BiobaseXNA 0.9.3.0 → 0.9.3.1

raw patch · 6 files changed

+210/−38 lines, 6 filesdep +QuickCheckdep +tastydep +tasty-quickcheckdep ~PrimitiveArraydep ~aesondep ~basePVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: QuickCheck, tasty, tasty-quickcheck, tasty-th

Dependency ranges changed: PrimitiveArray, aeson, base, binary, bytes, bytestring, cereal, cereal-vector, cmdargs, containers, csv, deepseq, file-embed, hashable, lens, primitive, split, text, tuple, vector, vector-binary-instances, vector-th-unbox

API changes (from Hackage documentation)

Files

• Biobase/Primary/Nuc/DNA.hs +5/−5
• Biobase/Primary/Nuc/XNA.hs +5/−5
• Biobase/Secondary/Diagrams.hs +26/−1
• BiobaseXNA.cabal +52/−27
• changelog.md +6/−0
• tests/properties.hs +116/−0

@@ -46,11 +46,11 @@   letterChar = dnaChar   charLetter = charDNA -instance (LetterChar DNA) => ToJSON (Primary DNA) where-  toJSON = toJSON . VU.toList . VU.map letterChar--instance (MkPrimary (VU.Vector Char) DNA) => FromJSON (Primary DNA) where-  parseJSON = fmap (primary :: String -> Primary DNA) . parseJSON+--instance (LetterChar DNA) => ToJSON (Primary DNA) where+--  toJSON = toJSON . VU.toList . VU.map letterChar+--+--instance (MkPrimary (VU.Vector Char) DNA) => FromJSON (Primary DNA) where+--  parseJSON = fmap (primary :: String -> Primary DNA) . parseJSON  acgt :: [Letter DNA] acgt = [A .. T]

@@ -49,11 +49,11 @@   letterChar = xnaChar   charLetter = charXNA -instance (LetterChar XNA) => ToJSON (Primary XNA) where-  toJSON = toJSON . VU.toList . VU.map letterChar--instance (MkPrimary (VU.Vector Char) XNA) => FromJSON (Primary XNA) where-  parseJSON = fmap (primary :: String -> Primary XNA) . parseJSON+--instance (LetterChar XNA) => ToJSON (Primary XNA) where+--  toJSON = toJSON . VU.toList . VU.map letterChar+--+--instance (MkPrimary (VU.Vector Char) XNA) => FromJSON (Primary XNA) where+--  parseJSON = fmap (primary :: String -> Primary XNA) . parseJSON  charXNA = toUpper >>> \case     'A' -> A

@@ -20,6 +20,7 @@ import           GHC.Generics import qualified Data.Vector.Unboxed as VU import           Text.Printf+import           Control.DeepSeq  import           Biobase.Primary.Nuc import           Biobase.Secondary.Basepair@@ -31,7 +32,7 @@ -- paired if @unD1S VU.! k >=0 0@ Unpaired status is @-1@.  newtype D1Secondary = D1S {unD1S :: VU.Vector Int}-  deriving (Read,Show,Eq,Generic)+  deriving (Read,Show,Eq,Generic,NFData)  instance Binary    D1Secondary instance Serialize D1Secondary@@ -264,4 +265,28 @@   t' = either error id . dotBracket2pairlist ["()"] $ t   ss = if sPairs then s' \\ t' else []   tt = if tPairs then t' \\ s' else []++-- | Calculate the distance between two 'D1Secondary' structures, that live+-- in the same underlying space. In particular, this probably only works+-- for structures on the same primary sequence.+--+-- This function assumes somewhat dense structures, as it is @O(2n)@ with+-- @n@ the length of the underlying vectors.+--+-- @(i,k)@ vs @(j,l)@+--+-- TODO error out on weird inputs!++d1Distance :: D1Secondary -> D1Secondary -> Int+d1Distance (D1S x) (D1S y)+--  | VU.length x /= VU.length y = error "d1Distance called on vectors with differing lengths!"+  | otherwise = (`div` 2) . VU.sum $ VU.zipWith chk (x VU.++ xx) (y VU.++ yy)+  where xx = VU.replicate (VU.length y - VU.length x) (-2)+        yy = VU.replicate (VU.length x - VU.length y) (-2)+        chk i j | i==j             = 0+                | i <  0 && j <  0 = 0+                | i >= 0 && j >= 0 = 2+                | otherwise        = 1+        {-# Inline chk #-}+{-# NoInline d1Distance #-} 

@@ -1,25 +1,25 @@ name:           BiobaseXNA-version:        0.9.3.0+version:        0.9.3.1 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 - 2015+copyright:      Christian Hoener zu Siederdissen, 2011 - 2017 category:       Bioinformatics synopsis:       Efficient RNA/DNA representations license:        GPL-3 license-file:   LICENSE build-type:     Simple stability:      experimental-tested-with:    GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1+tested-with:    GHC == 7.10.3, GHC == 8.0.1 cabal-version:  >= 1.10.0 description:                 This is a base library for bioinformatics with emphasis on RNA                 and DNA primary structure as well as amino acid sequences.                 .-                Provided are efficient encodings for short sequences, as-                required by RNA folding tools. Extended RNA secondary-                structures can be represented as well.+                Provided are efficient encodings for short (limited by the+                amount of RAM) sequences, as required by RNA folding tools.+                Extended RNA secondary structures can be represented as well.                 .                 Contains data from:                 .@@ -48,28 +48,29 @@  library   build-depends: base                     >= 4.7      &&  < 5.0-               , aeson                    >= 0.8      &&  < 1.1-               , binary                   >= 0.7      &&  < 0.8-               , bytes                    >= 0.15     &&  < 0.16-               , bytestring               >= 0.10     &&  < 0.11-               , cereal                   >= 0.4      &&  < 0.6-               , cereal-vector            >= 0.2      &&  < 0.3-               , containers               >= 0.5      &&  < 0.6-               , csv                      >= 0.1      &&  < 0.2-               , deepseq                  >= 1.3      &&  < 1.5-               , file-embed               >= 0.0.8    &&  < 0.1-               , hashable                 >= 1.2      &&  < 1.3-               , lens                     >= 4.0      &&  < 5.0-               , primitive                >= 0.5      &&  < 0.7-               , split                    >= 0.2      &&  < 0.3-               , text                     >= 1.0      &&  < 1.3-               , tuple                    >= 0.3      &&  < 0.4-               , vector                   >= 0.10     &&  < 0.12-               , vector-binary-instances  >= 0.2      &&  < 0.3-               , vector-th-unbox          >= 0.2      &&  < 0.3+               , aeson                    >= 0.8+               , binary                   >= 0.7+               , bytes                    >= 0.15+               , bytestring               >= 0.10+               , cereal                   >= 0.4+               , cereal-vector            >= 0.2+               , containers               >= 0.5+               , csv                      >= 0.1+               , deepseq                  >= 1.3+               , file-embed               >= 0.0.8+               , hashable                 >= 1.2+               , lens                     >= 4.0+               , primitive                >= 0.5+               , QuickCheck               >= 2.7+               , split                    >= 0.2+               , text                     >= 1.0+               , tuple                    >= 0.3+               , vector                   >= 0.10+               , vector-binary-instances  >= 0.2+               , vector-th-unbox          >= 0.2                --                , bimaps                   == 0.1.0.*-               , PrimitiveArray           == 0.7.1.*+               , PrimitiveArray           == 0.8.0.*   exposed-modules:     Biobase.Primary     Biobase.Primary.AA@@ -118,7 +119,7 @@ executable SubOptDistance   build-depends: base                , BiobaseXNA-               , cmdargs      >= 0.10   && < 0.11+               , cmdargs      >= 0.10   main-is:     SubOptDistance.hs   hs-source-dirs:@@ -131,6 +132,30 @@                     , ScopedTypeVariables   ghc-options:     -O2++++test-suite properties+  type:+    exitcode-stdio-1.0+  main-is:+    properties.hs+  ghc-options:+    -threaded -rtsopts -with-rtsopts=-N+  hs-source-dirs:+    tests+  default-language:+    Haskell2010+  default-extensions: TemplateHaskell+                    , ScopedTypeVariables+  build-depends: base+               , QuickCheck         >= 2.7+               , tasty              >= 0.11+               , tasty-quickcheck   >= 0.8+               , tasty-th           >= 0.1+               , vector+               --+               , BiobaseXNA   

@@ -1,3 +1,9 @@+0.9.3.1+-------++- removed upper version bounds, bumped dependent versions+- added d1Distance for fast basepair distance calculations+ 0.9.3.0 ------- 

