Nussinov78 (empty) → 0.0.1.0
raw patch · 6 files changed
+1022/−0 lines, 6 filesdep +ADPfusiondep +BiobaseXNAdep +PrimitiveArraysetup-changed
Dependencies added: ADPfusion, BiobaseXNA, PrimitiveArray, base, mtl, primitive, vector
Files
- BioInf/Nussinov78.hs +167/−0
- C/nussinov.c +61/−0
- LICENSE +675/−0
- Nussinov78.cabal +96/−0
- Nussinov78.hs +21/−0
- Setup.hs +2/−0
+ BioInf/Nussinov78.hs view
@@ -0,0 +1,167 @@+{-# LANGUAGE PackageImports #-}+{-# LANGUAGE ScopedTypeVariables #-}+{-# LANGUAGE DoAndIfThenElse #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE FlexibleContexts #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE TypeFamilies #-}+{-# LANGUAGE NoMonomorphismRestriction #-}++-- | Strict, scalar nussinov78 algorithm.++module BioInf.Nussinov78 where++import Control.Arrow (first,second,(***))+import Control.Monad+import Control.Monad.Primitive+import Control.Monad.ST+import Control.Monad.State.Lazy+import "PrimitiveArray" Data.Array.Repa.Index+import qualified Data.Vector.Fusion.Stream as P+import qualified Data.Vector.Fusion.Stream.Monadic as S+import qualified Data.Vector.Unboxed as VU++import Biobase.Primary+import Biobase.Secondary.Vienna++import Data.PrimitiveArray+import Data.PrimitiveArray.Unboxed.Zero++import ADP.Fusion+import ADP.Fusion.Monadic+import ADP.Fusion.Monadic.Internal++++-- | Simple RNA folding with basepair maximization.++nussinov78 inp = arr `seq` bt where+ (_,Z:._:.n) = bounds arr+ arr = runST (nussinov78Fill . mkPrimary $ inp)+ bt = nussinov78BT (mkPrimary inp) arr+{-# NOINLINE nussinov78 #-}++-- | The actual Nussinov78 folding algorithm.++nussinov78Fill :: Primary -> ST s (Arr0 DIM2 Int)+nussinov78Fill inp = do+ let base = base' inp+ {-# INLINE base #-}+ let n = let (_,Z:.l) = bounds inp in l+1+ s <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 0 []++ fillTable s (+ nil <<< empty |||+ left <<< base -~~ s |||+ right <<< s ~~- base |||+ pair <<< base -~~ s ~~- base |||+ split <<< s +~+ s ... h+ )+ freeze s+{-# INLINE nussinov78Fill #-}++-- | Fill the single table with values in an orderly fashion. The order in+-- which we fill depends on the algorithm.++fillTable :: PrimMonad m => MArr0 (PrimState m) DIM2 Int -> (DIM2 -> m Int) -> m ()+fillTable tbl f = do+ let (_,Z:.n:._) = boundsM tbl+ forM_ [n,n-1..0] $ \i -> forM_ [i..n] $ \j -> do+ v <- f (Z:.i:.j)+ writeM tbl (Z:.i:.j) v+ return ()+{-# INLINE fillTable #-}++-- | Request the single character enclosed by (i,i+1), with i+1==j++base' :: Primary -> DIM2 -> (Scalar Nuc)+base' inp (Z:.i:.j) = Scalar $ inp ! (Z:.i)+{-# INLINE base' #-}++-- | True, if the subword at ij is empty.++empty :: DIM2 -> Scalar Bool+empty (Z:.i:.j) = Scalar $ i==j++-- | The base case of our recursion.++nil :: Bool -> Int+nil b = if b then 0 else -999999++-- | A single nucleotide to the left. Note that "x" is monadic. In 'nussinov'+-- we are in the ST monad, here we just know that we are in a monad.++left :: Nuc -> Int -> Int+left l x = x+{-# INLINE left #-}++-- | A single nucleotide to the right.++right :: Int -> Nuc -> Int+right x r = x+{-# INLINE right #-}++-- | Pair function++pair :: Nuc -> Int -> Nuc -> Int+pair l x r+ | basepair l r = x+1+ | otherwise = -999999+{-# INLINE pair #-}++-- | Combine the partition of x next-to y.++split :: Int -> Int -> Int+split = (+)+{-# INLINE split #-}++-- | Determine if two characters form a legal basepair.++basepair l r+ | mkViennaPair (l,r) /= vpNS = True+basepair _ _ = False+{-# INLINE basepair #-}++-- | the grammar makes sure that we at least have "nil #<< empty" in the stream+h = S.foldl1' max+{-# INLINE h #-}++++-- * backtrace secondary structures++type Backtrace = (Int,String)++nussinov78BT :: Primary -> Arr0 DIM2 Int -> [Backtrace]+nussinov78BT inp s = P.toList $ grammar (Z:.0:.n) where+ base = base' inp+ n = let (_,(Z:._:.l)) = bounds s in l+ s' :: DIM2 -> Scalar (DIM2,Int)+ s' ij = Scalar $ (ij,s!ij)++ grammar :: DIM2 -> P.Stream Backtrace+ grammar = (+ nilBT <<< empty |||+ leftBT <<< base -~~ s' |||+ rightBT <<< s' ~~- base |||+ pairBT <<< base -~~ s' ~~- base |||+ splitBT <<< s' +~+ s' ..@ hBT)++ nilBT :: Bool -> (Int, P.Stream Backtrace)+ nilBT b = if b then (0, P.singleton (0,"")) else (0, P.empty)++ leftBT :: Nuc -> (DIM2,Int) -> (Int, P.Stream Backtrace)+ leftBT _ (ij,x) = (x, P.map (second ("."++)) $ grammar ij)++ rightBT :: (DIM2,Int) -> Nuc -> (Int, P.Stream Backtrace)+ rightBT (ij,x) _ = (x, P.map (second (++".")) $ grammar ij)++ pairBT :: Nuc -> (DIM2,Int) -> Nuc -> (Int, P.Stream Backtrace)+ pairBT l (ij,x) r = if basepair l r then (x+1, P.map (second (\a -> "("++a++")")) $ grammar ij) else (0, P.empty)++ splitBT :: (DIM2,Int) -> (DIM2,Int) -> (Int, P.Stream Backtrace)+ splitBT (ij,x) (kl,y) = (x+y, P.concatMap (\(s1,bts1) -> P.map (\(s2,bts2) -> (s1+s2,bts1++bts2)) $ grammar kl) $ grammar ij)++ hBT ij = P.concatMap (\(score,bts) -> P.map (first (const score)) bts) . P.filter (\(score,bts) -> score == s!ij)+
+ C/nussinov.c view
@@ -0,0 +1,61 @@+//#include <stdlib.h>+//#include <stdio.h>++int main () {+ char *p;+ int n;+ int e;+ while (1==scanf ("%as", &p)) { // only GNU C+ n = strlen(p);+ e = nussinov (n, p);+ printf ("%s %d\n", p, e);+ free(p);+ p=0;+ };+ return 0;+}++int nussinov (int n, char *p) {+ int l = n*n;+ int i;+ int j;+ int k;+ int at;+ int cur;+ int new;+ int *mat = calloc (l, sizeof(int));+// printf (">>> %d\n", n);+ for (i = n-1; i>=0; i--) for (j=i; j<n; j++) {+ at = i * (n-1) + j;+ if (i==j) { //empty+ cur = 0;+ }+ if (i<j) { //left+ new = mat[(i+1)*(n-1) + j];+ if (cur < new) cur = new;+ };+ if (i<j) { //right+ new = mat[i*(n-1) + j-1];+ if (cur < new) cur = new;+ };+ if (i<j) { //pair+ new = i+1>=j ? 0 : mat[(i+1)*(n-1) +j-1];+ switch (p[i]) {+ case 'C': new += p[j]=='G' ? 1 : -999999; break;+ case 'G': new += p[j]=='C' || p[j]=='U' ? 1 : -999999; break;+ case 'A': new += p[j]=='U' ? 1 : -999999; break;+ case 'U': new += p[j]=='A' || p[j]=='G' ? 1 : -999999; break;+ default: new = -999999;+ };+ if (cur < new) cur = new;+ };+ for (k = i+1; k<j; k++) { //split+ new = mat[i*(n-1) + k] + mat[(k+1)*(n-1) + j];+ if (cur < new) cur = new;+ };+ mat[at] = cur;+// printf ("... i %d %c j %d %c : %d\n", i, p[i], j, p[j], cur);+ };+ free (mat);+ return cur;+}
