BiobaseXNA 0.9.3.1 → 0.11.1.1
raw patch · 23 files changed
Files
- Biobase/Primary/AA.hs +65/−47
- Biobase/Primary/Hashed.hs +6/−6
- Biobase/Primary/IUPAC.hs +29/−27
- Biobase/Primary/Letter.hs +86/−42
- Biobase/Primary/Nuc/Conversion.hs +90/−61
- Biobase/Primary/Nuc/DNA.hs +25/−19
- Biobase/Primary/Nuc/RNA.hs +36/−23
- Biobase/Primary/Nuc/XNA.hs +16/−16
- Biobase/Primary/Pretty.hs +4/−4
- Biobase/Primary/Trans.hs +45/−42
- Biobase/Primary/Unknown.hs +15/−20
- Biobase/Secondary.hs +7/−7
- Biobase/Secondary/Basepair.hs +92/−144
- Biobase/Secondary/Constraint.hs +0/−107
- Biobase/Secondary/Convert.hs +93/−0
- Biobase/Secondary/Diagrams.hs +9/−7
- Biobase/Secondary/Isostericity.hs +13/−10
- Biobase/Secondary/New.hs +101/−0
- Biobase/Secondary/Vienna.hs +26/−72
- BiobaseXNA.cabal +64/−43
- LICENSE +24/−669
- README.md +2/−1
- changelog.md +13/−0
Biobase/Primary/AA.hs view
@@ -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
Biobase/Primary/Hashed.hs view
@@ -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
Biobase/Primary/IUPAC.hs view
@@ -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)
Biobase/Primary/Letter.hs view
@@ -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 #-}
Biobase/Primary/Nuc/Conversion.hs view
@@ -1,16 +1,19 @@ -{-# Language CPP #-}--#if __GLASGOW_HASKELL__ < 710-{-# LANGUAGE OverlappingInstances #-}-#endif+-- {-# Language CPP #-}+-- +-- #if __GLASGOW_HASKELL__ < 710+-- {-# LANGUAGE OverlappingInstances #-}+-- #endif -- | Convert between different nucleotide representations module Biobase.Primary.Nuc.Conversion where +import Control.Lens (iso, from) import qualified Data.Vector.Unboxed as VU +import Biobase.Types.BioSequence (Transcribe(..),RNA,DNA)+ import Biobase.Primary.Letter (Letter(..), Primary) import qualified Biobase.Primary.Nuc.DNA as D import qualified Biobase.Primary.Nuc.RNA as R@@ -84,67 +87,93 @@ --- * Reverse-complement of characters.+-- ** Transcription between RNA and DNA. Both on the individual sequence level,+-- and on the level of primary sequence data. --- | Produce the complement of a RNA or DNA sequence. Does intentionally--- not work for XNA sequences as it is not possible to uniquely translate--- @A@ into either @U@ or @T@.+instance Transcribe (Letter RNA n) where+ type TranscribeTo (Letter RNA n) = Letter DNA n+ transcribe = iso rnaTdna dnaTrna+ {-# Inline transcribe #-} -class Complement s t where- complement :: s -> t+instance Transcribe (Letter DNA n) where+ type TranscribeTo (Letter DNA n) = Letter RNA n+ transcribe = from transcribe+ {-# Inline transcribe #-} --- | To 'transcribe' a DNA sequence into RNA we reverse the complement of--- the sequence.+instance Transcribe (Primary RNA n) where+ type TranscribeTo (Primary RNA n) = Primary DNA n+ transcribe = iso (VU.map rnaTdna) (VU.map dnaTrna)+ {-# Inline transcribe #-} -transcribe :: Primary D.DNA -> Primary R.RNA-transcribe = VU.reverse . complement+instance Transcribe (Primary DNA n) where+ type TranscribeTo (Primary DNA n) = Primary RNA n+ transcribe = iso (VU.map dnaTrna) (VU.map rnaTdna)+ {-# Inline transcribe #-} -instance Complement (Letter R.RNA) (Letter R.RNA) where- complement = \case- R.A -> R.U- R.C -> R.G- R.G -> R.C- R.U -> R.A- R.N -> R.N -instance Complement (Letter D.DNA) (Letter D.DNA) where- complement = \case- D.A -> D.T- D.C -> D.G- D.G -> D.C- D.T -> D.A- D.N -> D.N--instance Complement (Letter D.DNA) (Letter R.RNA) where- complement = \case- D.A -> R.U- D.C -> R.G- D.G -> R.C- D.T -> R.A- D.N -> R.N--instance Complement (Letter R.RNA) (Letter D.DNA) where- complement = \case- R.A -> D.T- R.C -> D.G- R.G -> D.C- R.U -> D.A- R.N -> D.N--#if __GLASGOW_HASKELL__ >= 710-instance {-# OVERLAPPING #-}-#else-instance-#endif- ( Complement s t, VU.Unbox s, VU.Unbox t)- => Complement (VU.Vector s) (VU.Vector t)- where complement = VU.map complement+-- TODO to be removed soon -#if __GLASGOW_HASKELL__ >= 710-instance {-# Overlappable #-}-#else-instance-#endif- ( Complement s t, Functor f) => Complement (f s) (f t)- where complement = fmap complement+---- * Reverse-complement of characters.