BiobaseTurner (empty) → 0.0.2.1

raw patch · 6 files changed

+1066/−0 lines, 6 filesdep +Biobasedep +FileManipdep +HsToolssetup-changed

Dependencies added: Biobase, FileManip, HsTools, ParsecTools, PrimitiveArray, base, containers, parsec, primitive, split

Files

Biobase/Turner.hs +41/−0
Biobase/Turner/Import.hs +176/−0
Biobase/Turner/Tables.hs +133/−0
BiobaseTurner.cabal +39/−0
LICENSE +675/−0
Setup.hs +2/−0

+ Biobase/Turner.hs view

@@ -0,0 +1,41 @@+{-# LANGUAGE TypeSynonymInstances #-}++-- | Mathews / Turner nearest neighbor energy tables for interactions between+-- RNA-RNA and DNA-DNA. Using lazy tables for easy filling of missing data.+-- Transform tables into uvectors for efficient access.++module Biobase.Turner where++import Biobase.RNA (Nucleotide)+import qualified Biobase.Turner.Tables as T++++-- | Data structure containing all necessary tables for the Turner 2004 model.+-- Note the temperature, using an additional function, rescaling becomes+-- possible. A Show and a Read instance are automatically derived but one+-- should use the Turner and/or Vienna import/export facilities. All data uses+-- complete tables, where any base can pair with any other. Missing data ('.'+-- in tables) is given by 'Nothing', otherwise we have 'Just Int'.+-- +-- In general, have a look here:+-- \url{http://rna.urmc.rochester.edu/NNDB/turner04/index.html} where+-- parameters are explained.+-- +-- Conversion from Turner to Vienna is only possible in one direction as a+-- number of parameters are not used in Vienna RNA Folding.++++-- We are missing tables for DNA-RNA data: helixdr.dat, stackdr.dat,+-- stackdr.dh.  Several other files have unknown data, too. These are:+-- dnadynalign*, fam\_hmm\_pars.dat, helix.dat, int22-exp.dh++type TurnerTables = T.Turner2004 Basepair Nucleotide Double++type TurnerEntropy  = TurnerTables+type TurnerEnthalpy = TurnerTables+type Temperature    = Double+type TurnerSet      = (Temperature,TurnerEntropy,TurnerEnthalpy)++type Basepair = (Nucleotide,Nucleotide)

