Biobase (empty) → 0.0.2.0

raw patch · 8 files changed

+1122/−0 lines, 8 filesdep +PrimitiveArraydep +arraydep +basesetup-changed

Dependencies added: PrimitiveArray, array, base, primitive, vector

Files

• Biobase.cabal +39/−0
• Biobase/Constants.hs +29/−0
• Biobase/RNA.hs +210/−0
• Biobase/Structure.hs +58/−0
• Biobase/Structure/DotBracket.hs +37/−0
• Biobase/Structure/Shapes.hs +72/−0
• LICENSE +675/−0
• Setup.hs +2/−0

@@ -0,0 +1,39 @@+name:           Biobase+version:        0.0.2.0+author:         Christian Hoener zu Siederdissen+maintainer:     choener@tbi.univie.ac.at+homepage:       http://www.tbi.univie.ac.at/~choener/Haskell/+copyright:      Christian Hoener zu Siederdissen, 2010+category:       Bioinformatics+synopsis:       Base library for bioinformatics+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.4.0+description:+                Base library for bioinformatics providing a number of im- and+                export functions for commonly used filetypes. Provided are+                functions and Haskell data types for RNA primary and secondary+                structure. Otherwise, this library provides the basis for other+                libraries to build on.++++library+  build-depends:+    array,+    base >= 4 && < 5,+    vector >= 0.6 && < 7,+    primitive >= 0.3 && < 0.4,+    PrimitiveArray >= 0.0.2.1 && < 0.0.3++  exposed-modules:+    Biobase.Constants+    Biobase.RNA+    Biobase.Structure+    Biobase.Structure.DotBracket+    Biobase.Structure.Shapes++  ghc-options:+    -O2

@@ -0,0 +1,29 @@++-- | Define several constants used throughout all libraries depending on+-- Biobase.++module Biobase.Constants where++++-- * energy "Infinities" for Int's++-- | maxBound on Int is problematic, if we try something like maxBound ++-- maxBound which happens very often. 'eInf' is used for settings like lookup+-- tables, etc while comparisons are against 'eMax'.+-- Both values need to be small enough not to overflow in typical situations.++eInf :: Int+eInf = 10000000++eMax :: Int+eMax = eInf `div` 10++++-- * floating infinity++-- here, we choose a real infinity and let the ieee handle it++fInf :: Double+fInf = 1/0

