BiobaseTurner 0.1.1.0 → 0.2.0.0

raw patch · 3 files changed

+68/−47 lines, 3 filesdep +repadep +vectordep ~BiobaseXNAdep ~PrimitiveArrayPVP ok

version bump matches the API change (PVP)

Dependencies added: repa, vector

Dependency ranges changed: BiobaseXNA, PrimitiveArray

API changes (from Hackage documentation)

Files

• Biobase/Turner.hs +21/−15
• Biobase/Turner/Import.hs +32/−27
• BiobaseTurner.cabal +15/−5

@@ -1,3 +1,4 @@+{-# LANGUAGE TypeOperators #-}  -- | The 'Turner2004' data structure reflects the RNA (and DNA) energy -- parameters known as the Turner 2004 data set.@@ -10,41 +11,48 @@  import Data.ByteString import Data.Map as M+import Data.Array.Repa.Index  import Biobase.Primary import Biobase.Secondary import Data.PrimitiveArray-import Data.PrimitiveArray.Ix+import Data.PrimitiveArray.Unboxed  -- | The parameters. Turner parameters are set by the Import module for -- nucleotides n,a,c,g,u. All values that are not read (or are ".") will end up -- with a value > 100K. ----- [1] Yes, such instances are easily created, but I don't want to pull in--- another library and I don't want to create an Ix instance here.--- -- TODO use 'Energy' instead of 'Double'+--+-- TODO specialized shape types for pairs? +type PP = (Z:.Nuc:.Nuc:.Nuc:.Nuc)+type PN = (Z:.Nuc:.Nuc:.Nuc)+type PNN = (Z:.Nuc:.Nuc:.Nuc:.Nuc)+type PPNN = PP:.Nuc:.Nuc+type PPNNN = PPNN:.Nuc+type PPNNNN = PPNNN:.Nuc+ data Turner2004 = Turner2004-  { stack :: PrimArray (Pair,Pair) Double+  { stack :: PrimArray PP Double   , dangle3 :: PrimArray PN Double   , dangle5 :: PrimArray PN Double-  , hairpinL :: PrimArray Int Double+  , hairpinL :: PrimArray DIM1 Double   , hairpinMM :: PrimArray PNN Double   , hairpinLookup :: M.Map ByteString Double   , hairpinGGG :: Double   , hairpinCslope :: Double   , hairpinCintercept :: Double   , hairpinC3 :: Double-  , bulgeL :: PrimArray Int Double+  , bulgeL :: PrimArray DIM1 Double   , bulgeSingleC :: Double-  , iloop1x1 :: PrimArray (Pair,Pair,(Nuc,Nuc)) Double-  , iloop2x1 :: PrimArray (Pair,Pair,(Nuc,Nuc,Nuc)) Double-  , iloop2x2 :: PrimArray (Pair,Pair,(Nuc,Nuc,Nuc,Nuc)) Double -- yeah, 6-tuple ix instances :-( [1]+  , iloop1x1 :: PrimArray PPNN Double+  , iloop2x1 :: PrimArray PPNNN Double+  , iloop2x2 :: PrimArray PPNNNN Double   , iloopMM :: PrimArray PNN Double   , iloop2x3MM :: PrimArray PNN Double   , iloop1xnMM :: PrimArray PNN Double-  , iloopL :: PrimArray Int Double+  , iloopL :: PrimArray DIM1 Double   , multiMM :: PrimArray PNN Double   , ninio :: Double   , maxNinio :: Double@@ -54,13 +62,11 @@   , multiAsym :: Double   , multiStrain :: Double   , extMM :: PrimArray PNN Double-  , coaxial :: PrimArray (Pair,Pair) Double -- no intervening unpaired nucleotides+  , coaxial :: PrimArray PP Double -- no intervening unpaired nucleotides   , coaxStack :: PrimArray PNN Double   , tStackCoax :: PrimArray PNN Double   , largeLoop :: Double   , termAU :: Double   , intermolecularInit :: Double-  } deriving (Read,Show)+  } deriving (Show) -type PNN = (Pair,Nuc,Nuc)-type PN  = (Pair,Nuc)

@@ -1,3 +1,5 @@+{-# LANGUAGE PatternGuards #-}+{-# LANGUAGE TupleSections #-} {-# LANGUAGE NoMonomorphismRestriction #-} {-# LANGUAGE OverloadedStrings #-} @@ -46,6 +48,7 @@ import qualified Data.List as L import System.FilePath.Posix import Data.Maybe (fromJust)+import Data.Array.Repa.Index  import Biobase.Primary import Biobase.Secondary@@ -83,17 +86,17 @@   cstack'     <- blockFromFile $ fp </> prefix ++ "coaxstack" <.> suffix   tstack'     <- blockFromFile $ fp </> prefix ++ "tstackcoax" <.> suffix   return Turner2004-    { stack         = fromAssocs minPP  maxPP  infE $ L.zip keysPP  stack'-    , dangle3       = fromAssocs minPB  maxPB  infE $ L.zip keysPB  dangle3'-    , dangle5       = fromAssocs minPB  maxPB  infE $ L.zip keysPB  dangle5'-    , hairpinL      = fromAssocs 0      30     infE $ L.zip [1..30] hairpinL'+    { stack         = fromAssocs minPP  maxPP   infE $ L.zip keysPP  stack'+    , dangle3       = fromAssocs minPB  maxPB   infE $ L.zip keysPB  dangle3'+    , dangle5       = fromAssocs minPB  maxPB   infE $ L.zip keysPB  dangle5'+    , hairpinL      = fromAssocs (Z:.0) (Z:.30) infE $ L.zip d1_30 hairpinL'     , hairpinMM     = fromAssocs minPBB maxPBB infE $ L.zip keysPBB hairpinMM'     , hairpinLookup = M.fromList $ hairpinLk3 ++ hairpinLk4 ++ hairpinLk6     , hairpinGGG    = L.head $ imisc' !! 8     , hairpinCslope = L.head $ imisc' !! 9     , hairpinCintercept = L.head $ imisc' !! 10     , hairpinC3     = L.head $ imisc' !! 11-    , bulgeL        = fromAssocs 0      30     infE $ L.zip [1..30] bulgeL'+    , bulgeL        = fromAssocs (Z:.0)      (Z:.30)     infE $ L.zip d1_30 bulgeL'     , bulgeSingleC  = L.head $ imisc' !! 13     , iloop1x1      = fromAssocs minPPBB   maxPPBB   infE $ L.zip keysPPBB   iloop1x1'     , iloop2x1      = fromAssocs minPPBBB  maxPPBBB  infE $ L.zip keysPPBBB  iloop2x1'@@ -101,7 +104,7 @@     , iloopMM       = fromAssocs minPBB    maxPBB    infE $ L.zip keysPBB    iloopMM'     , iloop2x3MM    = fromAssocs minPBB    maxPBB    infE $ L.zip keysPBB    iloop2x3MM'     , iloop1xnMM    = fromAssocs minPBB    maxPBB    infE $ L.zip keysPBB    iloop1xnMM'-    , iloopL        = fromAssocs 0      30     infE $ L.zip [1..30] iloopL'+    , iloopL        = fromAssocs (Z:.0)    (Z:.30)   infE $ L.zip d1_30      iloopL'     , multiMM       = fromAssocs minPBB    maxPBB    infE $ L.zip keysPBB    multiMM'     , ninio = L.head $ imisc' !! 2     , maxNinio = L.head $ imisc' !! 1@@ -119,32 +122,34 @@     , intermolecularInit = L.head $ imisc' !! 12     } -minPP     = (minP,minP)-maxPP     = (maxP,maxP)-minP      = (nN,nN)-maxP      = (nU,nU)-minPB     = (minP,nN)-maxPB     = (maxP,nU)-minPBB    = (minP,nN,nN)-maxPBB    = (maxP,nU,nU)-minPPBB   = (minP,minP,(nN,nN))-maxPPBB   = (maxP,maxP,(nU,nU))-minPPBBB  = (minP,minP,(nN,nN,nN))-maxPPBBB  = (maxP,maxP,(nU,nU,nU))-minPPBBBB = (minP,minP,(nN,nN,nN,nN))-maxPPBBBB = (maxP,maxP,(nU,nU,nU,nU))+minPP     = Z:.nN:.nN:.nN:.nN -- (minP,minP)+maxPP     = Z:.nU:.nU:.nU:.nU -- (maxP,maxP)+minP      = Z:.nN:.nN -- (nN,nN)+maxP      = Z:.nU:.nU -- (nU,nU)+minPB     = minP:.nN -- (minP,nN)+maxPB     = maxP:.nU -- (maxP,nU)+minPBB    = minPB:.nN -- (minP,nN,nN)+maxPBB    = maxPB:.nU -- (maxP,nU,nU)+minPPBB   = minPP:.nN:.nN -- (minP,minP,(nN,nN))+maxPPBB   = maxPP:.nU:.nU -- (maxP,maxP,(nU,nU))+minPPBBB  = minPPBB:.nN -- (minP,minP,(nN,nN,nN))+maxPPBBB  = maxPPBB:.nU -- (maxP,maxP,(nU,nU,nU))+minPPBBBB = minPPBBB:.nN -- (minP,minP,(nN,nN,nN,nN))+maxPPBBBB = maxPPBBB:.nU -- (maxP,maxP,(nU,nU,nU,nU)) -keysPP     = [((k1,k2),(k4,k3)) | k1 <- acgu, k3 <- acgu, k2 <- acgu, k4 <- acgu]-keysPB     = [((k1,k2),k3) | k1 <- acgu, k2 <- acgu, k3 <- acgu]-keysPBB    = [ ((k1,k2),k3,k4)+d1_30 = L.map (Z:.) [1..30]++keysPP     = [{- ((k1,k2),(k4,k3)) -} Z:.k1:.k2:.k4:.k3 | k1 <- acgu, k3 <- acgu, k2 <- acgu, k4 <- acgu]+keysPB     = [{- ((k1,k2),k3) -} Z:.k1:.k2:.k3 | k1 <- acgu, k2 <- acgu, k3 <- acgu]+keysPBB    = [ {- ((k1,k2),k3,k4) -} Z:.k1:.k2:.k3:.k4              | k1 <- acgu, k3 <- acgu, k2 <- acgu, k4 <- acgu]-keysPPBB   = [ ((k1,k2),(k4,k3),(k5,k6))+keysPPBB   = [ {- ((k1,k2),(k4,k3),(k5,k6)) -} Z:.k1:.k2:.k4:.k3:.k5:.k6              | (k1,k2) <- plist11, k5 <- acgu, (k3,k4) <- plist11, k6 <- acgu]-keysPPBBB  = [ ((k1,k2),(k4,k3),(k5,k6,k7))+keysPPBBB  = [ {- ((k1,k2),(k4,k3),(k5,k6,k7)) -} Z:.k1:.k2:.k4:.k3:.k5:.k6:.k7              | (k1,k2) <- plist11, k6 <- acgu, k5 <- acgu, (k3,k4) <- plist11, k7 <- acgu]-keysPPBBBBrna = [ ((k1,k2),(k4,k3),(k5,k6,k7,k8))+keysPPBBBBrna = [ {- ((k1,k2),(k4,k3),(k5,k6,k7,k8)) -} Z:.k1:.k2:.k4:.k3:.k5:.k6:.k7:.k8                 | (k1,k2) <- plist22rna, (k3,k4) <- plist22rna, k5 <- acgu, k8 <- acgu, k6 <- acgu, k7 <- acgu]-keysPPBBBBdna = [ ((k1,k2),(k4,k3),(k5,k6,k7,k8))+keysPPBBBBdna = [ {- ((k1,k2),(k4,k3),(k5,k6,k7,k8)) -} Z:.k1:.k2:.k4:.k3:.k5:.k6:.k7:.k8                 | (k1,k2) <- plist22dna, (k3,k4) <- plist22dna, k5 <- acgu, k8 <- acgu, k6 <- acgu, k7 <- acgu]  plist11 = [(nA,nU),(nC,nG),(nG,nC),(nU,nA),(nG,nU),(nU,nG)]

@@ -1,9 +1,9 @@ name:           BiobaseTurner-version:        0.1.1.0+version:        0.2.0.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/-copyright:      Christian Hoener zu Siederdissen, 2010,2011+copyright:      Christian Hoener zu Siederdissen, 2010-2012 category:       Bioinformatics synopsis:       Import Turner RNA parameters license:        GPL-3@@ -26,6 +26,10 @@                 enumerations, which we handle rather... simplistically. We                 cannot fix one asymmetry case in dnastack.dh, as we do not                 change sources.+                .+                BIG FAT WARNING indexing now depends on repa shapes and index+                representations. (with a good reason coming soon). For now,+                just assume that this has performance benefits.  library   build-depends:@@ -36,13 +40,19 @@     filepath,     iteratee,     split,-    BiobaseXNA,-    PrimitiveArray+    BiobaseXNA >= 0.6.0.0,+    vector >= 0.9,+    repa >= 2.0,+    PrimitiveArray >= 0.1.1.2    exposed-modules:     Biobase.Turner     Biobase.Turner.Import    ghc-options:-    -O2+    -Odph -funbox-strict-fields -fspec-constr++source-repository head+  type: git+  location: git://github.com/choener/BiobaseTurner