GenussFold (empty) → 0.0.0.1

raw patch · 8 files changed

+1055/−0 lines, 8 filesdep +ADPfusiondep +FormalGrammarsdep +GenussFoldsetup-changed

Dependencies added: ADPfusion, FormalGrammars, GenussFold, PrimitiveArray, ansi-wl-pprint, base, bytestring, cmdargs, containers, data-default, lens, mtl, semigroups, template-haskell, text, transformers, unordered-containers, vector

Files

• BioInf/GenussFold.hs +7/−0
• BioInf/GenussFold/PKN.hs +140/−0
• GenussFold.cabal +117/−0
• LICENSE +675/−0
• README.md +74/−0
• Setup.hs +2/−0
• changelog.md +7/−0
• src/GenussFold.hs +33/−0

@@ -0,0 +1,7 @@++module BioInf.GenussFold+  ( pknPairMax+  ) where++import BioInf.GenussFold.PKN (pknPairMax)+

@@ -0,0 +1,140 @@++module BioInf.GenussFold.PKN where++import           Control.Applicative+import           Control.Monad+import           Control.Monad.ST+import           Data.Char (toUpper,toLower)+import           Data.List+import           Data.Vector.Fusion.Util+import           Language.Haskell.TH+import           Language.Haskell.TH.Syntax+import qualified Data.Vector.Fusion.Stream as S+import qualified Data.Vector.Fusion.Stream.Monadic as SM+import qualified Data.Vector.Unboxed as VU+import           Text.Printf++import           ADP.Fusion+import           Data.PrimitiveArray as PA hiding (map)++import           FormalLanguage++++-- | Define signature and grammar++[formalLanguage|+Verbose++Grammar: PKN+N: S+{-+ - <U,2> is a split non-terminal.+ -+ - We explicitly introduce <U> and <V> as we want to have @pk1@ and @pk2@+ - in place. In principle, we could make use of an intermediate recursive+ - syntactic variable to ease the memory load, but this is simpler.+ -}+N: <U,2>+N: <V,2>+T: c+S: S+S -> unp <<< S c+S -> jux <<< S c S c+S -> nil <<< e+S -> pse <<< U V U V++<U,U> -> pk1 <<< [S,-] [c,-] <U,U> [-,S] [-,c]+<U,U> -> nll <<< [e,e]++<V,V> -> pk2 <<< [S,-] [c,-] <V,V> [-,S] [-,c]+<V,V> -> nll <<< [e,e]+//+Emit: PKN+|]++makeAlgebraProduct ''SigPKN++bpmax :: Monad m => SigPKN m Int Int Char+bpmax = SigPKN+  { unp = \ x c     -> x+  , jux = \ x c y d -> if c `pairs` d then x + y + 1 else -999999+  , pse = \ () () x y -> x + y+  , nil = \ ()      -> 0+  , pk1 = \ (Z:.x:.()) (Z:.a:.()) y (Z:.():.z) (Z:.():.b) -> if a `pairs` b then x + y + z + 1 else -888888+  , pk2 = \ (Z:.x:.()) (Z:.a:.()) y (Z:.():.z) (Z:.():.b) -> if a `pairs` b then x + y + z + 1 else -888888+  , nll = \ (Z:.():.()) -> 0+  , h   = SM.foldl' max (-999999)+  }+{-# INLINE bpmax #-}++pairs !c !d+  =  c=='A' && d=='U'+  || c=='C' && d=='G'+  || c=='G' && d=='C'+  || c=='G' && d=='U'+  || c=='U' && d=='A'+  || c=='U' && d=='G'+{-# INLINE pairs #-}++-- |+--+-- TODO It could be beneficial to introduce+-- @type Splitted = Either String (String,String)@+-- or something isomorphic. While [String] works, it allows for too many+-- possibilities here! ([] ist lightweight, on the other hand ...)++pretty :: Monad m => SigPKN m [String] [[String]] Char+pretty = SigPKN+  { unp = \ [x] c     -> [x ++ "."]+  , jux = \ [x] c [y] d -> [x ++ "(" ++ y ++ ")"]+  , pse = \ () () [x1,x2] [y1,y2] -> [x1 ++ y1 ++ x2 ++ y2]+  , nil = \ ()      -> [""]+  , pk1 = \ (Z:.[x]:.()) (Z:.a:.()) [y1,y2] (Z:.():.[z]) (Z:.():.b) -> [x ++ "[" ++ y1 , y2 ++ z ++ "]"]+  , pk2 = \ (Z:.[x]:.()) (Z:.a:.()) [y1,y2] (Z:.():.[z]) (Z:.():.b) -> [x ++ "{" ++ y1 , y2 ++ z ++ "}"]+  , nll = \ (Z:.():.()) -> ["",""]+  , h   = SM.toList+  }+{-# INLINE pretty #-}++-- |+--+-- @+-- [{]}(())+-- caguagcu+-- [ ]+--  { }+--     (())+-- @++pknPairMax :: Int -> String -> (Int,[[String]])+pknPairMax k inp = (d, take k bs) where+  i = VU.fromList . Prelude.map toUpper $ inp+  n = VU.length i+  !(Z:.t:.u:.v) = runInsideForward i+  d = unId $ axiom t+  bs = runInsideBacktrack i (Z:.t:.u:.v)+{-# NOINLINE pknPairMax #-}++type X = ITbl Id Unboxed Subword Int+type T = ITbl Id Unboxed (Z:.Subword:.Subword) Int++runInsideForward :: VU.Vector Char -> Z:.X:.T:.T+runInsideForward i = mutateTablesWithHints (Proxy :: Proxy MonotoneMCFG)+                   $ gPKN bpmax+                        (ITbl 0 0 EmptyOk (PA.fromAssocs (subword 0 0) (subword 0 n) (-666999) []))+                        (ITbl 0 0 (Z:.EmptyOk:.EmptyOk) (PA.fromAssocs (Z:.subword 0 0:.subword 0 0) (Z:.subword 0 n:.subword 0 n) (-777999) []))+                        (ITbl 0 0 (Z:.EmptyOk:.EmptyOk) (PA.fromAssocs (Z:.subword 0 0:.subword 0 0) (Z:.subword 0 n:.subword 0 n) (-888999) []))+                        (chr i)+  where n = VU.length i+{-# NoInline runInsideForward #-}++runInsideBacktrack :: VU.Vector Char -> Z:.X:.T:.T -> [[String]]+runInsideBacktrack i (Z:.t:.u:.v) = unId $ axiom b+  where !(Z:.b:._:._) = gPKN (bpmax <|| pretty)+                          (toBacktrack t (undefined :: Id a -> Id a))+                          (toBacktrack u (undefined :: Id a -> Id a))+                          (toBacktrack v (undefined :: Id a -> Id a))+                          (chr i)+{-# NoInline runInsideBacktrack #-}+

