList $ tbl^.codonToAminoAcid + , _aminoAcidtoCodons = M.fromList . map (charAA *** map felement) . M.toList $ tbl^.aminoAcidtoCodons + , _tableID = tbl^.tableID + , _tableName = tbl^.tableName + } where ftriplet :: Codon Char -> Codon (Letter DNA n) + ftriplet = over each charDNA + felement :: TranslationElement Char Char -> TranslationElement (Letter DNA n) (Letter AA n) + felement = over (baseCodon.each) charDNA . over aminoAcid charAA --- | Raw codon table +instance Translation (Codon (Letter DNA n)) where + type TargetType (Codon (Letter DNA n)) = Letter AA n + type CodonType (Codon (Letter DNA n)) = Letter DNA n + type AAType (Codon (Letter DNA n)) = Letter AA n + translate tbl t = maybe Unknown _aminoAcid $ M.lookup t (tbl^.codonToAminoAcid) + {-# Inline translate #-} + translateAllFrames = translate + {-# Inline translateAllFrames #-} -codonListEmbedded :: ByteString -codonListEmbedded = $(embedFile "sources/codontable") +instance Translation (Primary DNA n) where + type TargetType (Primary DNA n) = Primary AA n + type CodonType (Primary DNA n) = Letter DNA n + type AAType (Primary DNA n) = Letter AA n + -- | + -- + -- TODO we could consider returning @Nothing@ in case the input is not + -- power-of-three. + translate tbl xs = VU.unfoldrN (VU.length xs `div` 3) go xs + where go (VU.splitAt 3 -> (hs,ts)) + | VU.length hs < 3 = Nothing + | otherwise = Just (aa,ts) + where [a,b,c] = VU.toList hs + aa = translate tbl $ Codon a b c + {-# Inline translate #-} + translateAllFrames tbl xs = VU.unfoldrN (VU.length xs) go 0 + where go 0 = Just (Undef,1) + go 1 = Just (Undef,2) + go k = Just (translate tbl $ Codon (xs VU.! (k-2)) (xs VU.! (k-1)) (xs VU.! k), k+1) + {-# Inlinable translateAllFrames #-} diff --git a/Biobase/Primary/Unknown.hs b/Biobase/Primary/Unknown.hs --- a/Biobase/Primary/Unknown.hs +++ b/Biobase/Primary/Unknown.hs @@ -1,10 +1,13 @@ --- | A 'Letter' with unknown annotation. We sometimes want to encode that --- we are dealing with @Letter@s in an alphabet, but we do not want to --- commit to a certain alphabet (just yet). +-- | A 'Letter' with unknown annotation. We sometimes want to encode that we +-- are dealing with @Letter@s in an alphabet, but we do not want to commit to a +-- certain alphabet (just yet). -- -- This module allows us to make explicit that we do not know the specific -- alphabet type yet. +-- +-- One should NEVER blindly coerce, since the order and limits of @Letter@'s +-- might well be different. module Biobase.Primary.Unknown where @@ -44,44 +47,36 @@ -- | Creating an unknown letter. -unk :: Int -> Letter Unknown +unk ∷ Int → Letter Unknown n unk = Letter -- *** instances -instance Show (Letter Unknown) where +instance Show (Letter Unknown n) where show (Letter i) = "U " ++ show i -instance Read (Letter Unknown) where +instance Read (Letter Unknown n) where readPrec = parens $ do Lex.Ident u <- lexP case u of - "U" -> unk <$> readPrec - _ -> RP.pfail + "U" → unk <$> readPrec + _ → RP.pfail -instance Enum (Letter Unknown) where +instance Enum (Letter Unknown n) where succ (Letter x) = Letter $ x+1 pred (Letter x) = Letter $ x-1 toEnum = Letter fromEnum = getLetter -instance MkPrimary (VU.Vector Int) Unknown where +instance MkPrimary (VU.Vector Int) Unknown n where primary = VU.map Letter {-# Inline primary #-} -instance