+--+---- | Produce the complement of a RNA or DNA sequence. Does intentionally+---- not work for XNA sequences as it is not possible to uniquely translate+---- @A@ into either @U@ or @T@.+--+--class Complement s t where+-- complement :: s -> t+--+---- | To 'transcribe' a DNA sequence into RNA we reverse the complement of+---- the sequence.+--+--transcribe :: Primary D.DNA -> Primary R.RNA+--transcribe = VU.reverse . complement+--+--instance Complement (Letter R.RNA) (Letter R.RNA) where+-- complement = \case+-- R.A -> R.U+-- R.C -> R.G+-- R.G -> R.C+-- R.U -> R.A+-- R.N -> R.N+--+--instance Complement (Letter D.DNA) (Letter D.DNA) where+-- complement = \case+-- D.A -> D.T+-- D.C -> D.G+-- D.G -> D.C+-- D.T -> D.A+-- D.N -> D.N+--+--instance Complement (Letter D.DNA) (Letter R.RNA) where+-- complement = \case+-- D.A -> R.U+-- D.C -> R.G+-- D.G -> R.C+-- D.T -> R.A+-- D.N -> R.N+--+--instance Complement (Letter R.RNA) (Letter D.DNA) where+-- complement = \case+-- R.A -> D.T+-- R.C -> D.G+-- R.G -> D.C+-- R.U -> D.A+-- R.N -> D.N+--+-- #if __GLASGOW_HASKELL__ >= 710+-- instance {-# OVERLAPPING #-}+-- #else+-- instance+-- #endif+-- ( Complement s t, VU.Unbox s, VU.Unbox t)+-- => Complement (VU.Vector s) (VU.Vector t)+-- where complement = VU.map complement+-- +-- #if __GLASGOW_HASKELL__ >= 710+-- instance {-# Overlappable #-}+-- #else+-- instance+-- #endif+-- ( Complement s t, Functor f) => Complement (f s) (f t)+-- where complement = fmap complement
Biobase/Primary/Nuc/DNA.hs view
@@ -1,6 +1,8 @@ module Biobase.Primary.Nuc.DNA where +import Control.Category ((>>>))+import Control.Lens (Iso', iso) import Data.Aeson import Data.Char (toUpper) import Data.Ix (Ix(..))@@ -14,26 +16,23 @@ import qualified Data.Vector.Generic as VG import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU-import Control.Category ((>>>)) +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"@@ -42,7 +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 @@ -52,7 +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@@ -71,25 +70,32 @@ N -> 'N' {-# INLINE dnaChar #-} -instance Show (Letter DNA) where+-- | An isomorphism from 'Char' to 'Letter DNA'. This assumes that the+-- 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 n)+cdna = iso charDNA dnaChar++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
Biobase/Primary/Nuc/RNA.hs view
@@ -1,12 +1,17 @@ module Biobase.Primary.Nuc.RNA where +import Control.Category ((>>>))+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 import qualified Data.Text as T@@ -14,29 +19,25 @@ import qualified Data.Vector.Generic as VG import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU-import Control.Category ((>>>))-import qualified Data.ByteString.Builder as BB +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"@@ -45,14 +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.@@ -63,10 +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@@ -83,23 +84,35 @@ G -> 'G' U -> 'U' N -> 'N'+ _ -> '\9888' {-# INLINE rnaChar #-} -instance Show (Letter RNA) where+-- | 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 n)+crna = iso charRNA rnaChar++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) ]+