+ LICENSE view
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+ Nussinov78.cabal view
@@ -0,0 +1,96 @@+name: Nussinov78+version: 0.0.1.0+author: Christian Hoener zu Siederdissen, 2011-2012+copyright: Christian Hoener zu Siederdissen, 2011-2012+homepage: http://www.tbi.univie.ac.at/~choener/adpfusion+maintainer: choener@tbi.univie.ac.at+category: Bioinformatics+license: GPL-3+license-file: LICENSE+build-type: Simple+stability: experimental+cabal-version: >= 1.6.0+synopsis:+ Nussinov78 using the ADPfusion library.+description:+ The Nussinov78 RNA secondary structure prediction algorithm+ using the ADPfusion framework.+ .+ This algorithm is simple enough to be used as a tutorial-type+ example. It also shows that efficient code is possible. The+ ADPfusion code compared to C is slower by a factor of only 1.8.+ We plan to improve upon this.+ .+ A number of helper functions currently present in+ BioInf.Nussinov78 will later move in their own library.+ .+ If possible, build using the GHC llvm backend, and GHC-7.2.2.+ GHC-7.4.x produces very bad code on my system, please benchmark+ using 7.2.2.+ .+ For comparison, a version of the algorithm written in C is+ available under C/nussinov.c. Use at least+ "gcc -O3 nussinov.c".++Extra-Source-Files:+ C/nussinov.c++Flag llvm+ description: build using llvm backend+ default: True++++library+ build-depends:+ base >= 4 && < 5,+ mtl,+ primitive == 0.4.* ,+ vector == 0.9.* ,+ PrimitiveArray == 0.2.1.1 ,+ BiobaseXNA == 0.6.2.2 ,+ ADPfusion == 0.0.1.0+ exposed-modules:+ BioInf.Nussinov78+ ghc-options:+ -Odph+ -funbox-strict-fields+ -fspec-constr+ -funfolding-use-threshold100+ -funfolding-keeness-factor100+ if flag (llvm)+ ghc-options:+ -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts++++executable Nussinov78+ build-depends:+ base >= 4 && < 5,+ mtl,+ primitive == 0.4.* ,+ vector == 0.9.* ,+ PrimitiveArray == 0.2.1.1 ,+ BiobaseXNA == 0.6.2.2 ,+ ADPfusion == 0.0.1.0+ main-is:+ Nussinov78.hs+ other-modules:+ BioInf.Nussinov78+ ghc-options:+ -rtsopts+ -Odph+ -funbox-strict-fields+ -fspec-constr+ -funfolding-use-threshold100+ -funfolding-keeness-factor100+ if flag (llvm)+ ghc-options:+ -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts++++source-repository head+ type: git+ location: git://github.com/choener/Nussinov78+
+ Nussinov78.hs view
@@ -0,0 +1,21 @@++-- | Simple wrapper for Nussinov78. We take at most 10 backtracking results --+-- unlimited backtracking would produce an exponential amount of backtracking+-- results. The ambiguity is part of the original algorithm!++module Main where++import Text.Printf++import BioInf.Nussinov78++++main = do+ xs <- fmap lines getContents+ mapM_ doNussinov78 xs++doNussinov78 inp = do+ putStrLn inp+ let rs = nussinov78 inp+ mapM_ (\(e,bt) -> putStr bt >> printf " %5d\n" e) $ take 10 rs
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain