BiobaseTypes 0.1.2.1 → 0.1.3.0

raw patch · 5 files changed

+376/−21 lines, 5 filesdep +bytestringdep +containersdep +lensdep ~deepseqPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: bytestring, containers, lens, mtl, utf8-string

Dependency ranges changed: deepseq

API changes (from Hackage documentation)

Files

• Biobase/Types/Energy.hs +17/−16
• Biobase/Types/Sequence.hs +199/−0
• Biobase/Types/Structure.hs +138/−0
• BiobaseTypes.cabal +17/−5
• changelog.md +5/−0

@@ -7,8 +7,10 @@ module Biobase.Types.Energy where  import Control.DeepSeq+import Control.Lens import Data.Aeson (FromJSON, ToJSON) import Data.Binary (Binary)+import Data.Data import Data.Default import Data.Hashable import Data.Serialize (Serialize)@@ -28,31 +30,30 @@ -- -- TODO shall we phantom-type the actual units? -newtype DeltaGibbs = DG { getDG :: Double }-  deriving (Eq,Ord,Num,Fractional,Read,Show,Generic)--+newtype DG = DG { dG :: Double }+  deriving (Eq,Ord,Num,Fractional,Read,Show,Generic,Data,Typeable)+makeLenses ''DG -derivingUnbox "DeltaGibbs"-  [t| DeltaGibbs -> Double |]  [| getDG |]  [| DG |]+derivingUnbox "DG"+  [t| DG -> Double |]  [| dG |]  [| DG |] -instance Hashable  DeltaGibbs-instance Binary    DeltaGibbs-instance Serialize DeltaGibbs-instance FromJSON  DeltaGibbs-instance ToJSON    DeltaGibbs-instance NFData    DeltaGibbs+instance Hashable  DG+instance Binary    DG+instance Serialize DG+instance FromJSON  DG+instance ToJSON    DG+instance NFData    DG -deriving instance NumericalExtremes DeltaGibbs-deriving instance NumericalEpsilon  DeltaGibbs+deriving instance NumericalExtremes DG+deriving instance NumericalEpsilon  DG -instance Default DeltaGibbs where+instance Default DG where   def = maxLarge   {-# Inline def #-}   --- | @round $ DeltaGibbs / 100@.+-- | @round $ DG / 100@.  newtype DeltaDekaGibbs = DekaG { getDekaG :: Int }   deriving (Eq,Ord,Num,Read,Show,Generic)