@@ -0,0 +1,117 @@+name:           GenussFold+version:        0.0.0.1+author:         Christian Hoener zu Siederdissen, 2015+copyright:      Christian Hoener zu Siederdissen, 2015+homepage:       https://github.com/choener/GenussFold+bug-reports:    https://github.com/choener/GenussFold/issues+maintainer:     choener@bioinf.uni-leipzig.de+category:       Formal Languages, Bioinformatics+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.10.0+tested-with:    GHC == 7.8.4, GHC == 7.10.1+synopsis:       MCFGs for Genus-1 RNA Pseudoknots+description:+                <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>+                .+                Genus-1 RNA pseudoknot grammars implemented with a multiple+                context-free language. Compared to the usual implementations+                that are based on explicit recursions, an implementation based+                on a formal grammar is much more pleasing to write.+                .+                Consult the README for details.+                .+                * @BioInf.GenussFold.PKN@: Recursive pseudoknots with a simple+                  basepair maximization scoring scheme.+                .++++Extra-Source-Files:+  README.md+  changelog.md++++flag debug+  description:  dump intermediate Core files+  default:      False+  manual:       True++++library+  build-depends: base                   >= 4.7      && < 4.9+               , ADPfusion              >= 0.4.1    && < 0.4.2+               , ansi-wl-pprint         >= 0.6.7    && < 0.6.8+--               , BiobaseTurner          >= 0.3.2    && < 0.3.3+--               , BiobaseTypes           >= 0.1.1    && < 0.1.2+               , bytestring             >= 0.10     && < 0.11+               , containers+               , data-default           >= 0.5      && < 0.6+               , FormalGrammars         >= 0.2.1    && < 0.2.2+               , lens                   >= 4.0      && < 5.0+               , mtl                    >= 2.0      && < 3.0+               , PrimitiveArray         >= 0.6.0    && < 0.6.2+               , semigroups             >= 0.16     && < 0.17+               , template-haskell+               , text                   >= 1.0      && < 1.3+               , transformers           >= 0.3      && < 0.5+               , unordered-containers   >= 0.2      && < 0.3+               , vector                 >= 0.10     && < 0.11+  exposed-modules:+    BioInf.GenussFold+    BioInf.GenussFold.PKN+  default-language:+    Haskell2010+  default-extensions: BangPatterns+                    , DataKinds+                    , DeriveDataTypeable+                    , FlexibleContexts+                    , KindSignatures+                    , MultiParamTypeClasses+                    , QuasiQuotes+                    , TemplateHaskell+                    , TypeFamilies+                    , TypeOperators+  ghc-options:+    -O2+    -funbox-strict-fields+    -fcpr-off+    -fno-liberate-case+  if flag(debug)+    ghc-options:+      -ddump-to-file+      -ddump-simpl+      -ddump-stg+      -dsuppress-all++++-- Wrapper for the library++executable GenussFold+  build-depends: base+               , cmdargs          >= 0.10   && < 0.11+               , FormalGrammars+               , GenussFold+  hs-source-dirs:+    src+  default-language:+    Haskell2010+  default-extensions: DeriveDataTypeable+                    , RecordWildCards+  main-is:+    GenussFold.hs+  ghc-options:+    -O2+    -funbox-strict-fields++++source-repository head+  type: git+  location: git://github.com/choener/GenussFold+

