BiobaseTypes 0.2.0.0 → 0.2.0.1

raw patch · 7 files changed

+235/−66 lines, 7 filesdep +streamingdep ~QuickCheckdep ~lensPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: streaming

Dependency ranges changed: QuickCheck, lens

API changes (from Hackage documentation)

Files

• Biobase/Types/BioSequence.hs +52/−14
• Biobase/Types/Index.hs +8/−5
• Biobase/Types/Location.hs +102/−0
• Biobase/Types/Strand.hs +33/−16
• BiobaseTypes.cabal +34/−30
• LICENSE +1/−1
• changelog.md +5/−0

@@ -4,6 +4,8 @@ -- that act on known types. -- -- Unknown bio sequences should be tagged with @Void@.+--+-- TODO give (lens) usage examples  module Biobase.Types.BioSequence where @@ -17,10 +19,13 @@ import           GHC.Exts (IsString(..)) import           GHC.Generics (Generic) import qualified Data.ByteString.Char8 as BS+import qualified Data.ByteString.UTF8 as BSU+import qualified Streaming.Prelude as SP+import qualified Streaming as S import qualified Test.QuickCheck as TQ import           Test.QuickCheck (Arbitrary(..))-import qualified Data.ByteString.UTF8 as BSU +import           Biobase.Types.Location import           Biobase.Types.Strand import qualified Biobase.Types.Index as BTI @@ -76,6 +81,10 @@  -- * RNA +-- |+--+-- TODO write that converts explicitly+ mkRNAseq ∷ ByteString → BioSequence RNA mkRNAseq = BioSequence . BS.map go . BS.map toUpper   where go x | x `elem` acgu = x@@ -162,10 +171,10 @@  -- | Phantom-typed over two types, the type @w@ of the identifier, which can be -- descriptive ("FirstInput") and the second type, identifying what kind of--- sequence types we are dealing with. Finally, the third type fixes the index--- type of the infix.+-- sequence types we are dealing with. Finally, the third type provides+-- location information and should be location or streamed location. -data BioSequenceWindow w ty k = BioSequenceWindow+data BioSequenceWindow w ty loc = BioSequenceWindow   { _bswIdentifier ∷ !(SequenceIdentifier w)     -- ^ Identifier for this window. Typically some fasta identifier   , _bswPrefix     ∷ !(BioSequence ty)@@ -174,23 +183,18 @@     -- ^ The actual sequence, the infix   , _bswSuffix     ∷ !(BioSequence ty)     -- ^ any suffix-  , _bswStrand     ∷ !Strand-    -- ^ strand information. Probably '+' but arbitrary-  , _bswIndex ∷ !(BTI.Index k)-    -- ^ Provide the index for the left-most character of the @bswSequence@ on-    -- '+' on '-' as well, but to be interpreted on the '+' strand.-    -- TODO this actually needs a more complicated encoding...!+  , _bswLocation   ∷ !loc   }   deriving (Data, Typeable, Generic, Eq, Ord, Read, Show) makeLenses ''BioSequenceWindow -instance Reversing (BioSequenceWindow w ty k) where+instance (Reversing loc) ⇒ Reversing (BioSequenceWindow w ty loc) where   {-# Inlinable reversing #-}   reversing bsw = bsw                 & bswPrefix .~ (bsw^.bswSuffix.reversed)                 & bswSuffix .~ (bsw^.bswPrefix.reversed)                 & bswSequence .~ (bsw^.bswSequence.reversed)-                & bswStrand .~ (bsw^.bswStrand.reversed)+                & bswLocation .~ (bsw^.bswLocation.reversed)  -- | A lens into the full sequence information of a sequence window. One should -- *NOT* modify the length of the individual sequences.@@ -206,8 +210,26 @@                   & bswSequence._BioSequence .~ ifx                   & bswSuffix._BioSequence .~ sfx +-- | For each element, attach the prefix as well.+--+-- @1 2 3 4@ -> @01 12 23 34@ +attachPrefixes ∷ (Monad m) ⇒ SP.Stream (SP.Of (BioSequenceWindow w ty k)) m r → SP.Stream (SP.Of (BioSequenceWindow w ty k)) m r+{-# Inlinable attachPrefixes #-}+attachPrefixes  =+  let go (Left pfx) w = Right (set bswPrefix pfx w)+      go (Right p)  w = Right (set bswPrefix (view bswSequence p) w)+  in  SP.map (\(Right w) → w) . SP.drop 1 . SP.scan go (Left $ BioSequence "") id +-- | For each element, attach the suffix as well.+--+-- @1 2 3 4@ -> @12 23 34 40@++attachSuffixes ∷ (Monad m) ⇒ SP.Stream (SP.Of (BioSequenceWindow w ty k)) m r → SP.Stream (SP.Of (BioSequenceWindow w ty k)) m r+{-# Inlinable attachSuffixes #-}+attachSuffixes xs = undefined++ -- * DNA/RNA  -- | Simple case translation from @U@ to @T@. with upper and lower-case@@ -302,10 +324,26 @@   complement ∷ Iso' f f  instance Complement (BioSequence DNA) where-  complement = iso (over _BioSequence (BS.map dnaComplement)) (over _BioSequence (BS.map dnaComplement))   {-# Inline complement #-}+  complement = let f = (over _BioSequence (BS.map dnaComplement))+                   {-# Inline f #-}+               in  iso f f  instance Complement (BioSequence RNA) where-  complement = iso (over _BioSequence (BS.map rnaComplement)) (over _BioSequence (BS.map rnaComplement))   {-# Inline complement #-}+  complement = let f = (over _BioSequence (BS.map rnaComplement))+                   {-# Inline f #-}+               in  iso f f++instance (Complement (BioSequence ty)) ⇒ Complement (BioSequenceWindow w ty k) where+  {-# Inline complement #-}+  complement = let g = view complement+                   f = (\w → over bswSuffix g . over bswPrefix g . over bswSequence g $ w)+                   {-# Inline g #-}+                   {-# Inline f #-}+               in  iso f f++reverseComplement ∷ (Complement f, Reversing f) ⇒ Iso' f f+{-# Inline reverseComplement #-}+reverseComplement = reversed . complement 