@@ -0,0 +1,199 @@++-- | Wrappers around biosequences.++module Biobase.Types.Sequence where++import           Control.Lens+import           Control.DeepSeq+import           Data.ByteString (ByteString)+import           Data.Char (ord,chr,toUpper)+import           Data.Data (Data)+import           Data.Typeable (Typeable)+import           GHC.Generics (Generic)+import qualified Data.ByteString.Char8 as BS+import qualified Data.ByteString.UTF8 as BSU+import           GHC.Exts (IsString(..))++++-- | A sequence identifier. Just a newtype wrapped text field. Because we can+-- never know what people are up to, this is utf8-encoded.+--+-- TODO Provide @Iso'@ for @Text@, too?++newtype SequenceID = SequenceID { _sequenceID ∷ ByteString }+  deriving (Data, Typeable, Generic, Eq, Ord, Read, Show, IsString)+makeLenses ''SequenceID++instance NFData SequenceID++-- | Convert to a string in a unicode-aware manner.++sequenceIDstring ∷ Iso' SequenceID String+sequenceIDstring = sequenceID . iso BSU.toString BSU.fromString+{-# Inline sequenceIDstring #-}++++-- | A short RNA sequence.+--+-- It is an instance of 'Ixed' to allow @RNAseq (BS.pack "cag") ^? ix 2 == Just 'g'@.++newtype RNAseq = RNAseq { _rnaseq ∷ ByteString }+  deriving (Data, Typeable, Generic, Eq, Ord, Read, Show)+makeLenses ''RNAseq++instance NFData RNAseq++type instance Index RNAseq = Int++type instance IxValue RNAseq = Char++instance Ixed RNAseq where+  ix k = rnaseq . ix k . iso (chr . fromIntegral) (fromIntegral . ord)+  {-# Inline ix #-}++deriving instance Reversing RNAseq++mkRNAseq ∷ ByteString → RNAseq+mkRNAseq = RNAseq . BS.map go . BS.map toUpper+  where go x | x `elem` acgu = x+             | otherwise     = 'N'+        acgu ∷ String+        acgu = "ACGU"++instance IsString RNAseq where+  fromString = mkRNAseq . BS.pack++++-- | A short DNA sequence.+--+-- Note everything really long should be handled by specialized libraries with+-- streaming capabilities.++newtype DNAseq = DNAseq { _dnaseq ∷ ByteString }+  deriving (Data, Typeable, Generic, Eq, Ord, Read, Show)+makeLenses ''DNAseq++instance NFData DNAseq++type instance Index DNAseq = Int++type instance IxValue DNAseq = Char++instance Ixed DNAseq where+  ix k = dnaseq . ix k . iso (chr . fromIntegral) (fromIntegral . ord)+  {-# Inline ix #-}++mkDNAseq ∷ ByteString → DNAseq+mkDNAseq = DNAseq . BS.map go . BS.map toUpper+  where go x | x `elem` acgt = x+             | otherwise     = 'N'+        acgt ∷ String+        acgt = "ACGT"++instance IsString DNAseq where+  fromString = mkDNAseq . BS.pack++deriving instance Reversing DNAseq++-- | Simple case translation from @U@ to @T@. with upper and lower-case+-- awareness.++rna2dna ∷ Char → Char+rna2dna = \case+  'U' → 'T'+  'u' → 't'+  x   → x+{-# Inline rna2dna #-}++-- | Single character RNA complement.++rnaComplement ∷ Char → Char+rnaComplement = \case+  'A' → 'U'+  'a' → 'u'+  'C' → 'G'+  'c' → 'g'+  'G' → 'C'+  'g' → 'c'+  'U' → 'A'+  'u' → 'a'+  x   → x+{-# Inline rnaComplement #-}++-- | Simple case translation from @T@ to @U@ with upper- and lower-case+-- awareness.++dna2rna ∷ Char → Char+dna2rna = \case+  'T' → 'U'+  't' → 'u'+  x   → x+{-# Inline dna2rna #-}++-- | Single character DNA complement.++dnaComplement ∷ Char → Char+dnaComplement = \case+  'A' → 'T'+  'a' → 't'+  'C' → 'G'+  'c' → 'g'+  'G' → 'C'+  'g' → 'c'+  'T' → 'A'+  't' → 'a'+  x   → x+{-# Inline dnaComplement #-}++++-- | Transcribes a DNA sequence into an RNA sequence. Note that 'transcribe' is+-- actually very generic. We just define its semantics to be that of+-- biomolecular transcription.+--+-- 'transcribe' makes the assumption that, given @DNA -> RNA@, we transcribe+-- the coding strand.+-- <http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/transcription.html>+--+-- @@ DNAseq "ACGT" ^. transcribe == RNAseq "ACGU" RNAseq "ACGU" ^. transcribe+-- == DNAseq "ACGT" RNAseq "ACGU" ^. from transcribe :: DNAseq == DNAseq "ACGT"+-- @@++class Transcribe f where+  type TranscribeTo f ∷ *+  transcribe ∷ Iso' f (TranscribeTo f)++-- | Transcribe a DNA sequence into an RNA sequence. This does not @reverse@+-- the sequence!++instance Transcribe DNAseq where+  type TranscribeTo DNAseq = RNAseq+  transcribe = iso (RNAseq . BS.map dna2rna . _dnaseq) (DNAseq . BS.map rna2dna . _rnaseq)+  {-# Inline transcribe #-}++-- | Transcribe a RNA sequence into an DNA sequence. This does not @reverse@+-- the sequence!++instance Transcribe RNAseq where+  type TranscribeTo RNAseq = DNAseq+  transcribe = from transcribe+  {-# Inline transcribe #-}++++-- | The complement of a biosequence.++class Complement f where+  complement ∷ Iso' f f++instance Complement DNAseq where+  complement = iso (DNAseq . BS.map dnaComplement . _dnaseq) (DNAseq . BS.map dnaComplement . _dnaseq)+  {-# Inline complement #-}++instance Complement RNAseq where+  complement = iso (RNAseq . BS.map rnaComplement . _rnaseq) (RNAseq . BS.map rnaComplement . _rnaseq)+  {-# Inline complement #-}+