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@@ -0,0 +1,74 @@+[![Build Status](https://travis-ci.org/choener/GenussFold.svg?branch=master)](https://travis-ci.org/choener/GenussFold)++# GenussFold: RNA Pseudoknot Folding++[*generalized Algebraic Dynamic Programming Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)++The implementation makes use of the *gADP* technique and provides a larger+example on how to implement algorithms that require interleaved, split+syntactic variables.++Formal background can be found in this paper:++Maik Riechert, Christian Höner zu Siederdissen, and Peter F. Stadler  +*Algebraic dynamic programming for multiple context-free languages*  +2015, submitted  +[preprint](http://www.bioinf.uni-leipzig.de/Software/gADP/preprints/rie-hoe-2015.pdf)  ++++As an example, consider palindromic brackets `((()))`. Given two types of+brackets, these can be interleaved: `((( [[[ ))) ]]]`. Such interleaved,+long-range dependencies have been observed in human languages and, in+particular, in RNA bioinformatics.++RNA structures may form so-called pseudoknots, where the RNA structure does not+yield a planar structure (the canonical secondary structure) anymore, but+rather forms graphs with crossing edges. Using the idea of interleaved brackets+and given an input sequence `AAA CCC UUU GGG` (with artificial white space to+make this more clear), a pseudoknotted structure may be formed:++```+AAA CCC UUU GGG  +[[[ ((( ]]] )))+```++A formal grammar that parses such a structure requires the ability to denote+that a sub-structure has a "hole". We can write such a grammar as follows:++```+S     -> U V U V  +<U,U> -> [ε,ε]  +<U,U> -> [S,-] [a,-] <U,U> [-,S] [-,u]  +<V,V> -> [ε,ε]  +<V,V> -> [S,-] [c,-] <V,V> [-,S] [-,g]+```++The `PKN` grammar in GenussFold (for genus-1 structures, but much more+pleasurable to write) offers the required features:++1. state that a syntactic variable is split between two regions `<U,U>`+1. state that this split system is linearized and different symbols can be+   interleaved: `U V U V`+1. in addition, we allow syntactic variables of lower dimension (like `S`) to+   be used in dimensional stacks of symbols (`[S,-]`).++This system allows writing monotone multiple context-free grammars with good+performance -- we are reasonably close to C in running time performance.+Reasonable means around a factor of 2 slower.++++#### Performance comparison++C-code for running time performance comparison is available in the GenussFold+github repository. The direct URL is:+<https://github.com/choener/GenussFold/blob/master/C/genussfold.c>++#### Contact++Christian Hoener zu Siederdissen  +Leipzig University, Leipzig, Germany  +choener@bioinf.uni-leipzig.de  +http://www.bioinf.uni-leipzig.de/~choener/  +

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

@@ -0,0 +1,7 @@+0.0.0.1+-------++- initial checkin+- preparing travis.yml+- Pseudoknot-enabled Nussinov style RNA folding with basepair maximization.+

@@ -0,0 +1,33 @@++module Main where++import Control.Applicative ( (<$>) )+import Control.Monad (forM_)+import System.Console.CmdArgs+import Text.Printf++import BioInf.GenussFold++++data Options+  = Nussinov+    { coopts :: Int+    }+  deriving (Show,Data,Typeable)++oNussinov = Nussinov+  { coopts = 1 &= help "number of co-optimal backtracking results"+  }++main :: IO ()+main = do+  o <- cmdArgs $ modes [oNussinov]+  case o of+    Nussinov{..} -> do+      ls <- lines <$> getContents+      forM_ ls $ \l -> do+        let (r,bs) = pknPairMax coopts l+        printf "%s   %d\n" l r+        forM_ bs $ \[b] -> printf "%s   %d\n" b r+