Biobase/Primary/Nuc/XNA.hs view
@@ -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
Biobase/Primary/Pretty.hs view
@@ -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
Biobase/Primary/Trans.hs view
@@ -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 #-}
Biobase/Primary/Unknown.hs view
@@ -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--}
Biobase/Secondary.hs view
@@ -1,19 +1,19 @@ module Biobase.Secondary- ( module Biobase.Secondary.Basepair- , module Biobase.Secondary.Constraint- , module Biobase.Secondary.Diagrams+-- ( module Biobase.Secondary.Basepair+-- ( module Biobase.Secondary.Constraint+ ( module Biobase.Secondary.Diagrams , module Biobase.Secondary.Isostericity , module Biobase.Secondary.Pseudoknots , module Biobase.Secondary.Structure- , module Biobase.Secondary.Vienna+-- , module Biobase.Secondary.Vienna ) where -import Biobase.Secondary.Basepair-import Biobase.Secondary.Constraint+--import Biobase.Secondary.Basepair+--import Biobase.Secondary.Constraint import Biobase.Secondary.Diagrams import Biobase.Secondary.Isostericity import Biobase.Secondary.Pseudoknots import Biobase.Secondary.Structure-import Biobase.Secondary.Vienna+--import Biobase.Secondary.Vienna
Biobase/Secondary/Basepair.hs view
@@ -1,12 +1,11 @@ -{-# LANGUAGE FunctionalDependencies #-}---- {-# LANGUAGE OverlappingInstances #-}- -- | Secondary structure: define basepairs as Int-tuples, the three edges, a -- nucleotide can use for pairing and the cis/trans isomerism. Both edges and -- cis/trans come with a tag for "unknown". --+-- Since we often want to make "pairedness" explicit, we have a newtype for+-- this as well.+-- -- TODO set ext-annotations to be (isomerism,edge,edge) and have a asString -- instance to read "cWW" "tSH" and other notation. @@ -18,8 +17,9 @@ import Data.Ix (Ix(..)) import Data.List as L import Data.Primitive.Types-import Data.Serialize+import Data.Serialize (Serialize) import Data.Tuple (swap)+import Data.Vector.Fusion.Stream.Monadic (map,Step(..),flatten) import Data.Vector.Unboxed.Deriving import GHC.Base (remInt,quotInt) import GHC.Generics@@ -28,10 +28,95 @@ import qualified Data.Vector.Unboxed as VU import Text.Read +import Biobase.Types.BioSequence+import Data.PrimitiveArray hiding (Complement(..),map)+ import Biobase.Primary+import Biobase.Primary.Nuc.RNA+import Biobase.Primary.Nuc +-- * Newtype for efficient basepair encoding.++-- | Encode a base pair as a single @Int@.++newtype Basepair = BP { getBP :: Int }+ deriving (Eq,Ord,Ix,Generic)++derivingUnbox "Basepair"+ [t| Basepair -> Int |] [| getBP |] [| BP |]++instance Binary Basepair+instance Serialize Basepair+instance FromJSON Basepair+instance ToJSON Basepair++instance Index Basepair where+ newtype LimitType Basepair = LtBP Basepair++instance IndexStream z => IndexStream (z:.Basepair) where+ 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+ | otherwise = return $ Yield (z:.BP k) (z,k+1)+ {-# Inline [0] mk #-}+ {-# Inline [0] step #-}+ {-# Inline streamUp #-}+ 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+ | otherwise = return $ Yield (z:.BP k) (z,k-1)+ {-# Inline [0] mk #-}+ {-# Inline [0] step #-}+ {-# Inline streamDown #-}++instance IndexStream Basepair++pattern AA = BP 0+pattern AC = BP 1+pattern AG = BP 2+pattern AU = BP 3+pattern CA = BP 4+pattern CC = BP 5+pattern CG = BP 6+pattern CU = BP 7+pattern GA = BP 8+pattern GC = BP 9+pattern GG = BP 10+pattern GU = BP 11+pattern UA = BP 12+pattern UC = BP 13+pattern UG = BP 14+pattern UU = BP 15+pattern NS = BP 16+pattern NoBP = BP 17++{-+class MkBasepair a where+ mkBasepair :: a -> Basepair+ fromBasepair :: Basepair -> a++-- | If we get a "legal" base pair, we just create it, all other+-- combinations yield 'NoBP'. Non-standard base pairs have to be created+-- explicitly using @NS@. When going back to @a@, non-standard and no pair+-- yield @(N,N)@.