@@ -0,0 +1,138 @@++-- | Wrappers for structural data. Encoded as bytestrings. This differs from+-- @BiobaseXNA@, where specialized encodings are used. These structures are+-- supposedly "short", they need to fit into a strict bytestring.+--+-- TODO Consider where to move each type. There are merge possibilities between+-- BiobaseXNA and BiobaseTypes.++module Biobase.Types.Structure where++import           Control.DeepSeq+import           Control.Lens+import           Control.Monad.Error.Class+import           Control.Monad (foldM,unless)+import           Data.ByteString (ByteString)+import           Data.Data+import           Data.Set (Set)+import           GHC.Generics (Generic)+import qualified Data.ByteString.Char8 as BS8+import qualified Data.List as L+import qualified Data.Set as Set++++-- | Secondary structure using @()@ for paired elements, and @.@ for unpaired+-- ones. It is assumed that the @()@ match up. These structures from a Monoid.++newtype RNAss = RNAss { _rnass ∷ ByteString }+  deriving (Eq,Ord,Show,Read,Data,Typeable,Generic,Monoid)+makeLenses ''RNAss++instance NFData RNAss++-- | Ensemble structure encoding. *Very* different type ctor name chosen! The+-- structure of this string makes verification much more complicated.+--+-- TODO describe encoding used by RNAfold for the ensemble string.++newtype RNAensembleStructure = RNAes { _rnaes ∷ ByteString }+  deriving (Eq,Ord,Show,Read,Data,Typeable,Generic)+makeLenses ''RNAensembleStructure++instance NFData RNAensembleStructure++-- | Cofolded structure.++data RNAds = RNAds+  { _rnadsL ∷ !ByteString+  , _rnadsR ∷ !ByteString+  }+  deriving (Eq,Ord,Show,Read,Data,Typeable,Generic)+makeLenses ''RNAds++instance NFData RNAds++-- | A Prism that turns ByteStrings with a single @&@ into @RNAds@.++rnads ∷ Prism' ByteString RNAds+rnads = prism (\(RNAds l r) → BS8.concat [l, "&", r])+              (\s → case BS8.split '&' s of [l,r] → Right (RNAds l r) ; _ → Left s)+{-# Inline rnads #-}++-- | Isomorphism from @RNAds@ to @(RNAss,RNAss)@. The @RNAss@ are only+-- legal if taken both: @rnassFromDimer . both@.++rnads2rnassPair ∷ Iso' RNAds (RNAss, RNAss)+rnads2rnassPair = iso (\(RNAds l r) → (RNAss l, RNAss r)) (\(RNAss l, RNAss r) → RNAds l r)+{-# Inline rnads2rnassPair #-}++-- | Try to create a dimeric structure.++mkRNAds ∷ (Monad m, MonadError RNAStructureError m) ⇒ ByteString → m RNAds+mkRNAds q = BS8.split '&' q & \case+    [l,r] → do+      -- TODO can still fail with unmatched brackets.+      return $ RNAds+        { _rnadsL = l+        , _rnadsR = r+        }+    _     → throwError $ RNAStructureError "mkRNAds: not a dimer" q+{-# Inline mkRNAds #-}++-- | Capture what might be wrong with the RNAss.++data RNAStructureError = RNAStructureError+  { _rnaStructureError  ∷ String+  , _rnaOffender        ∷ ByteString+  }+  deriving (Show,Generic)++instance NFData RNAStructureError++-- | Verifies that the given RNAss is properly formatted. Otherwise, error out.+--+-- TODO Implement! Check with BiobaseXNA and the stack effort in there. This+-- might influence if the verification goes into BiobaseXNA and happens via an+-- @Iso'@.++verifyRNAss ∷ (Monad m, MonadError RNAStructureError m) ⇒ RNAss → m RNAss+verifyRNAss ss = do+  return ss++newtype RNApset = RNApset { _rnapset ∷ Set (Int,Int) }+  deriving (Read,Show,Eq,Ord,Generic)+makeLenses ''RNApset++instance NFData RNApset++-- | Transform an 'RNAss' into a set of base pairs @(i,j)@. The pairs are+-- 0-based.++rnassPairSet+  ∷ (MonadError String m)+  ⇒ RNAss+  → m RNApset+rnassPairSet (RNAss s2) = do+  let go (set,ks  ) (i,'(') = return (set,i:ks)+      go (set,i:is) (j,')') = return (Set.insert (i,j) set, is)+      go (set,[]  ) (j,')') = throwError $ "unequal brackets in \"" ++ BS8.unpack s2 ++ "\" at position: " ++ show j+      go (set,ks  ) (_,'.') = return (set,ks)+  (set,ss) ← foldM go (Set.empty,[]) . L.zip [0..] $ BS8.unpack s2+  unless (null ss) $ throwError $ "unequal brackets in \"" ++ BS8.unpack s2 ++ "\" with opening bracket(s): " ++ show ss+  return $ RNApset set+{-# Inlinable rnassPairSet #-}++-- | RNA pair set, but a transformation error calls @error@.++rnassPairSet' ∷ RNAss → RNApset+rnassPairSet' = either error id . rnassPairSet++-- | Calculates the number of different base pairs betwwen two structures.++pairDist ∷ RNApset → RNApset → Int+pairDist (RNApset p1) (RNApset p2) = Set.size z1 + Set.size z2+  where i = Set.intersection p1 p2+        z1 = p1 `Set.difference` i+        z2 = p2 `Set.difference` i+