@@ -0,0 +1,210 @@+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE StandaloneDeriving #-}+{-# LANGUAGE TypeSynonymInstances #-}+{-# LANGUAGE PatternGuards #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE FlexibleInstances #-}++-- | Encodings for nucleotides and pairs. Currently very ViennaRNA-centric.+-- This might change over time.+--+-- TODO do not export Nucleotide ctor?++module Biobase.RNA where++import Data.Char (toUpper)+import Data.Ix+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 Data.PrimitiveArray+import Data.PrimitiveArray.Ix++++-- * single nucleotide encoding++newtype Nucleotide = Nucleotide Int+  deriving (Eq,Ord,Ix)++(nucE:nucA:nucC:nucG:nucU:_) = map Nucleotide [0..]++nucCharList :: [(Int,Char)]+nucCharList = zip [0..] "EACGU"+charNucList :: [(Char,Int)]+charNucList = zip "EACGU" [0..]++deriving instance Prim Nucleotide+deriving instance VGM.MVector VU.MVector Nucleotide+deriving instance VG.Vector VU.Vector Nucleotide+deriving instance VU.Unbox Nucleotide++-- TODO maybe use 'assert' and do not catch errors in optimized operation?!++instance Enum Nucleotide where+  toEnum x+    | x>=0 && x<=4 = Nucleotide x+    | otherwise    = error $ "can't make to enum" ++ show x+  fromEnum (Nucleotide x) = x+  {-# INLINE toEnum #-}+  {-# INLINE fromEnum #-}++instance Bounded Nucleotide where+  minBound = nucE+  maxBound = nucU++instance Show Nucleotide where+  show (Nucleotide x)+    | Just s <- x `lookup` nucCharList = [s]++instance Read Nucleotide where+  readsPrec p [] = []+  readsPrec p (x:xs)+    | x ==' ' = readsPrec p xs+    | Just n <- x `lookup` charNucList = [(Nucleotide n,xs)]+    | otherwise = []++charToNucleotide :: Char -> Nucleotide+charToNucleotide = f . toUpper where+  f x+    | Just n <- x `lookup` charNucList = Nucleotide n+    | otherwise = nucE++nucleotideToChar :: Nucleotide -> Char+nucleotideToChar (Nucleotide n) = f n where+  f x+    | Just c <- x `lookup` nucCharList = c++++-- * Represent nucleotide sequences using an unboxed vector.++type Primary = PrimArray Int Nucleotide++instance Show Primary where+  show p = "mkPrimary " ++ unPrimary p++class MkPrimary a where+  mkPrimary :: a -> Primary+  unPrimary :: Primary -> a++instance MkPrimary String where+  mkPrimary xs = fromList 0 (length xs -1) $ map charToNucleotide xs+  unPrimary v = map nucleotideToChar $ toList v+  {-# INLINE mkPrimary #-}+  {-# INLINE unPrimary #-}++instance MkPrimary (VU.Vector Char) where+  mkPrimary = mkPrimary . VU.toList+  unPrimary = VU.fromList . unPrimary+  {-# INLINE mkPrimary #-}+  {-# INLINE unPrimary #-}++++-- * Encoding of Watson-Crick and Wobble Pairs in the Vienna RNA package style.++newtype ViennaPair = ViennaPair Int+  deriving (Eq,Ord,Ix)++(vpNP:vpCG:vpGC:vpGU:vpUG:vpAU:vpUA:vpNS:_) = map ViennaPair [0..]++vpStrList :: [(Int,String)]+vpStrList = zip [0..] ["NP","CG","GC","GU","UG","AU","UA","NS"]+strVpList :: [(String,Int)]+strVpList = zip ["NP","CG","GC","GU","UG","AU","UA","NS"] [0..]++deriving instance VGM.MVector VU.MVector ViennaPair+deriving instance VG.Vector VU.Vector ViennaPair+deriving instance VU.Unbox ViennaPair++instance Enum ViennaPair where+  toEnum x+    | x>=0 && x<=7 = ViennaPair x+    | otherwise    = error $ "can't make to enum" ++ show x+  fromEnum (ViennaPair x) = x+  {-# INLINE toEnum #-}+  {-# INLINE fromEnum #-}++instance Bounded ViennaPair where+  minBound = vpNP+  maxBound = vpNS++instance Show ViennaPair where+  show (ViennaPair x)+    | Just s <- x `lookup` vpStrList = s++instance Read ViennaPair where+  readsPrec p [] = []+  readsPrec p [x] = []+  readsPrec p (x:y:xs)+    | x ==' ' = readsPrec p (y:xs)+    | Just n <- (x:y:[]) `lookup` strVpList = [(ViennaPair n,xs)]+    | otherwise = []++++-- * convenience lists++acgu = [nucA .. nucU]+acguStr = map show acgu+acguPairs = [(b1,b2) | b1<-acgu, b2<-acgu]+eacgu = [nucE .. nucU]+npnsP = [vpNP .. vpNS]+cguaP = [vpCG .. vpUA]+cgnsP = [vpCG .. vpNS]++++-- * Transformations between Nucleotide and ViennaPair++toPair :: Nucleotide -> Nucleotide -> ViennaPair+toPair x y+  | x==nucC&&y==nucG = vpCG+  | x==nucG&&y==nucC = vpGC+  | x==nucG&&y==nucU = vpGU+  | x==nucU&&y==nucG = vpUG+  | x==nucA&&y==nucU = vpAU+  | x==nucU&&y==nucA = vpUA+  | otherwise        = vpNP+{-# INLINE toPair #-}++pairs :: Nucleotide -> Nucleotide -> Bool+pairs a b = (>vpNP) $ toPair a b+{-# INLINE pairs #-}++vienna2Tuple p+  | p==vpCG = (nucC,nucG)+  | p==vpGC = (nucG,nucC)+  | p==vpGU = (nucG,nucU)+  | p==vpUG = (nucU,nucG)+  | p==vpAU = (nucA,nucU)+  | p==vpUA = (nucU,nucA)+  | otherwise = error "non-standard pairs can't be backcasted"+{-# INLINE vienna2Tuple #-}++vienna2RevTuple p+  | p==vpCG = (nucG,nucC)+  | p==vpGC = (nucC,nucG)+  | p==vpGU = (nucU,nucG)+  | p==vpUG = (nucG,nucU)+  | p==vpAU = (nucU,nucA)+  | p==vpUA = (nucA,nucU)+  | otherwise = error "non-standard pairs can't be backcasted"+{-# INLINE vienna2RevTuple #-}++tuple2Vienna (b1,b2)+  | b1==nucC&&b2==nucG = vpCG+  | b1==nucG&&b2==nucC = vpGC+  | b1==nucG&&b2==nucU = vpGU+  | b1==nucU&&b2==nucG = vpUG+  | b1==nucA&&b2==nucU = vpAU+  | b1==nucU&&b2==nucA = vpUA+  | otherwise = vpNS+{-# INLINE tuple2Vienna #-}++tuple2RevVienna (a,b) = tuple2Vienna (b,a)+{-# INLINE tuple2RevVienna #-}+