@@ -18,6 +18,7 @@   , Index   ) where +import Data.Coerce import Data.Proxy import GHC.TypeLits import Text.Printf@@ -40,11 +41,13 @@ -- as @0 :: Index 0@ gives @1 :: Index 1@ for example. I.e. valid indices -- become valid indices. -reIndex :: forall n m . (KnownNat n, KnownNat m) => Index n -> Index m-reIndex (Index i) = Index $ i - n + m-  where n = fromIntegral $ natVal (Proxy :: Proxy n)-        m = fromIntegral $ natVal (Proxy :: Proxy m)+reIndex ∷ Index n → Index m {-# Inline reIndex #-}+reIndex = coerce+--reIndex :: forall n m . (KnownNat n, KnownNat m) => Index n -> Index m+--reIndex (Index i) = Index $ i - n + m+--  where n = fromIntegral $ natVal (Proxy :: Proxy n)+--        m = fromIntegral $ natVal (Proxy :: Proxy m)  -- | Helper function that allows @addition@ of an 'Index' and an 'Int', -- with the 'Int' on the right.@@ -57,7 +60,7 @@ -- with the 'Int' on the right.  (-.) :: forall t . KnownNat t => Index t -> Int -> Index t-(-.) i n = checkIndex $ unsafePlus i n+(-.) i n = checkIndex $ unsafePlus i (negate n) {-# Inline (-.) #-}  -- | Unsafe plus.

@@ -0,0 +1,102 @@++-- | Annotate the genomic @Location@ of features or elements. A @Location@ is+-- always contiguous, using strand, 0-based position, and length.+-- Transformation to different systems of annotation is made possible.++module Biobase.Types.Location where++import Control.Lens hiding (Index, index)+import GHC.Generics (Generic)+import GHC.TypeNats+import Prelude hiding (length)++import Biobase.Types.Index+import Biobase.Types.Strand++++-- | Location information.++data Location = Location+  { _lStrand ∷ !Strand+  -- ^ On which strand are we+  , _lStart  ∷ !(Index 0)+  -- ^ Start, 0-based+  , _lLength ∷ !Int+  -- ^ number of characters in this location+  , _lTotalLength ∷ !Int+  -- ^ the total length of the "contig" (or whatever) this location is positioned in.+  } deriving (Eq,Ord,Read,Show,Generic)+makeLenses ''Location+makePrisms ''Location++instance Reversing Location where+  {-# Inline reversing #-}+  reversing = undefined+++-- | An isomorphism between locations, and triples of @Strand,Start,End@, where+-- end is inclusive. For @length==0@ locations, this will mean @start<end@ on+-- the plus strand.+--+-- This should hold for all @k@, in @Index k@.++startEndInclusive ∷ (KnownNat k) ⇒ Iso' Location (Strand, (Index k, Index k), Int)+{-# Inline startEndInclusive #-}+startEndInclusive = iso l2r r2l+  where l2r z = let s = z^.lStrand; f = z^.lStart; l = z^.lLength+                in  (s, (reIndex f, reIndex $ f +. l -. 1), z^.lTotalLength)+        r2l (s,(f,t),ttl) = Location s (reIndex f) (delta f t + 1) ttl++++-- | During streaming construction, it is possible that we know a feature is on+-- the @-@ strand, but the length of the contig is not known yet.+--+-- @+-- 0         1         2+-- 012345678901234567890+--   >---                    +        2 4    Location +  2 4+--      <---                 Reversed 5 4    Location - 12 4+-- 098765432109876543210+-- 2         1         0+-- @+--+-- ++data PartialLocation+  -- | Location, when it is not yet known how long the contig will be.+  = PartialLocation+      { _plStrand ∷ !Strand+      , _plStart  ∷ !(Index 0)+      , _plLength ∷ !Int+      }+  -- | The reversed strand. However, we have an @plEnd@, not a @plStart@ now!+  | ReversedPartialLocation+      { _plStrand ∷ !Strand+      , _plEnd    ∷ !(Index 0)+      , _plLength ∷ !Int+      }+  deriving (Eq,Ord,Read,Show,Generic)+makeLenses ''PartialLocation+makePrisms ''PartialLocation++-- | Reversing a reversible location means moving the start to the end.++instance Reversing PartialLocation where+  {-# Inline reversing #-}+  reversing = \case+    PartialLocation s t l → ReversedPartialLocation (s^.reversed) t l++-- An isomorphism between a 'Location' and the pair @('PartialLocation',Int)@+-- exists.++locationPartial ∷ Iso' Location (PartialLocation,Int)+{-# Inline locationPartial #-}+locationPartial = iso l2r r2l where+  l2r l = (PartialLocation (view lStrand l) (view lStart l) (view lLength l), l^.lTotalLength)+  r2l (p,z) = case p of PartialLocation s t l → Location s t l z+                        ReversedPartialLocation s e l+                          | s `elem` [PlusStrand,MinusStrand] → Location s (index $ z- getIndex e -l) l z+                          | otherwise                         → Location s e l z+

@@ -1,9 +1,11 @@  -- | Strand information. A newtyped version, complete with serialization,--- pattern synonyms, being a @PrimitiveArray@ index type, etc.+-- pattern synonyms, being a @PrimitiveArray@ index type, etc. The strand+-- information includes @+@, @-@, as well as the (GFF3) @.@ not stranded, and+-- @?@ for unknown strand information. ----- TODO will be expanded to encode biological sense information more--- clearly: <http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29>.+-- TODO will be expanded to encode biological sense information more clearly:+-- <http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29>.  module Biobase.Types.Strand where @@ -33,8 +35,10 @@   deriving (Eq,Ord,Generic,Data,Typeable)  instance Show Strand where-  show PlusStrand  = "PlusStrand"-  show MinusStrand = "MinusStrand"+  show PlusStrand    = "PlusStrand"+  show MinusStrand   = "MinusStrand"+  show NotStranded   = "NotStranded"+  show UnknownStrand = "UnknownStrand"  instance Read Strand where   readsPrec _ xs = do@@ -42,29 +46,42 @@     case pm of       "PlusStrand" → return (PlusStrand, s)       "MinusStrand" → return (MinusStrand, s)+      "NotStranded" → return (NotStranded, s)+      "UnknownStrand" → return (UnknownStrand, s)       [x] | x `elem` ("+Pp" ∷ String) → return (PlusStrand,s)           | x `elem` ("-Mm" ∷ String) → return (MinusStrand,s)+          | x `elem` ("."   ∷ String) → return (NotStranded,s)+          | x `elem` ("?"   ∷ String) → return (UnknownStrand,s)       _ → []  instance Bounded Strand where   minBound = PlusStrand-  maxBound = MinusStrand+  maxBound = UnknownStrand  instance Enum Strand where-  succ PlusStrand = MinusStrand-  succ MinusStrand = error "succ MinusStrand"-  pred MinusStrand = PlusStrand-  pred PlusStrand = error "pred PlusStrand"-  toEnum i | i>=0 && i<=1 = Strand i+  succ (Strand k)+    | k <  0 = error "succ undefined strand"+    | k == 3 = error "succ UnknownStrand"+    | k >  3 = error "succ undefined strand"+    | otherwise = Strand (k+1)+  pred (Strand k)+    | k <  0 = error "pred undefined strand"+    | k == 0 = error "pred UnknownStrand"+    | k >  3 = error "pred undefined strand"+    | otherwise = Strand (k-1)+  toEnum i | i>=0 && i<=3 = Strand i   toEnum i                = error $ "toEnum (Strand)" ++ show i   fromEnum = getStrand  instance Reversing Strand where-  reversing PlusStrand = MinusStrand+  reversing PlusStrand  = MinusStrand   reversing MinusStrand = PlusStrand+  reversing x           = x -pattern PlusStrand  = Strand 0-pattern MinusStrand = Strand 1+pattern PlusStrand    = Strand 0+pattern MinusStrand   = Strand 1+pattern NotStranded   = Strand 2+pattern UnknownStrand = Strand 3  -- TODO Sense and Antisense are somewhat different @@ -114,11 +131,11 @@           {-# Inline [0] step #-}   {-# Inline streamDown #-} -instance IndexStream Strand+-- instance IndexStream Strand  instance Arbitrary Strand where   arbitrary = do-    b <- choose (0,1)+    b <- choose (0,3)     return $ Strand b   shrink (Strand j)     | 0<j = [Strand $ j-1]

