BiobaseTurner 0.2.2.4 → 0.3.0.0

raw patch · 3 files changed

+211/−139 lines, 3 filesdep +conduitdep +lensdep +primitivedep −iterateedep ~BiobaseXNAdep ~PrimitiveArraydep ~splitPVP ok

version bump matches the API change (PVP)

Dependencies added: conduit, lens, primitive, repa

Dependencies removed: iteratee

Dependency ranges changed: BiobaseXNA, PrimitiveArray, split, vector

API changes (from Hackage documentation)

Files

• Biobase/Turner.hs +117/−47
• Biobase/Turner/Import.hs +75/−72
• BiobaseTurner.cabal +19/−20

@@ -1,3 +1,9 @@+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE StandaloneDeriving #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE TemplateHaskell #-} {-# LANGUAGE TypeOperators #-}  -- | The 'Turner2004' data structure reflects the RNA (and DNA) energy@@ -6,26 +12,85 @@ -- In general, have a look here: -- <http://rna.urmc.rochester.edu/NNDB/turner04/index.html> where parameters -- are explained.+--+-- TODO need a "Functor" instance over elements "e". Or alternatively, generic+-- programming to capture stuff going on in 'e'  module Biobase.Turner where -import Data.ByteString-import Data.Map as M++import Control.Lens import Data.Array.Repa.Index+import Data.ByteString (ByteString(..))+import qualified Data.ByteString+import qualified Data.Map as M+import qualified Data.Vector as V+import qualified Data.Vector.Unboxed as VU+import qualified Data.Vector.Generic as VG+import qualified Data.Vector.Generic.Mutable as VGM+import Data.Primitive.Types  import Biobase.Primary import Biobase.Secondary-import Data.PrimitiveArray-import Data.PrimitiveArray.Unboxed.Zero+import Data.PrimitiveArray as PA+import Data.PrimitiveArray.Zero --- | 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.------ TODO use 'Energy' instead of 'Double'------ TODO specialized shape types for pairs? ++-- | The actual Turner parameters return energies in Double format.++newtype Energy = Energy Double+  deriving (Eq,Ord,Num,Read,Show)++deriving instance Prim Energy+deriving instance VGM.MVector VU.MVector Energy+deriving instance VG.Vector   VU.Vector  Energy+deriving instance VU.Unbox Energy++-- | The Turner model with 'Energy's.++type Turner2004 = Turner2004Model Energy++-- | The Turner energy tables. Parametrized over the storing vector type 'v'+-- and the actual element type 'e'.++data Turner2004Model e = Turner2004Model+  { _stack              :: !(Unboxed PP e)+  , _dangle3            :: !(Unboxed PN e)+  , _dangle5            :: !(Unboxed PN e)+  , _hairpinL           :: !(VU.Vector e)+  , _hairpinMM          :: !(Unboxed PNN e)+  , _hairpinLookup      :: !(M.Map ByteString e)+  , _hairpinGGG         :: !e+  , _hairpinCslope      :: !e+  , _hairpinCintercept  :: !e+  , _hairpinC3          :: !e+  , _bulgeL             :: !(VU.Vector e)+  , _bulgeSingleC       :: !e+  , _iloop1x1           :: !(Unboxed PPNN e)+  , _iloop2x1           :: !(Unboxed PPNNN e)+  , _iloop2x2           :: !(Unboxed PPNNNN e)+  , _iloopMM            :: !(Unboxed PNN e)+  , _iloop2x3MM         :: !(Unboxed PNN e)+  , _iloop1xnMM         :: !(Unboxed PNN e)+  , _iloopL             :: !(VU.Vector e)+  , _multiMM            :: !(Unboxed PNN e)+  , _ninio              :: !e+  , _maxNinio           :: !e+  , _multiOffset        :: !e+  , _multiNuc           :: !e+  , _multiHelix         :: !e+  , _multiAsym          :: !e+  , _multiStrain        :: !e+  , _extMM              :: !(Unboxed PNN e)+  , _coaxial            :: !(Unboxed PP e) -- no intervening unpaired nucleotides+  , _coaxStack          :: !(Unboxed PNN e)+  , _tStackCoax         :: !(Unboxed PNN e)+  , _largeLoop          :: !e+  , _termAU             :: !e+  , _intermolecularInit :: !e+  } deriving (Show)+ type PP = (Z:.Nuc:.Nuc:.Nuc:.Nuc) type PN = (Z:.Nuc:.Nuc:.Nuc) type PNN = (Z:.Nuc:.Nuc:.Nuc:.Nuc)@@ -33,40 +98,45 @@ type PPNNN = PPNN:.Nuc type PPNNNN = PPNNN:.Nuc -data Turner2004 = Turner2004-  { stack :: Arr0 PP Double-  , dangle3 :: Arr0 PN Double-  , dangle5 :: Arr0 PN Double-  , hairpinL :: Arr0 DIM1 Double-  , hairpinMM :: Arr0 PNN Double-  , hairpinLookup :: M.Map ByteString Double-  , hairpinGGG :: Double-  , hairpinCslope :: Double-  , hairpinCintercept :: Double-  , hairpinC3 :: Double-  , bulgeL :: Arr0 DIM1 Double-  , bulgeSingleC :: Double-  , iloop1x1 :: Arr0 PPNN Double-  , iloop2x1 :: Arr0 PPNNN Double-  , iloop2x2 :: Arr0 PPNNNN Double-  , iloopMM :: Arr0 PNN Double-  , iloop2x3MM :: Arr0 PNN Double-  , iloop1xnMM :: Arr0 PNN Double-  , iloopL :: Arr0 DIM1 Double-  , multiMM :: Arr0 PNN Double-  , ninio :: Double-  , maxNinio :: Double-  , multiOffset :: Double-  , multiNuc :: Double-  , multiHelix :: Double-  , multiAsym :: Double-  , multiStrain :: Double-  , extMM :: Arr0 PNN Double-  , coaxial :: Arr0 PP Double -- no intervening unpaired nucleotides-  , coaxStack :: Arr0 PNN Double-  , tStackCoax :: Arr0 PNN Double-  , largeLoop :: Double-  , termAU :: Double-  , intermolecularInit :: Double-  } deriving ()+makeLenses ''Turner2004Model++-- | Map a function over all 'e' elements.++emap :: (VU.Unbox e, VU.Unbox e') => (e -> e') -> Turner2004Model e -> Turner2004Model e'+emap f Turner2004Model{..} = Turner2004Model+  { _stack              = PA.map f _stack+  , _dangle3            = PA.map f _dangle3+  , _dangle5            = PA.map f _dangle5+  , _hairpinL           = VU.map f _hairpinL+  , _hairpinMM          = PA.map f _hairpinMM+  , _hairpinLookup      = M.map f _hairpinLookup+  , _hairpinGGG         = f _hairpinGGG+  , _hairpinCslope      = f _hairpinCslope+  , _hairpinCintercept  = f _hairpinCintercept+  , _hairpinC3          = f _hairpinC3+  , _bulgeL             = VU.map f _bulgeL+  , _bulgeSingleC       = f _bulgeSingleC+  , _iloop1x1           = PA.map f _iloop1x1+  , _iloop2x1           = PA.map f _iloop2x1+  , _iloop2x2           = PA.map f _iloop2x2+  , _iloopMM            = PA.map f _iloopMM+  , _iloop2x3MM         = PA.map f _iloop2x3MM+  , _iloop1xnMM         = PA.map f _iloop1xnMM+  , _iloopL             = VU.map f _iloopL+  , _multiMM            = PA.map f _multiMM+  , _ninio              = f _ninio+  , _maxNinio           = f _maxNinio+  , _multiOffset        = f _multiOffset+  , _multiNuc           = f _multiNuc+  , _multiHelix         = f _multiHelix+  , _multiAsym          = f _multiAsym+  , _multiStrain        = f _multiStrain+  , _extMM              = PA.map f _extMM+  , _coaxial            = PA.map f _coaxial+  , _coaxStack          = PA.map f _coaxStack+  , _tStackCoax         = PA.map f _tStackCoax+  , _largeLoop          = f _largeLoop+  , _termAU             = f _termAU+  , _intermolecularInit = f _intermolecularInit+  } 

@@ -41,14 +41,15 @@ import Data.ByteString.Char8 as BS import Data.ByteString.Lex.Double import Data.Char-import Data.Iteratee as I-import Data.Iteratee.Char as I-import Data.Iteratee.IO as I+import Data.Conduit as C+import Data.Conduit.Binary as C+import Data.Conduit.List as CL import Data.List.Split import Data.Map as M import Data.Maybe (fromJust) import qualified Data.List as L import System.FilePath.Posix+import qualified Data.Vector.Unboxed as VU  import Biobase.Primary import Biobase.Secondary@@ -72,7 +73,7 @@   hairpinLk4 <- tabFromFile   $ fp </> prefix ++ "tloop"    <.> suffix   hairpinLk6 <- tabFromFile   $ fp </> prefix ++ "hexaloop" <.> suffix   let (dangle3',dangle5') = L.splitAt (L.length dangle' `div` 2) dangle'-  let (_:iloopL':bulgeL':hairpinL':[]) = L.transpose $ splitEvery 4 loop'+  let (_:iloopL':bulgeL':hairpinL':[]) = L.transpose $ chunksOf 4 loop'   iloop1x1'   <- blockFromFile $ fp </> prefix ++ "int11" <.> suffix   iloop2x1'   <- blockFromFile $ fp </> prefix ++ "int21" <.> suffix   iloop2x2'   <- blockFromFile $ fp </> prefix ++ "int22" <.> suffix@@ -85,41 +86,41 @@   coaxial'    <- blockFromFile $ fp </> prefix ++ "coaxial" <.> suffix   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 (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 (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'-    , iloop2x2      = fromAssocs minPPBBBB maxPPBBBB infE $ L.zip (if (prefix == "" || suffix == "dh") then keysPPBBBBrna else keysPPBBBBdna) iloop2x2'-    , 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 (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-    , multiOffset = (imisc' !! 3) !! 0-    , multiNuc = (imisc' !! 3) !! 1-    , multiHelix = (imisc' !! 3) !! 2-    , multiAsym = L.head $ imisc' !! 5-    , multiStrain = L.head $ imisc' !! 6-    , extMM      = fromAssocs minPBB maxPBB infE $ L.zip keysPBB extMM'-    , coaxial    = fromAssocs minPP  maxPP  infE $ L.zip keysPP  coaxial'-    , coaxStack  = fromAssocs minPBB maxPBB infE $ L.zip keysPBB cstack'-    , tStackCoax = fromAssocs minPBB maxPBB infE $ L.zip keysPBB tstack'-    , largeLoop = L.head $ imisc' !! 0-    , termAU = L.head $ imisc' !! 7-    , intermolecularInit = L.head $ imisc' !! 12+  return Turner2004Model+    { _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           = VU.fromList $ infE : 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         = Energy . L.head $ imisc' !! 8+    , _hairpinCslope      = Energy . L.head $ imisc' !! 9+    , _hairpinCintercept  = Energy . L.head $ imisc' !! 10+    , _hairpinC3          = Energy . L.head $ imisc' !! 11+    , _bulgeL             = VU.fromList $ infE : bulgeL' -- fromAssocs (Z:.0)      (Z:.30)     infE $ L.zip d1_30 bulgeL'+    , _bulgeSingleC       = Energy . L.head $ imisc' !! 13+    , _iloop1x1           = fromAssocs minPPBB   maxPPBB   infE $ L.zip keysPPBB   iloop1x1'+    , _iloop2x1           = fromAssocs minPPBBB  maxPPBBB  infE $ L.zip keysPPBBB  iloop2x1'+    , _iloop2x2           = fromAssocs minPPBBBB maxPPBBBB infE $ L.zip (if (prefix == "" || suffix == "dh") then keysPPBBBBrna else keysPPBBBBdna) iloop2x2'+    , _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             = VU.fromList $ infE : iloopL' -- fromAssocs (Z:.0)    (Z:.30)   infE $ L.zip d1_30      iloopL'+    , _multiMM            = fromAssocs minPBB    maxPBB    infE $ L.zip keysPBB    multiMM'+    , _ninio              = Energy . L.head $ imisc' !! 2+    , _maxNinio           = Energy . L.head $ imisc' !! 1+    , _multiOffset        = Energy $ (imisc' !! 3) !! 0+    , _multiNuc           = Energy $ (imisc' !! 3) !! 1+    , _multiHelix         = Energy $ (imisc' !! 3) !! 2+    , _multiAsym          = Energy . L.head $ imisc' !! 5+    , _multiStrain        = Energy . L.head $ imisc' !! 6+    , _extMM              = fromAssocs minPBB maxPBB infE $ L.zip keysPBB extMM'+    , _coaxial            = fromAssocs minPP  maxPP  infE $ L.zip keysPP  coaxial'+    , _coaxStack          = fromAssocs minPBB maxPBB infE $ L.zip keysPBB cstack'+    , _tStackCoax         = fromAssocs minPBB maxPBB infE $ L.zip keysPBB tstack'+    , _largeLoop          = Energy . L.head $ imisc' !! 0+    , _termAU             = Energy . L.head $ imisc' !! 7+    , _intermolecularInit = Energy . L.head $ imisc' !! 12     }  minPP     = Z:.nN:.nN:.nN:.nN -- (minP,minP)@@ -156,67 +157,69 @@ plist22rna = [(nA,nU),(nC,nG),(nG,nC),(nG,nU),(nU,nA),(nU,nG)] plist22dna = [(nA,nT),(nC,nG),(nG,nC),(nT,nA),(nG,nT),(nT,nG)] -infE = 999999 :: Double---- * Iteratee stuff---- | Transform input stream into list of list of doubles+infE = Energy 999999 -eneeBlocks :: (Functor m, Monad m) => Enumeratee ByteString [[Double]] m a-eneeBlocks = enumLinesBS ><> mapStream f ><> I.filter (not . L.null) where-  f x-    | "5'" `isPrefixOf` y = []-    | "3'" `isPrefixOf` y = []-    | "." `isPrefixOf`  y = values y-    | Just (d,xs) <- readDouble y = values y-    | otherwise = [] -- error $ BS.unpack x-    where y = BS.dropWhile isSpace x+-- * Conduit stuff  -- | extract values. "." - values are extracted as > 100k -values :: ByteString -> [Double]+values :: ByteString -> [Energy] values xs   | BS.null ys     = []   | "." `isPrefixOf` ys     = infE : values (BS.drop 1 ys)   | Just (d,zs) <- readDouble ys-    = d : values zs+    = Energy d : values zs   where ys = BS.dropWhile isSpace xs  -- | Iteratee to parse tabulated loops (hairpins). -iTabulated :: (Functor m, Monad m) => Iteratee ByteString m [(ByteString,Double)]-iTabulated = joinI $ enumLinesBS ><> I.filter (BS.all isSpace) $ g where+parseTabulated :: Monad m => Sink ByteString m [(ByteString,Energy)]+parseTabulated = C.lines =$ CL.filter (not . BS.all isSpace) =$ g where   g = do-    I.drop 2-    joinI $ mapStream f stream2stream+    CL.drop 2+    xs <- CL.map f =$ consume+    return xs   f x-    | Just (d,_) <- readDouble v = (k,d)+    | Just (d,_) <- readDouble v = (k,Energy d)     | otherwise = error $ "tabulated: <" ++ BS.unpack x ++ ">"     where (k,v) = second (BS.dropWhile isSpace) . BS.span (not . isSpace) . BS.dropWhile isSpace $ x  -- | Convenience function -blockFromFile :: FilePath -> IO [Double]+blockFromFile :: FilePath -> IO [Energy] blockFromFile fp = do-  i <- enumFile 8192 fp . joinI $ eneeBlocks stream2list-  xs <- run i+  xs <- runResourceT $ sourceFile fp $$ parseBlocks =$ consume   if (allEq $ L.map L.length xs)     then return $ L.concat xs     else error $ "in file: " ++ fp ++ " we have unequal line lengths" +-- | Transform input stream into list of list of doubles++parseBlocks :: Monad m => Conduit ByteString m [Energy]+parseBlocks = C.lines =$= CL.map f =$= CL.filter (not . L.null) where+  f x+    | "5'" `isPrefixOf` y = []+    | "3'" `isPrefixOf` y = []+    | "." `isPrefixOf`  y = values y+    | Just (d,xs) <- readDouble y = values y+    | otherwise = [] -- error $ BS.unpack x+    where y = BS.dropWhile isSpace x+++ -- | Parses the miscloop table ----- NOTO extra brownie points for miscloop.dat for providing data in a form that+-- NOTE extra brownie points for miscloop.dat for providing data in a form that -- does not conform to normal number encoding. -iMiscLoop :: (Functor m, Monad m) => Iteratee ByteString m [[Double]]-iMiscLoop = joinI $ enumLinesBS ><> I.groupBy (\x y -> not $ BS.null y) $ f where+parseMiscLoop :: Monad m => Sink ByteString m [[Double]]+parseMiscLoop = C.lines =$ CL.groupBy (\x y -> not $ BS.null y) =$ f where   f = do-    I.drop 1-    xs <- fmap (L.map (L.map (readD) . BS.words . L.last)) $ stream2list-    return xs+    CL.drop 1+    xs <- consume+    return . L.map (L.map readD . BS.words . L.last) $ xs  -- | Parses stupidly encoded values like ".6" and "-.0". @@ -231,12 +234,12 @@ -- |  miscFromFile :: FilePath -> IO [[Double]]-miscFromFile fp = run =<< enumFile 8192 fp iMiscLoop+miscFromFile fp = runResourceT $ sourceFile fp $$ parseMiscLoop  -- | -tabFromFile :: FilePath -> IO [(ByteString,Double)]-tabFromFile fp = run =<< enumFile 8192 fp iTabulated+tabFromFile :: FilePath -> IO [(ByteString,Energy)]+tabFromFile fp = runResourceT $ sourceFile fp $$ parseTabulated  allEq [] = True allEq (x:xs) = L.all (==x) xs

@@ -1,9 +1,9 @@ name:           BiobaseTurner-version:        0.2.2.4+version:        0.3.0.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/-copyright:      Christian Hoener zu Siederdissen, 2010-2012+copyright:      Christian Hoener zu Siederdissen, 2010-2013 category:       Bioinformatics synopsis:       Import Turner RNA parameters license:        GPL-3@@ -19,32 +19,31 @@                 The file structure is geared towards humans, not machines. If                 you need to be able to export, send a mail.                 .-                This is the 2011 post-library split version, hence not-                deprecated anymore.-                .                 NOTE This is rather fragile as some files use different index-                enumerations, which we handle rather... simplistically. We-                cannot fix one asymmetry case in dnastack.dh, as we do not-                change sources.+                enumerations, which we handle rather... simplistically.                 .-                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.+                In principle, all parameters should be symmetric regarding the+                stem direction. However, there is one asymmetry case in+                dnastack.dh. We do not fix this problem as we do not change the+                source files.    library   build-depends:     base >3 && <5,-    bytestring        >= 0.9,-    bytestring-lexing >= 0.4,-    containers     >= 0.4,-    filepath       >= 1,-    iteratee       >= 0.8.8,-    split          >= 0.1.4,-    vector         == 0.9.*   ,-    BiobaseXNA     == 0.6.2.5 ,-    PrimitiveArray == 0.2.2.0+    bytestring        >= 0.9    ,+    bytestring-lexing >= 0.4    ,+    conduit           >= 0.5    ,+    containers        >= 0.4    ,+    filepath          >= 1      ,+    lens              >= 3.8    ,+    primitive         >= 0.5    ,+    repa              >= 3.2    ,+    split             >= 0.2    ,+    vector            >= 0.10   ,+    BiobaseXNA        >= 0.7    ,+    PrimitiveArray    >= 0.5    exposed-modules:     Biobase.Turner