@@ -0,0 +1,58 @@++--+-- Basic definitions for RNA secondary structure.+--++-- TODO would RNA tertiary structure be here as well?+-- TODO maybe, we should just put the sequence into Secondary as well?++{-# LANGUAGE RecordWildCards #-}++module Biobase.Structure where++import Data.List (sort,groupBy)++import Biobase.RNA++++-- | A complex of one or more primary and secondary structures++data Complex = Complex+  { comments :: String+  , structures :: [(Primary,Secondary)]+  }+  deriving (Show)++++-- | A secondary structure. It is explicit that we store the length of the+-- sequence. (length n, last index (n-1) problem)++data Secondary = Secondary+  { len      :: Int+  , pairings :: [(Int,Int)]+  }+  deriving (Show)++++-- | secondary structure representation using an explicit tree, SSExt encodes+-- the length of the underlying sequence. Each node can contain additional+-- information under 'a'.+++data SSTree a = SSTree Int Int a [SSTree a]+              | SSExt  Int     a [SSTree a]+  deriving (Read,Show,Eq)++++-- | generate an SSTree from a secondary structure++toSSTree :: Secondary -> SSTree ()+toSSTree Secondary{..} = ext $ sort pairings where+  ext [] = SSExt len () []+  ext xs = SSExt len () . map tree $ groupBy (\l r -> snd l > fst r) xs+  tree [(i,j)]    = SSTree i j () []+  tree ((i,j):xs) = SSTree i j () . map tree $ groupBy (\l r -> snd l > fst r) xs

@@ -0,0 +1,37 @@++--+-- transform to and from dotbracket notation for RNA secondary structures.+--++{-# LANGUAGE RecordWildCards #-}++module Biobase.Structure.DotBracket where++import Data.Array.IArray+import Data.List (sort)++import Biobase.RNA+import Biobase.Structure++++-- | Given the secondary structure notation, generate the dot-bracket string.++dotbracket :: Secondary -> String+dotbracket Secondary{..} = elems rbr where+  arr = listArray (0,len-1) $ replicate len '.' :: Array Int Char+  lbr = arr // map (\(l,_) -> (l,'(')) pairings+  rbr = lbr // map (\(_,r) -> (r,')')) pairings++++-- | transforms a pseudoknot-free dotbracket string into a pairlist++dotbracketToPairlist :: String -> Secondary+dotbracketToPairlist str = Secondary (length str) (sort $ f 0 [] str) where+  f :: Int -> [Int] -> String -> [(Int,Int)]+  f _ st [] = []+  f k st ('.':xs) = f (k+1) st xs+  f k st ('(':xs) = f (k+1) (k:st) xs+  f k (s:st) (')':xs) = (s,k) : f (k+1) st xs+  f a b c = error $ show (a,b,c)