++instance MkBasepair (Letter RNA,Letter RNA) where+ mkBasepair (l,r)+ | l >= A && l <= U && r >= A && r <= U+ = BP $ 4 * getLetter l + getLetter r+ | otherwise = NoBP+ fromBasepair k+ | k == NoBP || k == NS = (N,N)+ | otherwise = let (l,r) = getBP k `divMod` 4 in (Letter l, Letter r)+ {-# Inline mkBasepair #-}+ {-# Inline fromBasepair #-}+-}++ -- * Newtypes for extended secondary structures -- ** Encode which of three edges is engaged in base pairing@@ -51,41 +136,7 @@ instance FromJSON Edge instance ToJSON Edge --- TODO Index instances! -{--instance (Shape sh,Show sh) => Shape (sh :. Edge) where- rank (sh:._) = rank sh + 1- zeroDim = zeroDim:.Edge 0- unitDim = unitDim:.Edge 1 -- TODO does this one make sense?- intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2- addDim (sh1:.Edge n1) (sh2:.Edge n2) = addDim sh1 sh2 :. Edge (n1+n2) -- TODO will not necessarily yield a valid Edge- size (sh1:.Edge n) = size sh1 * n- sizeIsValid (sh1:.Edge n) = sizeIsValid (sh1:.n)- toIndex (sh1:.Edge sh2) (sh1':.Edge sh2') = toIndex (sh1:.sh2) (sh1':.sh2')- fromIndex (ds:.Edge d) n = fromIndex ds (n `quotInt` d) :. Edge r where- r | rank ds == 0 = n- | otherwise = n `remInt` d- inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx- listOfShape (sh:.Edge n) = n : listOfShape sh- shapeOfList xx = case xx of- [] -> error "empty list in shapeOfList/Primary"- x:xs -> shapeOfList xs :. Edge x- deepSeq (sh:.n) x = deepSeq sh (n `seq` x)- {-# INLINE rank #-}- {-# INLINE zeroDim #-}- {-# INLINE unitDim #-}- {-# INLINE intersectDim #-}- {-# INLINE addDim #-}- {-# INLINE size #-}- {-# INLINE sizeIsValid #-}- {-# INLINE toIndex #-}- {-# INLINE fromIndex #-}- {-# INLINE inShapeRange #-}- {-# INLINE listOfShape #-}- {-# INLINE shapeOfList #-}- {-# INLINE deepSeq #-}--} -- | Human-readable Show instance. @@ -131,42 +182,7 @@ instance FromJSON CTisomerism instance ToJSON CTisomerism --- TODO Index instances -{--instance (Shape sh,Show sh) => Shape (sh :. CTisomerism) where- rank (sh:._) = rank sh + 1- zeroDim = zeroDim:.CT 0- unitDim = unitDim:.CT 1 -- TODO does this one make sense?- intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2- addDim (sh1:.CT n1) (sh2:.CT n2) = addDim sh1 sh2 :. CT (n1+n2) -- TODO will not necessarily yield a valid CT- size (sh1:.CT n) = size sh1 * n- sizeIsValid (sh1:.CT n) = sizeIsValid (sh1:.n)- toIndex (sh1:.CT sh2) (sh1':.CT sh2') = toIndex (sh1:.sh2) (sh1':.sh2')- fromIndex (ds:.CT d) n = fromIndex ds (n `quotInt` d) :. CT r where- r | rank ds == 0 = n- | otherwise = n `remInt` d- inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx- listOfShape (sh:.CT n) = n : listOfShape sh- shapeOfList xx = case xx of- [] -> error "empty list in shapeOfList/Primary"- x:xs -> shapeOfList xs :. CT x- deepSeq (sh:.n) x = deepSeq sh (n `seq` x)- {-# INLINE rank #-}- {-# INLINE zeroDim #-}- {-# INLINE unitDim #-}- {-# INLINE intersectDim #-}- {-# INLINE addDim #-}- {-# INLINE size #-}- {-# INLINE sizeIsValid #-}- {-# INLINE toIndex #-}- {-# INLINE fromIndex #-}- {-# INLINE inShapeRange #-}- {-# INLINE listOfShape #-}- {-# INLINE shapeOfList #-}- {-# INLINE deepSeq #-}--}- -- | Human-readable Show instance. instance Show CTisomerism where@@ -204,7 +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. @@ -216,7 +232,7 @@ -- | An extended basepair, with nucleotides an annotation. -type ExtPair = (Pair,ExtPairAnnotation)+type ExtPair n = (Pair n, ExtPairAnnotation) @@ -241,72 +257,4 @@ pattern TWH = (Trn,W,H) pattern TWS = (Trn,W,S) pattern TWW = (Trn,W,W)------ * tuple-like selection------ the 'lens' library provides combinators that should make this--- superfluous.