@@ -1,7 +1,7 @@ name:           BiobaseTypes-version:        0.1.2.1-author:         Christian Hoener zu Siederdissen, 2015 - 2016-copyright:      Christian Hoener zu Siederdissen, 2015 - 2016+version:        0.1.3.0+author:         Christian Hoener zu Siederdissen, 2015 - 2017+copyright:      Christian Hoener zu Siederdissen, 2015 - 2017 homepage:       https://github.com/choener/BiobaseTypes bug-reports:    https://github.com/choener/BiobaseTypes/issues maintainer:     choener@bioinf.uni-leipzig.de@@ -11,7 +11,7 @@ build-type:     Simple stability:      experimental cabal-version:  >= 1.10.0-tested-with:    GHC == 7.10.3, GHC == 8.0.1+tested-with:    GHC == 8.0.2, GHC == 8.2.1 synopsis:       Collection of types for bioinformatics description:                 Types used in a number of bioinformatics libraries.@@ -21,6 +21,8 @@                 * energies                 .                 * numerics+                .+                * biostring wrappers   @@ -34,18 +36,23 @@   build-depends: base                     >= 4.7      &&  < 5.0                , aeson                    >= 0.8                , binary                   >= 0.7+               , bytestring                , cereal                   >= 0.4                , cereal-text              >= 0.1                , cereal-vector            >= 0.2+               , containers                , data-default             >= 0.5-               , deepseq                  >= 1.3+               , deepseq                  >= 1.4                , hashable                 >= 1.2                , intern                   >= 0.9+               , lens                     >= 4.0+               , mtl                , primitive                >= 0.5                , QuickCheck               >= 2.7                , string-conversions       >= 0.4                , text                     >= 1.0                , text-binary              >= 0.2+               , utf8-string              >= 1.0                , vector                   >= 0.10                , vector-binary-instances  >= 0.2                , vector-th-unbox          >= 0.2@@ -63,17 +70,21 @@     Biobase.Types.Names.Internal     Biobase.Types.NumericalExtremes     Biobase.Types.Odds+    Biobase.Types.Sequence     Biobase.Types.Strand+    Biobase.Types.Structure     Biobase.Types.Taxonomy   default-language:     Haskell2010   default-extensions: BangPatterns                     , DataKinds+                    , DeriveDataTypeable                     , DeriveGeneric                     , FlexibleContexts                     , FlexibleInstances                     , GeneralizedNewtypeDeriving                     , KindSignatures+                    , LambdaCase                     , MultiParamTypeClasses                     , OverloadedStrings                     , PatternSynonyms@@ -82,6 +93,7 @@                     , TemplateHaskell                     , TypeFamilies                     , TypeOperators+                    , UnicodeSyntax   ghc-options:     -O2 -funbox-strict-fields 

@@ -1,3 +1,8 @@+0.1.3.0+-------++- "biostring" wrappers (ByteString based RNA, DNA, ... sequences)+ 0.1.2.1 -------