@@ -0,0 +1,72 @@++--+-- Shapes are a way of representing secondary structures in a more+-- coarse-grained way.++module Biobase.Structure.Shapes where++-- TODO replace the five functions with one! (not trivial, apparently)++import Data.List (mapAccumL)++import Biobase.RNA+import Biobase.Structure+import Biobase.Structure.DotBracket++++-- | given an SSTree, return the shape representation++toShape5 :: SSTree a -> String+toShape5 (SSTree i j _ []) = "[]"+toShape5 (SSTree i j _ xs@(x:y:_)) = "[" ++ concatMap toShape5 xs ++ "]"+toShape5 (SSTree _ _ _ [x]) = toShape5 x+toShape5 (SSExt len _ xs) = concatMap toShape5 xs++toShape4 :: SSTree a -> String+toShape4 (SSTree i j _ []) = "[]"+toShape4 (SSTree i j _ xs@(x:y:_)) = "[" ++ concatMap toShape4 xs ++ "]"+toShape4 (SSTree i j _ [x@(SSTree k l _ _)])+  | i+1<k && j-1>l = "[" ++ toShape4 x ++ "]"+  | otherwise      = toShape4 x+toShape4 (SSTree _ _ _ [x]) = toShape4 x+toShape4 (SSExt len _ xs) = concatMap toShape4 xs++toShape3 :: SSTree a -> String+toShape3 (SSTree i j _ []) = "[]"+toShape3 (SSTree i j _ xs@(x:y:_)) = "[" ++ concatMap toShape3 xs ++ "]"+toShape3 (SSTree i j _ [x@(SSTree k l _ _)])+  | i+1<k || j-1>l = "[" ++ toShape3 x ++ "]"+  | otherwise      = toShape3 x+toShape3 (SSTree _ _ _ [x]) = toShape3 x+toShape3 (SSExt len _ xs) = concatMap toShape3 xs++toShape2 :: SSTree a -> String+toShape2 (SSTree i j _ []) = "[]"+toShape2 (SSTree i j _ xs@(x:y:_)) = "[" ++ concatMap toShape2 xs ++ "]"+toShape2 (SSTree i j _ [x@(SSTree k l _ _)])+  | i+1<k || j-1>l = "[" ++ ['_' | i+1<k] ++ toShape2 x ++ ['_' | j-1>l] ++ "]"+  | otherwise      = toShape2 x+toShape2 (SSTree _ _ _ [x]) = toShape2 x+toShape2 (SSExt len _ xs) = concatMap toShape2 xs++toShape1 :: SSTree a -> String+toShape1 (SSTree i j _ []) = "[]"+toShape1 (SSTree i j _ xs@(x:y:_)) = "[" ++ mkDashes i (j-1) xs ++ "]"+toShape1 (SSTree i j _ [x@(SSTree k l _ _)])+  | i+1<k || j-1>l = "[" ++ ['_' | i+1<k] ++ toShape1 x ++ ['_' | j-1>l] ++ "]"+  | otherwise      = toShape1 x+toShape1 (SSTree _ _ _ [x]) = toShape1 x+toShape1 (SSExt _ _ []) = ""+toShape1 (SSExt len _ xs) = mkDashes 0 (len-1) xs+++mkDashes a z xs = (concat . snd $ mapAccumL (\acc t@(SSTree k l _ _) -> (l, ['_' | acc+1<k] ++ toShape1 t)) a xs) ++ ['_' | let (SSTree _ k _ _) = last xs, z > k]++toShape :: Int -> SSTree a -> String+toShape s+  | s==5 = toShape5+  | s==4 = toShape4+  | s==3 = toShape3+  | s==2 = toShape2+  | s==1 = toShape1

@@ -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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Of course, your program's commands+might be different; for a GUI interface, you would use an "about box".++  You should also get your employer (if you work as a programmer) or school,+if any, to sign a "copyright disclaimer" for the program, if necessary.+For more information on this, and how to apply and follow the GNU GPL, see+<http://www.gnu.org/licenses/>.++  The GNU General Public License does not permit incorporating your program+into proprietary programs.  If your program is a subroutine library, you+may consider it more useful to permit linking proprietary applications with+the library.  If this is what you want to do, use the GNU Lesser General+Public License instead of this License.  But first, please read+<http://www.gnu.org/philosophy/why-not-lgpl.html>.+

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