@@ -1,16 +1,16 @@+cabal-version:  2.2 name:           BiobaseTypes-version:        0.2.0.0+version:        0.2.0.1 author:         Christian Hoener zu Siederdissen, 2015 - 2019 copyright:      Christian Hoener zu Siederdissen, 2015 - 2019 homepage:       https://github.com/choener/BiobaseTypes bug-reports:    https://github.com/choener/BiobaseTypes/issues maintainer:     choener@bioinf.uni-leipzig.de category:       Data Structures, Bioinformatics-license:        BSD3+license:        BSD-3-Clause license-file:   LICENSE build-type:     Simple stability:      experimental-cabal-version:  >= 1.10.0 tested-with:    GHC == 8.4.4 synopsis:       Collection of types for bioinformatics description:@@ -30,7 +30,7 @@   -library+common deps   build-depends: base                     >= 4.7      &&  < 5.0                , aeson                    >= 0.8                , attoparsec               >= 0.13@@ -48,6 +48,7 @@                , mtl                , primitive                >= 0.5                , QuickCheck               >= 2.7+               , streaming                >= 0.1                , string-conversions       >= 0.4                , text                     >= 1.0                , text-binary              >= 0.2@@ -60,24 +61,6 @@                , ForestStructures         == 0.0.1.*                , PrimitiveArray           == 0.9.1.*                , SciBaseTypes             == 0.1.0.*-  exposed-modules:-    Biobase.Types.Accession-    Biobase.Types.BioSequence-    Biobase.Types.Bitscore-    Biobase.Types.Codon-    Biobase.Types.Energy-    Biobase.Types.Evalue-    Biobase.Types.Index-    Biobase.Types.Index.Type-    Biobase.Types.Names-    Biobase.Types.Names.Internal-    Biobase.Types.ReadingFrame-    Biobase.Types.Shape-    Biobase.Types.Strand-    Biobase.Types.Structure-    Biobase.Types.Taxonomy-    DP.Backtraced.BioSequence-    DP.Backtraced.Codon   default-language:     Haskell2010   default-extensions: BangPatterns@@ -95,6 +78,8 @@                     , OverloadedStrings                     , PatternSynonyms                     , PolyKinds+                    , RankNTypes+                    , RecordWildCards                     , ScopedTypeVariables                     , StandaloneDeriving                     , TemplateHaskell@@ -108,7 +93,34 @@   +library+  import:+    deps+  exposed-modules:+    Biobase.Types.Accession+    Biobase.Types.BioSequence+    Biobase.Types.Bitscore+    Biobase.Types.Codon+    Biobase.Types.Energy+    Biobase.Types.Evalue+    Biobase.Types.Index+    Biobase.Types.Index.Type+    Biobase.Types.Location+    Biobase.Types.Names+    Biobase.Types.Names.Internal+    Biobase.Types.ReadingFrame+    Biobase.Types.Shape+    Biobase.Types.Strand+    Biobase.Types.Structure+    Biobase.Types.Taxonomy+    DP.Backtraced.BioSequence+    DP.Backtraced.Codon+++ test-suite properties+  import:+    deps   type:     exitcode-stdio-1.0   main-is:@@ -117,15 +129,7 @@     -threaded -rtsopts -with-rtsopts=-N   hs-source-dirs:     tests-  default-language:-    Haskell2010-  default-extensions: ScopedTypeVariables-                    , TemplateHaskell-                    , UnicodeSyntax   build-depends: base-               , bytestring-               , lens-               , QuickCheck                , tasty              >= 0.11                , tasty-quickcheck   >= 0.8                , tasty-th           >= 0.1

@@ -1,4 +1,4 @@-Copyright Christian Hoener zu Siederdissen 2015+Copyright Christian Hoener zu Siederdissen 2015-2019  All rights reserved. 

@@ -1,3 +1,8 @@+0.2.0.1+-------++- minor version bumped due to OrderedBits+ 0.2.0.0 -------