---- | Selection of nucleotides and/or type classes independent of which type we--- are looking at.--class BaseSelect a b | a -> b where- -- | select first index or nucleotide- baseL :: a -> b- -- | select second index or nucleotide- baseR :: a -> b- -- | select both nucleotides as pair- baseP :: a -> (b,b)- -- | select basepair type if existing or return default cWW- baseT :: a -> ExtPairAnnotation- -- | update first index or nucleotide- updL :: b -> a -> a- -- | update second index or nucleotide- updR :: b -> a -> a- -- | update complete pair- updP :: (b,b) -> a -> a- -- | update basepair type, error if not possible due to type a- updT :: ExtPairAnnotation -> a -> a---- | extended pairtype annotation given--instance BaseSelect ((a,a),ExtPairAnnotation) a where- baseL ((a,_),_) = a- baseR ((_,b),_) = b- baseP (lr ,_) = lr- baseT (_,t) = t- updL n ((_,y),t) = ((n,y),t)- updR n ((x,_),t) = ((x,n),t)- updP n (_,t) = (n,t)- updT n (xy,_) = (xy,n)- {-# INLINE baseL #-}- {-# INLINE baseR #-}- {-# INLINE baseP #-}- {-# INLINE baseT #-}- {-# INLINE updL #-}- {-# INLINE updR #-}- {-# INLINE updP #-}- {-# INLINE updT #-}---- | simple cis/wc-wc basepairs--instance BaseSelect (a,a) a where- baseL (a,_) = a- baseR (_,a) = a- baseP = id- baseT _ = CWW- updL n (_,y) = (n,y)- updR n (x,_) = (x,n)- updP n _ = n- updT n xy = if n==CWW then xy else error $ "updT on standard pairs can not update to: " ++ show n- {-# INLINE baseL #-}- {-# INLINE baseR #-}- {-# INLINE baseP #-}- {-# INLINE baseT #-}- {-# INLINE updL #-}- {-# INLINE updR #-}- {-# INLINE updP #-}- {-# INLINE updT #-}
− Biobase/Secondary/Constraint.hs
@@ -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-
+ Biobase/Secondary/Convert.hs view
@@ -0,0 +1,93 @@++-- | This module gives functionality to convert between different variants+-- of secondary structure elements.++module Biobase.Secondary.Convert where++import Biobase.Types.BioSequence++import Biobase.Primary.Letter+import Biobase.Primary.Nuc.RNA+import Biobase.Secondary.Basepair+import Biobase.Secondary.Vienna (ViennaPair(..))+import qualified Biobase.Secondary.Vienna as SV+import qualified Biobase.Secondary.Basepair as SB++++-- | @basepairConvert@ converts between different secondary structure base+-- pair representations. In general, the conversion is lossy, in particular+-- when "downsizing", say to @ViennaPair@.++class BasepairConvert a b where+ basepairConvert :: a -> b++++-- ** @(RNA,RNA) <-> Basepair@++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 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)+ {-# Inline basepairConvert #-}++++-- ** @(RNA,RNA) <-> ViennaPair@++instance BasepairConvert (Letter RNA n, Letter RNA n) ViennaPair where+ basepairConvert = \case+ (C,G) -> SV.CG+ (G,C) -> SV.GC+ (G,U) -> SV.GU+ (U,G) -> SV.UG+ (A,U) -> SV.AU+ (U,A) -> SV.UA+ _ -> SV.NS+ {-# Inline basepairConvert #-}++instance BasepairConvert ViennaPair (Letter RNA n, Letter RNA n) where+ basepairConvert = \case+ SV.CG -> (C,G)+ SV.GC -> (G,C)+ SV.GU -> (G,U)+ SV.UG -> (U,G)+ SV.AU -> (A,U)+ SV.UA -> (U,A)+ SV.NS -> (N,N)+ {-# Inline basepairConvert #-}++++-- ** @Basepair <-> ViennaPair@++instance BasepairConvert Basepair ViennaPair where+ basepairConvert = \case+ SB.AU -> SV.AU+ SB.CG -> SV.CG+ SB.GC -> SV.GC+ SB.GU -> SV.GU+ SB.UA -> SV.UA+ SB.UG -> SV.UG+ _ -> SV.NS+ {-# Inline basepairConvert #-}++instance BasepairConvert ViennaPair Basepair where+ basepairConvert = \case+ SV.AU -> SB.AU+ SV.CG -> SB.CG+ SV.GC -> SB.GC+ SV.GU -> SB.GU+ SV.UA -> SB.UA+ SV.UG -> SB.UG+ _ -> SB.NS+ {-# Inline basepairConvert #-}+
Biobase/Secondary/Diagrams.hs view
@@ -30,6 +30,8 @@ -- | RNA secondary structure with 1-diagrams. Each nucleotide is paired with at -- most one other nucleotide. A nucleotide with index @k@ in @[0..len-1]@ is -- paired if @unD1S VU.! k >=0 0@ Unpaired status is @-1@.+--+-- TODO Provide @iso@ between @D1Secondary@ and @RNAss@. newtype D1Secondary = D1S {unD1S :: VU.Vector Int} deriving (Read,Show,Eq,Generic,NFData)@@ -184,13 +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. --@@ -251,11 +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.
Biobase/Secondary/Isostericity.hs view
@@ -13,9 +13,10 @@ 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 import qualified Data.ByteString.Char8 as BS import qualified Data.Map as M import Text.CSV@@ -42,7 +43,7 @@ -- -- TODO inClass missing -instance IsostericityLookup ExtPair where+instance IsostericityLookup (ExtPair n) where getClasses p | Just cs <- M.lookup p defaultIsostericityMap = cs@@ -53,18 +54,17 @@ -- -- TODO inClass missing -instance IsostericityLookup Pair where+instance IsostericityLookup (Pair n) where getClasses p | Just cs <- M.lookup (p,CWW) defaultIsostericityMap = cs | otherwise = []- inClass x = map (baseP.fst) -- remove extended information- . filter ((CWW==).baseT.fst) -- keep only cWW pairs (baseT-ype)- . filter ((x `elem`).snd) -- select based on class+ inClass x = map (sel1 . fst) -- remove extended information+ . filter ((CWW==). snd . fst) -- keep only cWW pairs (baseT-ype)+ . filter ((x `elem`).snd) -- select based on class $ M.assocs defaultIsostericityMap - -- ** default data -- | The default isostericity mapping.@@ -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 = $(makeRelativeToProject "sources/isostericity-detailed.csv" >>= embedFile)
+ Biobase/Secondary/New.hs view
@@ -0,0 +1,101 @@++-- | New parsers and structures for secondary structures. The structures here a strict.+--+-- TODO Parser should check if a @#Vienna Secondary Structure@ or @#Extended Secondary Structure@ precedes the entries.++module Biobase.Secondary.New where++import Control.Applicative+import Control.Lens+import Control.Monad.Except+import Data.Attoparsec.ByteString.Char8+import Data.ByteString.Char8 (ByteString,pack)+import Data.Functor+import Data.Tree+import Data.Vector (Vector, fromList)+import GHC.Generics (Generic)++++-- | A completely closed sub-structure. An unpaired region @.@ is closed. A+-- paired region @(r)@ is closed, where @r@ contains arbitrarily many unpaired+-- and paired elements.+--+-- TODO Should be extended with @Extended@, but this requires knowing which of+-- the ends overlap with paired: left, right, or both.++data SubStructure (t :: *) a+ = Unpaired { _label :: !a }+ | Paired { _label :: !a, _subStructures :: !(Vector (SubStructure t a)) }+ deriving (Show, Read, Functor, Traversable, Foldable, Generic, Eq, Ord)+makeLenses ''SubStructure+makePrisms ''SubStructure++-- | A full structure is composed of a number of sub-structures. The empty+-- structure is a full structure.++newtype FullStructure (t :: *) a+ = FullStructure { _fullStructure :: Vector (SubStructure t a) }+ deriving (Show, Read, Functor, Traversable, Foldable, Generic, Eq, Ord)+makeLenses ''FullStructure++++-- ** Parses a ViennaRNA secondary structure string.++pUnpaired :: Parser (SubStructure () ())+pUnpaired = Unpaired () <$ char '.'+{-# Inlinable pUnpaired #-}++pPaired :: Parser (SubStructure () ())+pPaired = Paired () <$ char '(' <*> (fromList <$> many pSubStructure) <* char ')'+{-# Inlinable pPaired #-}++pSubStructure :: Parser (SubStructure () ())+pSubStructure = pUnpaired <|> pPaired+{-# Inlinable pSubStructure #-}++pFullStructure :: Parser (FullStructure () ())+pFullStructure = FullStructure <$> fromList <$> many pSubStructure <* endOfInput+{-# Inlinable pFullStructure #-}++newtype StructureParseError = StructureParseError String+ deriving (Show)++parseVienna :: MonadError StructureParseError m ⇒ ByteString -> m (FullStructure () ())+parseVienna = either (throwError . StructureParseError) return . parseOnly pFullStructure+{-# Inlinable parseVienna #-}++++-- ** Transform into a @Tree@.++-- | Transform a 'FullStructure' into a 'Tree'.+--+-- Given a full structure generated like this:+-- @+-- s = either (error . show) id $ parseVienna $ pack ".()(())."+-- @+--+-- a tree of just the base paired can be created with+-- @+-- toTree (preview (_Paired._1)) () s+-- @++toTree+ :: (SubStructure t a -> Maybe b)+ -- ^ how to handle substructure elements? @Nothing@ means discard this+ -- substructure and all children.+ -> b+ -- ^ The root label+ -> FullStructure (t :: *) a+ -- ^ The @FullStructure@ to transform into a @Tree@.+ -> 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+{-# Inlinable toTree #-}+
Biobase/Secondary/Vienna.hs view
@@ -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@@ -32,95 +33,48 @@ 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 #-} -{--instance (Shape sh,Show sh) => Shape (sh :. ViennaPair) where- rank (sh:._) = rank sh + 1- zeroDim = zeroDim:.ViennaPair 0- unitDim = unitDim:.ViennaPair 1 -- TODO does this one make sense?- intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2- addDim (sh1:.ViennaPair n1) (sh2:.ViennaPair n2) = addDim sh1 sh2 :. ViennaPair (n1+n2) -- TODO will not necessarily yield a valid ViennaPair- size (sh1:.ViennaPair n) = size sh1 * n- sizeIsValid (sh1:.ViennaPair n) = sizeIsValid (sh1:.n)- toIndex (sh1:.ViennaPair sh2) (sh1':.ViennaPair sh2') = toIndex (sh1:.sh2) (sh1':.sh2')- fromIndex (ds:.ViennaPair d) n = fromIndex ds (n `quotInt` d) :. ViennaPair r where- r | rank ds == 0 = n- | otherwise = n `remInt` d- inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx- listOfShape (sh:.ViennaPair n) = n : listOfShape sh- shapeOfList xx = case xx of- [] -> error "empty list in shapeOfList/Primary"- x:xs -> shapeOfList xs :. ViennaPair x- deepSeq (sh:.n) x = deepSeq sh (n `seq` x)- {-# INLINE rank #-}- {-# INLINE zeroDim #-}- {-# INLINE unitDim #-}- {-# INLINE intersectDim #-}- {-# INLINE addDim #-}- {-# INLINE size #-}- {-# INLINE sizeIsValid #-}- {-# INLINE toIndex #-}- {-# INLINE fromIndex #-}- {-# INLINE inShapeRange #-}- {-# INLINE listOfShape #-}- {-# INLINE shapeOfList #-}- {-# INLINE deepSeq #-}--instance (Eq sh, Shape sh, Show sh, ExtShape sh) => ExtShape (sh :. ViennaPair) where- subDim (sh1:.ViennaPair n1) (sh2:.ViennaPair n2) = subDim sh1 sh2 :. (ViennaPair $ n1-n2)- rangeList (sh1:.ViennaPair n1) (sh2:.ViennaPair n2) = [sh:.ViennaPair n | sh <- rangeList sh1 sh2, n <- [n1 .. (n1+n2)]]- rangeStream (fs:.ViennaPair f) (ts:.ViennaPair t) = VM.flatten mk step Unknown $ rangeStream fs ts where- mk sh = return (sh :. f)- step (sh :. k)- | k>t = return $ VM.Done- | otherwise = return $ VM.Yield (sh :. ViennaPair k) (sh :. k +1)- {-# INLINE [1] mk #-}- {-# INLINE [1] step #-}- {-# INLINE rangeStream #-}--}- pattern NP = ViennaPair 0 :: ViennaPair pattern CG = ViennaPair 1 :: ViennaPair pattern GC = ViennaPair 2 :: ViennaPair@@ -128,9 +82,11 @@ pattern UG = ViennaPair 4 :: ViennaPair pattern AU = ViennaPair 5 :: ViennaPair pattern UA = ViennaPair 6 :: ViennaPair+-- | Non-standard base pair pattern NS = ViennaPair 7 :: ViennaPair pattern Undef = ViennaPair 8 :: ViennaPair +{- class MkViennaPair a where mkViennaPair :: a -> ViennaPair fromViennaPair :: ViennaPair -> a@@ -154,8 +110,9 @@ UA -> (U,A) _ -> error "non-standard pairs can't be backcasted" {-# 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@@ -164,8 +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)@@ -223,7 +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 |]