+ Biobase/Turner/Import.hs view

@@ -0,0 +1,176 @@+{-# LANGUAGE NoMonomorphismRestriction #-}++-- | Turner file parser. Returns a Turner2004 data structure. We store data in+-- the same way it is stored in the ViennaRNA package. Pairs are tuples+-- however.+--+-- How is 'stack' data stored:+--+-- AX+-- UY   ->  ((A,U),(Y,X))+--+-- How 'iloop1x1' is stored:+--+--  X+-- A G+-- U C  -> ((A,U),(C,G),X,Y)+--  Y+--+--  Now 'iloop1x2' is stored:+--+--  X+-- A  G+-- U  C  -> ((A,U),(C,G),X,C,Y), single (X) first, then 5' to 3'+--  YC+--+--  'iloop2x2' is stored:+--+--  XY+-- A  G+-- U  C  -> ((A,U),(C,G),X,Y,y,x), X-->Y then x<--y+--  xy+--+--TODO not sure if dangle3/dangle5 are correctly split or if they should switch++module Biobase.Turner.Import+  ( parseTurner+  ) where++import Control.Applicative+import Control.Arrow (first)+import Control.Monad+import Data.Either+import Data.List.Split (splitEvery)+import Data.List (transpose)+import qualified Data.Map as M+import System.FilePath.Find+import Text.Parsec hiding ((<|>), many)+import Text.Parsec.String++import Biobase.RNA+import Data.Ix.Tuple+import Data.PrimitiveArray+import Data.PrimitiveArray.Ix+import Text.Parsec.Numbers++import Biobase.Turner.Tables++++-- * Associate every file with a parse.++minp = (nucA,nucA)+maxp = (nucU,nucU)+minpb = (minp,nucA)+maxpb = (maxp,nucU)+minpp = (minp,minp)+maxpp = (maxp,maxp)+minppbb = (minp,minp,nucA,nucA)+maxppbb = (maxp,maxp,nucU,nucU)+minppbbb = (minp,minp,nucA,nucA,nucA)+maxppbbb = (maxp,maxp,nucU,nucU,nucU)+minppbbbb = (minp,minp,nucA,nucA,nucA,nucA)+maxppbbbb = (maxp,maxp,nucU,nucU,nucU,nucU)+minpbb = (minp,nucA,nucA)+maxpbb = (maxp,nucU,nucU)+-- (4,3) switched for vienna rna compatibility+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) | k1 <- acgu, k3 <- acgu, k2 <- acgu, k4 <- acgu]+plist11 = [(nucA,nucU),(nucC,nucG),(nucG,nucC),(nucU,nucA),(nucG,nucU),(nucU,nucG)]+plist22 = [(nucA,nucU),(nucC,nucG),(nucG,nucC),(nucG,nucU),(nucU,nucA),(nucU,nucG)]+-- (4,3) switched for vienna rna compatibility+keysppbb = [((k1,k2),(k4,k3),k5,k6) | (k1,k2) <- plist11, k5 <- acgu, (k3,k4) <- plist11, k6 <- acgu]+-- (4,3) switched for vienna rna compatibility+keysppbbb = [((k1,k2),(k4,k3),k5,k6,k7) | (k1,k2) <- plist11, k6 <- acgu, k5 <- acgu, (k3,k4) <- plist11, k7 <- acgu]+-- (4,3) switched for vienna rna compatibility, 5786 is 5'3' order top, bottom!+keysppbbbb = [((k1,k2),(k4,k3),k5,k6,k7,k8) | (k1,k2) <- plist22, (k3,k4) <- plist22, k5 <- acgu, k8 <- acgu, k6 <- acgu, k7 <- acgu]+z = 999999++++-- | Given the base dir and a suffix (.dat/.dh most likely), parse the relevant+-- files. The prefix can be used for, eg., dna file++parseTurner prefix basedir fsuffix = do+  vstack <- grabB basedir fsuffix $ prefix ++ "stack"+  vdangles <- grabB basedir fsuffix $ prefix ++ "dangle"+  vlengths <- grabB basedir fsuffix $ prefix ++ "loop"+  vhairmm <- grabB basedir fsuffix $ prefix ++ "tstackh"+  viloopmm <- grabB basedir fsuffix $ prefix ++ "tstacki"+  viloop23mm <- grabB basedir fsuffix $ prefix ++ "tstacki23"+  viloop1nmm <- grabB basedir fsuffix $ prefix ++ "tstacki1n"+  vmultimm <- grabB basedir fsuffix $ prefix ++ "tstackm"+  