@@ -0,0 +1,116 @@++module Main where++import           Control.Monad (join)+import           Data.Bits+import           Data.Function (on)+import           Data.Int (Int16(..))+import           Data.List (groupBy,sort,permutations,nub,(\\))+import           Data.Maybe (isJust)+import           Data.Word (Word)+import           Debug.Trace+import qualified Data.Vector.Unboxed as VU+import           Test.QuickCheck hiding ((.&.))+import           Test.Tasty+import           Test.Tasty.QuickCheck (testProperty)+import           Test.Tasty.TH++import           Biobase.Secondary.Diagrams+import           Biobase.Secondary.Basepair (PairIdx)++++newtype ArbitrarySSTree = ASST (SSTree PairIdx ())+  deriving (Show)++instance Arbitrary ArbitrarySSTree where+  arbitrary = ASST <$> sized arbitrarySSTree+    where+      arbitrarySSTree m = do+        Positive c <- arbitrary+        cs <- go 0 (c*m)+        let k = if null cs then 0 else 1 + maximum [ z | SSTree (_,z) _ _ <- cs ]+        return $ SSExtern k () cs+      go i j = do+        Positive c <- arbitrary+        Positive d <- arbitrary+        if i+c+d >= j+          then return []+          else do+            cs <- go (i+c+1) (i+c+d)+            let h = SSTree (i+c,i+c+d) () cs+            ts <- go (i+c+d+1) j+            return $ h:ts+{-+  shrink (ASST (SSExtern k () cs))+    | null cs = []+    | otherwise = [ ASST+-}++collectPairs (ASST (SSExtern k _ zs)) = (k, sort $ go zs)+  where go [] = []+        go (SSTree (i,j) _ cs : ss) = (i,j) : go cs ++ go ss++bld :: Int -> [PairIdx] -> D1Secondary+bld = curry mkD1S++prop_d1Distance a@(ASST _) b@(ASST _) = d1Distance x y == k+  where x = mkD1S (lx', x')+        y = mkD1S (ly', y')+        (lx', x') = collectPairs a+        (ly', y') = collectPairs b+        k = length $ (x' \\ y') ++ (y' \\ x')++---- | Check if both the memoized version and the population enumeration+---- produce the same multisets, but maybe in different order.+----+---- prop> \(n :: Int16) -> let b = popCount n in memoSorted b == enumSorted b+----+--+--prop_PopCountSet (NonZero (n' :: Int16)) = memo == enum+--  where b    = popCount n+--        memo = memoSorted b+--        enum = enumSorted b+--        n    = n' `mod` 12+--+--memoSorted, enumSorted :: Int -> [[Int]]+--+--memoSorted b = map sort . groupBy ((==) `on` popCount) $ VU.toList $ popCntMemoInt b+--enumSorted b = map sort                                $ [0] : [ roll (popPermutation b) (Just $ 2^k-1) | k <- [1..b] ]+--  where roll f (Just k) = k : roll f (f k)+--        roll _ Nothing  = []+--+--prop_lsb_Int (x :: Int) = lsbZ x == maybe (-1) id (maybeLsb x)+--+--prop_lsb_Word (x :: Word) = lsbZ x == maybe (-1) id (maybeLsb x)+--+--prop_OneBits_Int (x :: Int) = popCount x == length abl && and [ testBit x k | k <- abl ]+--  where abl = activeBitsL x+--+---- Tests if we actually generate all permutations.+--+--prop_allPermutations (a :: Int , b :: Int) = and $ zipWith cmp (sort qs) (sort $ nub ps)+--  where nbs = min a' b' -- number of 1 bits in set+--        sts = max a' b' -- set size+--        a' = a `mod` 8 -- finiteBitSize a+--        b' = b `mod` 8 -- finiteBitSize b+--        ps = permutations $ replicate (sts - nbs) False ++ replicate nbs True+--        qs = go (Just $ 2 ^ nbs - 1)+--        go :: Maybe Int -> [Int]+--        go Nothing  = []+--        go (Just k) = k : go (popPermutation sts k)+--        cmp k as = and [ if a then testBit k c else (not $ testBit k c) | (a,c) <- zip (reverse as) [0 .. ] ]+--+---- TODO popComplement+--+--prop_popShiftL_popShiftR (a::Word,b::Word) = s == l+--  where m = a .|. b+--        s = a .&. b+--        l = popShiftL m r+--        r = popShiftR m s++++main :: IO ()+main = $(defaultMainGenerator)+