ToJSON (Letter Unknown) where +instance ToJSON (Letter Unknown n) where toJSON = toJSON . getLetter -instance FromJSON (Letter Unknown) where +instance FromJSON (Letter Unknown n) where parseJSON = fmap Letter . parseJSON - -{- -instance ToJSON (Primary Unknown) where - toJSON = toJSON . map (show . getLetter) . VU.toList - -instance FromJSON (Primary Unknown) where - parseJSON = fmap (VU.fromList . map (Letter . read)) . parseJSON --} diff --git a/Biobase/Secondary.hs b/Biobase/Secondary.hs --- a/Biobase/Secondary.hs +++ b/Biobase/Secondary.hs @@ -1,8 +1,8 @@ module Biobase.Secondary -- ( module Biobase.Secondary.Basepair - ( module Biobase.Secondary.Constraint - , module Biobase.Secondary.Diagrams +-- ( module Biobase.Secondary.Constraint + ( module Biobase.Secondary.Diagrams , module Biobase.Secondary.Isostericity , module Biobase.Secondary.Pseudoknots , module Biobase.Secondary.Structure @@ -10,7 +10,7 @@ ) where --import Biobase.Secondary.Basepair -import Biobase.Secondary.Constraint +--import Biobase.Secondary.Constraint import Biobase.Secondary.Diagrams import Biobase.Secondary.Isostericity import Biobase.Secondary.Pseudoknots diff --git a/Biobase/Secondary/Basepair.hs b/Biobase/Secondary/Basepair.hs --- a/Biobase/Secondary/Basepair.hs +++ b/Biobase/Secondary/Basepair.hs @@ -19,7 +19,7 @@ import Data.Primitive.Types import Data.Serialize (Serialize) import Data.Tuple (swap) -import Data.Vector.Fusion.Stream.Monadic (map,Step(..)) +import Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import Data.Vector.Unboxed.Deriving import GHC.Base (remInt,quotInt) import GHC.Generics @@ -28,6 +28,7 @@ import qualified Data.Vector.Unboxed as VU import Text.Read +import Biobase.Types.BioSequence import Data.PrimitiveArray hiding (Complement(..),map) import Biobase.Primary @@ -51,10 +52,11 @@ instance FromJSON Basepair instance ToJSON Basepair -deriving instance Index Basepair +instance Index Basepair where + newtype LimitType Basepair = LtBP Basepair instance IndexStream z => IndexStream (z:.Basepair) where - streamUp (ls:.BP l) (hs:.BP h) = flatten mk step $ streamUp ls hs + streamUp (ls:..LtBP (BP l)) (hs:..LtBP (BP h)) = flatten mk step $ streamUp ls hs where mk z = return (z,l) step (z,k) | k > h = return $ Done @@ -62,7 +64,7 @@ {-# Inline [0] mk #-} {-# Inline [0] step #-} {-# Inline streamUp #-} - streamDown (ls:.BP l) (hs:.BP h) = flatten mk step $ streamDown ls hs + streamDown (ls:..LtBP (BP l)) (hs:..LtBP (BP h)) = flatten mk step $ streamDown ls hs where mk z = return (z,h) step (z,k) | k < l = return $ Done @@ -218,7 +220,7 @@ -- | A pair as a tuple containing 'Nuc's. -type Pair = (Letter RNA,Letter RNA) +type Pair n = (Letter RNA n, Letter RNA n) -- | Annotation for a basepair. @@ -230,7 +232,7 @@ -- | An extended basepair, with nucleotides an annotation. -type ExtPair = (Pair,ExtPairAnnotation) +type ExtPair n = (Pair n, ExtPairAnnotation) diff --git a/Biobase/Secondary/Constraint.hs b/Biobase/Secondary/Constraint.hs deleted file mode 100644 --- a/Biobase/Secondary/Constraint.hs +++ /dev/null @@ -1,107 +0,0 @@ - --- | Simple oldstyle RNAfold constraints. A constraint yields a bonus or --- malus to energy. - -module Biobase.Secondary.Constraint where - -import Data.Char (toLower) -import Data.Primitive.Types -import Prelude as P -import qualified Data.Vector.Generic as VG -import qualified Data.Vector.Generic.Mutable as VGM -import qualified Data.Vector.Unboxed as VU - -import Data.PrimitiveArray - -import Biobase.Secondary.Diagrams - - - --- | We can create a constraint from different sources. - -class MkConstraint a where - mkConstraint :: a -> Constraint - --- | A constraint is nothing more than a vector of constraint characters --- together with a possible pairing for each character. - -newtype Constraint = Constraint {unConstraint :: VU.Vector (Char,Int)} - deriving (Show,Read,Eq) - -bonusCC :: VU.Vector Char -bonusCC = VU.fromList "()<>|" -{-# NOINLINE bonusCC #-} - -nobonusCC :: VU.Vector Char -nobonusCC = VU.fromList ".x" -{-# NOINLINE nobonusCC #-} - --- | Given a 'Constraint', create an NxN matrix with bonus energies. These --- energies can be included in all pair-creating functions and will disallow or --- strongly favor certain pairings, while others will receive neither bonus nor --- malus. --- --- In case, a pair (i,j) is annotated as both, bonus- and malus-receiving, it --- will be set to receive a malus. This can happen, if something like "<" would --- give a bonus, but "x" gives a malus (and other cases). --- --- TODO and again, we should parametrize over "Energy", "Score", etc (that is, --- Prim a) - -bonusTable :: Double -> Double -> Constraint -> Unboxed (Z:.Int:.Int) Double -bonusTable bonus malus (Constraint constraint) = arr where - arr = fromAssocs (Z:.0:.0) (Z:.n:.n) 0 $ bonusBr ++ bonusAn ++ bonusBa ++ malusBr ++ malusAn ++ malusX - n = VU.length constraint -1 - infixl 1 `xor` - xor a b = a && not b || not a && b - -- "()" bonus energies - bonusBr = [ (Z:.i:.j,bonus) - | (i,('(',j)) <- zip [0..] $ VU.toList constraint - ] - malusBr = [ (Z:.i:.j,malus) - | i <- [0..n] - , j <- [i..n] - , let bi = constraint VU.! i - , let bj = constraint VU.! j - , fst bi == '(' && snd bi /= j || fst bj == ')' && snd bj /= i - ] - bonusAn = [ (Z:.i:.j,bonus) - | i<-[0..n] - , fst (constraint VU.! i) == '<' - , j<-[i+1..n] - ] ++ - [ (Z:.i:.j,bonus) - | j<-[0..n] - , fst (constraint VU.! j) == '>' - , i<-[0..j-1] - ] - malusAn = [ (Z:.i:.j,malus) - | i<-[0..n] - , j<-[i+1..n] - , fst (constraint VU.! j) == '<' - ] ++ - [ (Z:.i:.j,malus) - | i<-[0..n] - , j<-[i+1..n] - , fst (constraint VU.! i) == '>' - ] - bonusBa = [ (Z:.i:.j,bonus) - | i<-[0..n] - , j<-[i+1..n] - , fst (constraint VU.! i) == '|' || fst (constraint VU.! j) == '|' - ] - malusX = [ (Z:.i:.j,malus) - | i<-[0..n] - , j<-[i+1..n] - , fst (constraint VU.! i) == 'x' || fst (constraint VU.! j) == 'x' - ] - --- * Instances - -instance MkConstraint String where - mkConstraint xs = mkConstraint . VU.fromList . P.map toLower $ xs - -instance MkConstraint (VU.Vector Char) where - mkConstraint cs = Constraint $ VU.zip cs ks where - (D1S ks) = mkD1S cs - diff --git a/Biobase/Secondary/Convert.hs b/Biobase/Secondary/Convert.hs --- a/Biobase/Secondary/Convert.hs +++ b/Biobase/Secondary/Convert.hs @@ -4,6 +4,8 @@ module Biobase.Secondary.Convert where +import Biobase.Types.BioSequence + import Biobase.Primary.Letter import Biobase.Primary.Nuc.RNA import Biobase.Secondary.Basepair @@ -24,14 +26,14 @@ -- ** @(RNA,RNA) <-> Basepair@ -instance BasepairConvert (Letter RNA,Letter RNA) Basepair where +instance BasepairConvert (Letter RNA n,Letter RNA n) Basepair where basepairConvert (l,r) | l >= A && l <= U && r >= A && r <= U = BP $ 4 * getLetter l + getLetter r | otherwise = NoBP {-# Inline basepairConvert #-} -instance BasepairConvert Basepair (Letter RNA, Letter RNA) where +instance BasepairConvert Basepair (Letter RNA n, Letter RNA n) where basepairConvert k | k == NoBP || k == NS = (N,N) | otherwise = let (l,r) = getBP k `divMod` 4 in (Letter l, Letter r) @@ -41,7 +43,7 @@ -- ** @(RNA,RNA) <-> ViennaPair@ -instance BasepairConvert (Letter RNA, Letter RNA) ViennaPair where +instance BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair where basepairConvert = \case (C,G) -> SV.CG (G,C) -> SV.GC @@ -52,7 +54,7 @@ _ -> SV.NS {-# Inline basepairConvert #-} -instance BasepairConvert ViennaPair (Letter RNA, Letter RNA) where +instance BasepairConvert ViennaPair (Letter RNA n, Letter RNA n) where basepairConvert = \case SV.CG -> (C,G) SV.GC -> (G,C) diff --git a/Biobase/Secondary/Diagrams.hs b/Biobase/Secondary/Diagrams.hs --- a/Biobase/Secondary/Diagrams.hs +++ b/Biobase/Secondary/Diagrams.hs @@ -186,13 +186,13 @@ -- TODO Check size of hairpins and interior loops? isCanonicalStructure :: String -> Bool -isCanonicalStructure = all (`elem` "().") +isCanonicalStructure = all (flip (elem @[]) "().") -- | Is constraint type structure, i.e. there can also be symbols present -- that denote up- or downstream pairing. isConstraintStructure :: String -> Bool -isConstraintStructure = all (`elem` "().<>{}|") +isConstraintStructure = all (flip (elem @[]) "().<>{}|") -- | Take a structural string and split it into its constituents. -- @@ -253,11 +253,11 @@ g k st ('.':xs) = g (k+1) st xs g k st (x:xs) | l==x = g (k+1) (k:st) xs g k (s:st) (x:xs) | r==x = ((s,k):) <$> g (k+1) st xs - g k [] xs = fail $ printf "too many closing brackets at position %d: '%s' (dot-bracket: %s)" k xs str - g k st [] = fail $ printf "too many opening brackets, opening bracket(s) at: %s (dot-bracket: %s)" (show $ reverse st) str - g a b c = fail $ printf "unspecified error: %s (dot-bracket: %s)" (show (a,b,c)) str - f xs lr@(_:_:_:_) = fail $ printf "unsound dictionary: %s (dot-bracket: %s)" lr str - f xs lr = fail $ printf "unspecified error: dict: %s, input: %s (dot-bracket: %s)" lr xs str + g k [] xs = Left $ printf "too many closing brackets at position %d: '%s' (dot-bracket: %s)" k xs str + g k st [] = Left $ printf "too many opening brackets, opening bracket(s) at: %s (dot-bracket: %s)" (show $ reverse st) str + g a b c = Left $ printf "unspecified error: %s (dot-bracket: %s)" (show (a,b,c)) str + f xs lr@(_:_:_:_) = Left $ printf "unsound dictionary: %s (dot-bracket: %s)" lr str + f xs lr = Left $ printf "unspecified error: dict: %s, input: %s (dot-bracket: %s)" lr xs str -- | Calculates the distance between two vienna strings. diff --git a/Biobase/Secondary/Isostericity.hs b/Biobase/Secondary/Isostericity.hs --- a/Biobase/Secondary/Isostericity.hs +++ b/Biobase/Secondary/Isostericity.hs @@ -13,7 +13,7 @@ module Biobase.Secondary.Isostericity where import Data.ByteString.Char8 (ByteString) -import Data.FileEmbed (embedFile) +import Data.FileEmbed (makeRelativeToProject, embedFile) import Data.Function (on) import Data.List import Data.Tuple.Select @@ -43,7 +43,7 @@ -- -- TODO inClass missing -instance IsostericityLookup ExtPair where +instance IsostericityLookup (ExtPair n) where getClasses p | Just cs <- M.lookup p defaultIsostericityMap = cs @@ -54,7 +54,7 @@ -- -- TODO inClass missing -instance IsostericityLookup Pair where +instance IsostericityLookup (Pair n) where getClasses p | Just cs <- M.lookup (p,CWW) defaultIsostericityMap = cs @@ -77,7 +77,7 @@ -- | Process CSV list-of-lists to get the isostericity data. -mkIsostericityList :: [[[String]]] -> [(ExtPair, [String])] +mkIsostericityList :: [[[String]]] -> [(ExtPair n, [String])] mkIsostericityList gs = nubBy ((==) `on` fst) . concatMap turn . concatMap f $ gs where f g = map (\e -> ( ( let [x,y] = fst e in (charRNA x, charRNA y), read bpt @@ -86,11 +86,14 @@ ) $ map entry xs where bpt = head $ head g xs = tail g - entry x = (x!!0, map (filter (\z -> not $ z `elem` "()")) . takeWhile ('I' `elem`) . drop 2 $ x) + entry x = (x!!0, map (filter (\z -> not $ z `elem` bracket)) . takeWhile ('I' `elem`) . drop 2 $ x) + bracket :: String + bracket = "()" turn entry@(((x,y),(wc,tx,ty)), cs) = [entry, (((y,x),(wc,ty,tx)), cs)] -- | Simple parsing of raw CSV data. +parsedCSV :: [[[Field]]] parsedCSV = filter (not . null) gs where gs = map (filter ((""/=).head)) . groupBy (\x y -> ""/= (head y)) $ csv Right csv = parseCSV "isostericity/detailed" $ BS.unpack detailedCSV @@ -102,5 +105,5 @@ -- | Raw CSV data, embedded into the library. detailedCSV :: ByteString -detailedCSV = $(embedFile "sources/isostericity-detailed.csv") +detailedCSV = $(makeRelativeToProject "sources/isostericity-detailed.csv" >>= embedFile) diff --git a/Biobase/Secondary/New.hs b/Biobase/Secondary/New.hs --- a/Biobase/Secondary/New.hs +++ b/Biobase/Secondary/New.hs @@ -24,9 +24,9 @@ -- TODO Should be extended with @Extended@, but this requires knowing which of -- the ends overlap with paired: left, right, or both. -data SubStructure (t ∷ k) a - = Unpaired { _label ∷ !a } - | Paired { _label ∷ !a, _subStructures ∷ !(Vector (SubStructure t a)) } +data SubStructure (t :: *) a + = Unpaired { _label :: !a } + | Paired { _label :: !a, _subStructures :: !(Vector (SubStructure t a)) } deriving (Show, Read, Functor, Traversable, Foldable, Generic, Eq, Ord) makeLenses ''SubStructure makePrisms ''SubStructure @@ -34,8 +34,8 @@ -- | A full structure is composed of a number of sub-structures. The empty -- structure is a full structure. -newtype FullStructure (t ∷ k) a - = FullStructure { _fullStructure ∷ Vector (SubStructure t a) } +newtype FullStructure (t :: *) a + = FullStructure { _fullStructure :: Vector (SubStructure t a) } deriving (Show, Read, Functor, Traversable, Foldable, Generic, Eq, Ord) makeLenses ''FullStructure @@ -43,26 +43,26 @@ -- ** Parses a ViennaRNA secondary structure string. -pUnpaired ∷ Parser (SubStructure () ()) +pUnpaired :: Parser (SubStructure () ()) pUnpaired = Unpaired () <$ char '.' {-# Inlinable pUnpaired #-} -pPaired ∷ Parser (SubStructure () ()) +pPaired :: Parser (SubStructure () ()) pPaired = Paired () <$ char '(' <*> (fromList <$> many pSubStructure) <* char ')' {-# Inlinable pPaired #-} -pSubStructure ∷ Parser (SubStructure () ()) +pSubStructure :: Parser (SubStructure () ()) pSubStructure = pUnpaired <|> pPaired {-# Inlinable pSubStructure #-} -pFullStructure ∷ Parser (FullStructure () ()) +pFullStructure :: Parser (FullStructure () ()) pFullStructure = FullStructure <$> fromList <$> many pSubStructure <* endOfInput {-# Inlinable pFullStructure #-} newtype StructureParseError = StructureParseError String deriving (Show) -parseVienna ∷ MonadError StructureParseError m ⇒ ByteString → m (FullStructure () ()) +parseVienna :: MonadError StructureParseError m ⇒ ByteString -> m (FullStructure () ()) parseVienna = either (throwError . StructureParseError) return . parseOnly pFullStructure {-# Inlinable parseVienna #-} @@ -83,19 +83,19 @@ -- @ toTree - ∷ (SubStructure t a → Maybe b) + :: (SubStructure t a -> Maybe b) -- ^ how to handle substructure elements? @Nothing@ means discard this -- substructure and all children. - → b + -> b -- ^ The root label - → FullStructure (t ∷ k) a + -> FullStructure (t :: *) a -- ^ The @FullStructure@ to transform into a @Tree@. - → Tree b + -> Tree b toTree f r (FullStructure ts) = Node r $ fmap go ts ^.. traverse . _Just where go u@Unpaired{} = (`Node` []) <$> f u go p@Paired{} = case f p of - Nothing → Nothing - Just lbl → Just $ Node lbl $ (fmap go $ p^.subStructures) ^.. traverse . _Just + Nothing -> Nothing + Just lbl -> Just $ Node lbl $ (fmap go $ p^.subStructures) ^.. traverse . _Just {-# Inlinable toTree #-} diff --git a/Biobase/Secondary/Vienna.hs b/Biobase/Secondary/Vienna.hs --- a/Biobase/Secondary/Vienna.hs +++ b/Biobase/Secondary/Vienna.hs @@ -9,7 +9,7 @@ import Data.Primitive.Types import Data.Serialize (Serialize(..)) import Data.Tuple (swap) -import Data.Vector.Fusion.Stream.Monadic (map,Step(..)) +import Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import Data.Vector.Unboxed.Deriving import GHC.Base (remInt,quotInt) import GHC.Generics (Generic) @@ -20,6 +20,7 @@ import qualified Prelude as P import Data.PrimitiveArray hiding (Complement(..),map) +import Biobase.Types.BioSequence import Biobase.Primary.Letter import Biobase.Primary.Nuc @@ -32,46 +33,45 @@ newtype ViennaPair = ViennaPair { unViennaPair :: Int } deriving (Eq,Ord,Generic,Ix) +derivingUnbox "ViennaPair" + [t| ViennaPair -> Int |] + [| unViennaPair |] + [| ViennaPair |] + instance Binary (ViennaPair) instance Serialize (ViennaPair) instance FromJSON (ViennaPair) instance ToJSON (ViennaPair) instance Index ViennaPair where - linearIndex _ _ (ViennaPair p) = p + data LimitType ViennaPair + = Canonical | Extended + linearIndex _ (ViennaPair p) = p {-# Inline linearIndex #-} - smallestLinearIndex _ = error "still needed?" - {-# Inline smallestLinearIndex #-} - largestLinearIndex (ViennaPair p) = p - {-# Inline largestLinearIndex #-} - size _ (ViennaPair h) = h+1 + size h = case h of { Canonical → 7; Extended → 9 } {-# Inline size #-} - inBounds (ViennaPair l) (ViennaPair h) (ViennaPair p) = l <= p && p <= h + inBounds h (ViennaPair p) = 0 <= p && p < size h {-# Inline inBounds #-} instance IndexStream z => IndexStream (z:.ViennaPair) where - streamUp (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamUp ls hs - where mk z = return (z,l) + streamUp (ls:..l) (hs:..h) = flatten mk step $ streamUp ls hs + where mk z = return (z,size l - 1) step (z,k) - | k > h = return $ Done - | otherwise = return $ Yield (z:.ViennaPair k) (z,k+1) + | k > size h -1 = return $ Done + | otherwise = return $ Yield (z:.ViennaPair k) (z,k+1) {-# Inline [0] mk #-} {-# Inline [0] step #-} {-# Inline streamUp #-} - streamDown (ls:.ViennaPair l) (hs:.ViennaPair h) = flatten mk step $ streamDown ls hs - where mk z = return (z,h) + streamDown (ls:..l) (hs:..h) = flatten mk step $ streamDown ls hs + where mk z = return (z,size h - 1) step (z,k) - | k < l = return $ Done - | otherwise = return $ Yield (z:.ViennaPair k) (z,k-1) + | k < size l -1 = return $ Done + | otherwise = return $ Yield (z:.ViennaPair k) (z,k-1) {-# Inline [0] mk #-} {-# Inline [0] step #-} {-# Inline streamDown #-} instance IndexStream ViennaPair where - streamUp l h = map (\(Z:.k) -> k) $ streamUp (Z:.l) (Z:.h) - {-# Inline streamUp #-} - streamDown l h = map (\(Z:.k) -> k) $ streamDown (Z:.l) (Z:.h) - {-# Inline streamDown #-} @@ -112,7 +112,7 @@ {-# INLINE fromViennaPair #-} -} -isViennaPair :: Letter RNA -> Letter RNA -> Bool +isViennaPair :: Letter RNA m -> Letter RNA n -> Bool isViennaPair l r = l==C && r==G || l==G && r==C || l==A && r==U @@ -121,8 +121,8 @@ || l==U && r==G {-# INLINE isViennaPair #-} -viennaPairTable :: Unboxed (Z:.Letter RNA:.Letter RNA) ViennaPair -viennaPairTable = fromAssocs (Z:.N:.N) (Z:.U:.U) NS +viennaPairTable :: Unboxed (Z:.Letter RNA n:.Letter RNA n) ViennaPair +viennaPairTable = fromAssocs (ZZ:..LtLetter maxBound:..LtLetter maxBound) NS [ (Z:.C:.G , CG) , (Z:.G:.C , GC) , (Z:.G:.U , GU) @@ -180,7 +180,4 @@ cguaP = [CG .. UA] cgnsP = [CG .. NS] pairToString = [(CG,"CG"),(GC,"GC"),(UA,"UA"),(AU,"AU"),(GU,"GU"),(UG,"UG"),(NS,"NS"),(NP,"NP")] - -derivingUnbox "ViennaPair" - [t| ViennaPair -> Int |] [| unViennaPair |] [| ViennaPair |] diff --git a/BiobaseXNA.cabal b/BiobaseXNA.cabal --- a/BiobaseXNA.cabal +++ b/BiobaseXNA.cabal @@ -1,18 +1,18 @@ +cabal-version: 2.2 name: BiobaseXNA -version: 0.10.0.0 +version: 0.11.1.1 author: Christian Hoener zu Siederdissen maintainer: choener@bioinf.uni-leipzig.de homepage: https://github.com/choener/BiobaseXNA bug-reports: https://github.com/choener/BiobaseXNA/issues -copyright: Christian Hoener zu Siederdissen, 2011 - 2017 +copyright: Christian Hoener zu Siederdissen, 2011 - 2021 category: Bioinformatics synopsis: Efficient RNA/DNA/Protein Primary/Secondary Structure -license: GPL-3 +license: BSD-3-Clause license-file: LICENSE build-type: Simple stability: experimental -tested-with: GHC == 7.10.3, GHC == 8.0.1 -cabal-version: >= 1.10.0 +tested-with: GHC == 8.8, GHC == 8.10, GHC == 9.0 description: This is a base library for bioinformatics with emphasis on RNA and DNA primary structure as well as amino acid sequences. @@ -45,8 +45,7 @@ sources/iupac-nucleotides - -library +common deps build-depends: base >= 4.7 && < 5.0 , aeson >= 1.0 , attoparsec >= 0.13 @@ -57,6 +56,7 @@ , cereal-vector >= 0.2 , containers >= 0.5 , csv >= 0.1 + , data-default >= 0.7 , deepseq >= 1.3 , file-embed >= 0.0.8 , hashable >= 1.2 @@ -67,55 +67,37 @@ , split >= 0.2 , text >= 1.0 , tuple >= 0.3 - , vector >= 0.10 + , vector >= 0.11 , vector-binary-instances >= 0.2 , vector-th-unbox >= 0.2 -- , bimaps == 0.1.0.* - , BiobaseTypes == 0.1.3.* - , ForestStructures == 0.0.0.* - , PrimitiveArray == 0.8.0.* - exposed-modules: - Biobase.Primary - Biobase.Primary.AA - Biobase.Primary.Bounds - Biobase.Primary.Hashed - Biobase.Primary.IUPAC - Biobase.Primary.Letter - Biobase.Primary.Nuc - Biobase.Primary.Nuc.Conversion - Biobase.Primary.Nuc.DNA - Biobase.Primary.Nuc.RNA - Biobase.Primary.Nuc.XNA - Biobase.Primary.Pretty - Biobase.Primary.Trans - Biobase.Primary.Unknown - Biobase.Secondary - Biobase.Secondary.New - Biobase.Secondary.Basepair - Biobase.Secondary.Constraint - Biobase.Secondary.Convert - Biobase.Secondary.Diagrams - Biobase.Secondary.Isostericity - Biobase.Secondary.Pseudoknots - Biobase.Secondary.Structure - Biobase.Secondary.Vienna + , BiobaseENA == 0.0.0.* + , BiobaseTypes == 0.2.1.* + , DPutils == 0.1.1.* + , ForestStructures == 0.0.1.* + , PrimitiveArray == 0.10.1.* default-extensions: BangPatterns + , DataKinds + , DeriveDataTypeable + , DeriveFunctor , DeriveGeneric + , DeriveGeneric + , DeriveTraversable , EmptyDataDecls , FlexibleContexts , FlexibleInstances , GeneralizedNewtypeDeriving , LambdaCase - , PolyKinds - , DeriveFunctor - , DeriveTraversable - , DeriveGeneric , MultiParamTypeClasses , PatternSynonyms + , PolyKinds + , RankNTypes + , RecordWildCards , ScopedTypeVariables , StandaloneDeriving , TemplateHaskell + , TypeApplications , TypeFamilies , TypeOperators , UndecidableInstances @@ -127,8 +109,42 @@ -O2 -funbox-strict-fields +library + import: + deps + exposed-modules: + -- new + Biobase.Primary.AA + Biobase.Primary.Letter + Biobase.Primary.Nuc.RNA + Biobase.Primary.Unknown + -- old + Biobase.Primary + Biobase.Primary.Bounds + Biobase.Primary.Hashed + Biobase.Primary.IUPAC + Biobase.Primary.Nuc + Biobase.Primary.Nuc.Conversion + Biobase.Primary.Nuc.DNA + Biobase.Primary.Nuc.XNA + Biobase.Primary.Pretty + Biobase.Primary.Trans + Biobase.Secondary + Biobase.Secondary.New + Biobase.Secondary.Basepair +-- Biobase.Secondary.Constraint + Biobase.Secondary.Convert + Biobase.Secondary.Diagrams + Biobase.Secondary.Isostericity + Biobase.Secondary.Pseudoknots + Biobase.Secondary.Structure + Biobase.Secondary.Vienna + + executable SubOptDistance + import: + deps build-depends: base , BiobaseXNA , cmdargs >= 0.10 @@ -136,18 +152,12 @@ SubOptDistance.hs hs-source-dirs: src - default-language: - Haskell2010 - default-extensions: DeriveDataTypeable - , NoMonomorphismRestriction - , RecordWildCards - , ScopedTypeVariables - ghc-options: - -O2 test-suite properties + import: + deps type: exitcode-stdio-1.0 main-is: @@ -165,7 +175,6 @@ , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-th >= 0.1 - , vector -- , BiobaseXNA diff --git a/LICENSE b/LICENSE --- a/LICENSE +++ b/LICENSE @@ -1,675 +1,30 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. +Copyright Christian Hoener zu Siederdissen 2011-2019 - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: +All rights reserved. - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. + * Neither the name of Christian Hoener zu Siederdissen nor the names of other + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ -[![Build Status](https://travis-ci.org/choener/BiobaseXNA.svg?branch=master)](https://travis-ci.org/choener/BiobaseXNA) +![github action: master](https://github.com/choener/BiobaseXNA/actions/workflows/ci.yml/badge.svg?branch=master) +![github action: hackage](https://github.com/choener/SciBaseTypes/actions/workflows/hackage.yml/badge.svg) # BiobaseXNA diff --git a/changelog.md b/changelog.md --- a/changelog.md +++ b/changelog.md @@ -1,3 +1,11 @@ +0.11.0.1 +-------- + +- version bump + +0.11.0.0 +-------- + 0.10.0.0 --------