vextmm <- grabB basedir fsuffix $ prefix ++ "tstack"+  viloop11 <- grabB basedir fsuffix $ prefix ++ "int11"+  viloop12 <- grabB basedir fsuffix $ prefix ++ "int21"+  viloop22 <- grabB basedir fsuffix $ prefix ++ "int22"+  vlookups <- fmap (map (first (map charToNucleotide)) . concat) $ mapM (\f -> grabA basedir fsuffix $ prefix ++ f) ["triloop","tloop","hexaloop"]+  vmisc <- grabB basedir fsuffix $ prefix ++ "miscloop"+  let (vdangle3,vdangle5) = splitAt (length vdangles `div` 2) vdangles+  let (_:viloopl:vbulgel:vhairpinl:[]) = transpose $ splitEvery 4 vlengths+  return $ Turner2004+    { stack = fromAssocs minpp maxpp z $ zip keyspp vstack+    , dangle3 = fromAssocs minpb maxpb z $ zip keyspb vdangle3+    , dangle5 = fromAssocs minpb maxpb z $ zip keyspb vdangle5+    , hairpinL = fromAssocs 0 30 z $ zip [1..] vhairpinl+    , bulgeL = fromAssocs 0 30 z $ zip [1..] vbulgel+    , iloopL = fromAssocs 0 30 z $ zip [1..] viloopl+    , hairpinMM = fromAssocs minpbb maxpbb z $ zip keyspbb vhairmm+    , iloopMM = fromAssocs minpbb maxpbb z $ zip keyspbb viloopmm+    , iloop2x3MM = fromAssocs minpbb maxpbb z $ zip keyspbb viloop23mm+    , iloop1xnMM = fromAssocs minpbb maxpbb z $ zip keyspbb viloop1nmm+    , multiMM = fromAssocs minpbb maxpbb z $ zip keyspbb vmultimm+    , extMM = fromAssocs minpbb maxpbb z $ zip keyspbb vextmm+    , hairpinLookup = M.fromList vlookups+    , iloop1x1 = fromAssocs minppbb   maxppbb   z $ zip keysppbb   viloop11+    , iloop1x2 = fromAssocs minppbbb  maxppbbb  z $ zip keysppbbb  viloop12+    , iloop2x2 = fromAssocs minppbbbb maxppbbbb z $ zip keysppbbbb viloop22+    , ninio = vmisc !! 2+    , maxNinio = vmisc !! 1+    , multiOffset = vmisc !! 6+    , multiNuc = vmisc !! 7+    , multiHelix = vmisc !! 8+    , largeLoop = vmisc !! 0+    , termAU = vmisc !! 14+    , intermolecularInit = vmisc !! 19+    }++grabB basedir fsuffix fname = do+  p <- parseFromFile pBlockFile (basedir ++ "/" ++ fname ++ fsuffix)+  case p of+    (Right ans) -> return ans+    (Left err)  -> error $ show err++grabA basedir fsuffix fname = do+  p <- parseFromFile pAssocFile (basedir ++ "/" ++ fname ++ fsuffix)+  case p of+    (Right ans) -> return ans+    (Left err)  -> error $ show err++++-- * File parser: We do not want to understand the format, just extract all+-- data.++-- | Blocks of data.++pBlockFile = concat <$> many (try numberRow <|> infoRow) <* eof where+  -- a line with a least one number+  numberRow = many (char ' ') *> (number <* notFollowedBy (char '\'')) `sepEndBy1` (many $ char ' ') <* newline+  -- a number is a dot or some extended floating point number+  number = (try dotFloat) <|> (999999 <$ char '.') <|> parseExtFloat <?> "floating point number"++-- | A File with associations.++pAssocFile = concat <$> many1 (try assocRow <|> infoRow) where+  -- one assocs of string, value+  assocRow = (\a b -> [(a,b)]) <$ many (char ' ') <*> many1 (oneOf nuc) <* many (char ' ') <*> parseExtFloat <* many (char ' ')++-- a line with crap+infoRow = [] <$ anyChar `manyTill` newline++-- a rather stupid float+dotFloat = (\s a b -> read $ s:'0':a:b) <$> (char '-' <|> pure ' ') <*> char '.' <*> many1 digit++nuc = "ACGUT"