BiobaseXNA.cabal view
@@ -1,18 +1,18 @@+cabal-version: 2.2 name: BiobaseXNA-version: 0.9.3.1+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 representations-license: GPL-3+synopsis: Efficient RNA/DNA/Protein Primary/Secondary Structure+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.@@ -45,10 +45,10 @@ sources/iupac-nucleotides --library+common deps build-depends: base >= 4.7 && < 5.0- , aeson >= 0.8+ , aeson >= 1.0+ , attoparsec >= 0.13 , binary >= 0.7 , bytes >= 0.15 , bytestring >= 0.10@@ -56,46 +56,34 @@ , 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 , lens >= 4.0+ , mtl >= 2.0 , primitive >= 0.5 , QuickCheck >= 2.7 , 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.*- , 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.Basepair- Biobase.Secondary.Constraint- 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@@ -103,11 +91,17 @@ , LambdaCase , MultiParamTypeClasses , PatternSynonyms+ , PolyKinds+ , RankNTypes+ , RecordWildCards , ScopedTypeVariables+ , StandaloneDeriving , TemplateHaskell+ , TypeApplications , TypeFamilies , TypeOperators , UndecidableInstances+ , UnicodeSyntax , ViewPatterns default-language: Haskell2010@@ -115,8 +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@@ -124,18 +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:@@ -153,7 +175,6 @@ , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-th >= 0.1- , vector -- , BiobaseXNA
LICENSE view
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It is safest-to attach them to the start of each source file to most effectively-state the exclusion of warranty; and each file should have at least-the "copyright" line and a pointer to where the full notice is found.-- <one line to give the program's name and a brief idea of what it does.>- Copyright (C) <year> <name of author>-- This program is free software: you can redistribute it and/or modify- it under the terms of the GNU General Public License as published by- the Free Software Foundation, either version 3 of the License, or- (at your option) any later version.-- This program is distributed in the hope that it will be useful,- but WITHOUT ANY WARRANTY; without even the implied warranty of- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the- GNU General Public License for more details.-- You should have received a copy of the GNU General Public License- along with this program. If not, see <http://www.gnu.org/licenses/>.--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. - <program> Copyright (C) <year> <name of author>- 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-<http://www.gnu.org/licenses/>.+ * 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-<http://www.gnu.org/philosophy/why-not-lgpl.html>.+ * 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. 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README.md view
@@ -1,4 +1,5 @@-[](https://travis-ci.org/choener/BiobaseXNA)++ # BiobaseXNA
changelog.md view
@@ -1,3 +1,16 @@+0.11.0.1+--------++- version bump++0.11.0.0+--------++0.10.0.0+--------++- redesigned Biobase.Secondary.Basepair+ 0.9.3.1 -------