+ Biobase/Turner/Tables.hs view

@@ -0,0 +1,133 @@+{-# LANGUAGE TemplateHaskell #-}+{-# LANGUAGE DeriveFunctor #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE TypeSynonymInstances #-}++-- | Turner Nearest Neighbor Energy Tables}++-- TODO (Read) instance? (Vector has no Read instance...)++module Biobase.Turner.Tables where++import qualified Data.Map as M++import Data.PrimitiveArray+import Data.PrimitiveArray.Ix++++-- | A data structure describing all fields as used by the Turner 2004+-- parameter set. Some fields are commented out until they are being used.++data Turner2004 a b c = Turner2004+  { stack :: PrimArray (a,a) c+  , dangle3 :: PrimArray (a,b) c+  , dangle5 :: PrimArray (a,b) c+  , hairpinL :: PrimArray Int c+  , hairpinMM :: PrimArray (a,b,b) c+  , hairpinLookup :: M.Map [b] c+--  , hairpinGGG :: c+--  , hairpinCslope :: c+--  , hairpinCintercept :: c+--  , hairpinC3 :: c+  , bulgeL :: PrimArray Int c+--  , bulgeSingleC :: c+  , iloop1x1 :: PrimArray (a,a,b,b) c+  , iloop1x2 :: PrimArray (a,a,b,b,b) c+  , iloop2x2 :: PrimArray (a,a,b,b,b,b) c+  , iloopMM :: PrimArray (a,b,b) c+  , iloop2x3MM :: PrimArray (a,b,b) c+  , iloop1xnMM :: PrimArray (a,b,b) c+  , iloopL :: PrimArray Int c+  , multiMM :: PrimArray (a,b,b) c+  , ninio :: c+  , maxNinio :: c+  , multiOffset :: c+  , multiNuc :: c+  , multiHelix :: c+--  , multiAsym :: c+--  , multiStrain :: c+  , extMM :: PrimArray (a,b,b) c+--  , coaxStack :: PrimArray (a,a) c+--  , coaxStackOpen :: PrimArray (a,b,b) c+--  , coaxStackCont :: PrimArray (a,b,b) c+  , largeLoop :: Double+  , termAU :: c+  , intermolecularInit :: c+  }++++-- | Map functions over the payload.++dmap f Turner2004{..} = Turner2004+  { stack = amap f stack+  , dangle3 = amap f dangle3+  , dangle5 = amap f dangle5+  , hairpinL = amap f hairpinL+  , hairpinMM = amap f hairpinMM+  , hairpinLookup = fmap f hairpinLookup+--  , hairpinGGG = f hairpinGGG+--  , hairpinCslope = f hairpinCslope+--  , hairpinCintercept = f hairpinCintercept+--  , hairpinC3 = f hairpinC3+  , bulgeL = amap f bulgeL+--  , bulgeSingleC = f bulgeSingleC+  , iloop1x1 = amap f iloop1x1+  , iloop1x2 = amap f iloop1x2+  , iloop2x2 = amap f iloop2x2+  , iloopMM = amap f iloopMM+  , iloop2x3MM = amap f iloop2x3MM+  , iloop1xnMM = amap f iloop1xnMM+  , iloopL = amap f iloopL+  , multiMM = amap f multiMM+  , ninio = f ninio+  , maxNinio = f maxNinio+  , multiOffset = f multiOffset+  , multiNuc = f multiNuc+  , multiHelix = f multiHelix+--  , multiAsym = f multiAsym+--  , multiStrain = f multiStrain+  , extMM = amap f extMM+--  , coaxStack = amap f coaxStack+--  , coaxStackOpen = amap f coaxStackOpen+--  , coaxStackCont = amap f coaxStackCont+  , largeLoop = largeLoop+  , termAU = f termAU+  , intermolecularInit = f intermolecularInit+  }++++-- | Zip two payloads.+--+-- TODO right now, we have undefined behaviour when some arrrays are of different length++dZipWith f t1 t2 = Turner2004+  { stack = zipWithPA f (stack t1) (stack t2)+  , dangle3 = zipWithPA f (dangle3 t1) (dangle3 t2)+  , dangle5 = zipWithPA f (dangle5 t1) (dangle5 t2)+  , hairpinL = zipWithPA f (hairpinL t1) (hairpinL t2)+  , hairpinMM = zipWithPA f (hairpinMM t1) (hairpinMM t2)+  , hairpinLookup = undefined -- zipWithPA f (hairpinLookup t1) (hairpinLookup t2)+  , bulgeL = zipWithPA f (bulgeL t1) (bulgeL t2)+  , iloop1x1 = zipWithPA f (iloop1x1 t1) (iloop1x1 t2)+  , iloop1x2 = zipWithPA f (iloop1x2 t1) (iloop1x2 t2)+  , iloop2x2 = zipWithPA f (iloop2x2 t1) (iloop2x2 t2)+  , iloopMM = zipWithPA f (iloopMM t1) (iloopMM t2)+  , iloop2x3MM = zipWithPA f (iloop2x3MM t1) (iloop2x3MM t2)+  , iloop1xnMM = zipWithPA f (iloop1xnMM t1) (iloop1xnMM t2)+  , iloopL = zipWithPA f (iloopL t1) (iloopL t2)+  , multiMM = zipWithPA f (multiMM t1) (multiMM t2)+  , ninio = f (ninio t1) (ninio t2)+  , maxNinio = f (maxNinio t1) (maxNinio t2)+  , multiOffset = f (multiOffset t1) (multiOffset t2)+  , multiNuc = f (multiNuc t1) (multiNuc t2)+  , multiHelix = f (multiHelix t1) (multiHelix t2)+  , extMM = zipWithPA f (extMM t1) (extMM t2)+  , largeLoop = largeLoop t1 -- no zipping here! TODO make this a constant somewhere!+  , termAU = f (termAU t1) (termAU t2)+  , intermolecularInit = f (intermolecularInit t1) (intermolecularInit t2)+  }++zipWithPA f a1 a2 = let (l,u) = bounds a1 in fromList l u $ zipWith f (toList a1) (toList a2)

+ BiobaseTurner.cabal view

@@ -0,0 +1,39 @@+name:           BiobaseTurner+version:        0.0.2.1+author:         Christian Hoener zu Siederdissen+maintainer:     choener@tbi.univie.ac.at+copyright:      Christian Hoener zu Siederdissen, 2010+category:       Bioinformatics+synopsis:       RNA folding data structures.+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.4.0+description:+                Data structures and parsers for the Turner 2004 set of RNA parameters.+                - http://rna.urmc.rochester.edu/NNDB/index.html++++library+  build-depends:+    base >=4 && <5,+    containers,+    parsec >=3 && <4,+    primitive >=0.3 && <0.4,+    FileManip >=0.3.3 && <0.4,+    split >=0.1.2 && <0.2,++    Biobase >=0.0.2 && <0.0.3,+    HsTools >=0.0.1.1 && <0.0.2,+    ParsecTools >=0.0.2 && <0.0.3,+    PrimitiveArray >=0.0.2 && <0.0.3++  exposed-modules:+    Biobase.Turner+    Biobase.Turner.Import+    Biobase.Turner.Tables++  ghc-options:+    -O2

+ LICENSE view

@@ -0,0 +1,675 @@+              GNU GENERAL PUBLIC LICENSE+                Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++                     Preamble++  The GNU General Public License is a free, copyleft license for+software and other kinds of works.++  The licenses for most software and other practical works are designed+to take away your freedom to share and change the works.  By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users.  We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors.  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+ Setup.hs view

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain