RNAdraw (empty) → 0.2.0.1

raw patch · 9 files changed

+1167/−0 lines, 9 filesdep +BiobaseXNAdep +PrimitiveArraydep +QuasiTextsetup-changed

Dependencies added: BiobaseXNA, PrimitiveArray, QuasiText, array, base, bytestring, cmdargs, containers, repa, split, text, vector

Files

• BioInf/Secondary/Draw/DotBracket.hs +93/−0
• BioInf/ViennaRNA/DotPlot.hs +57/−0
• BioInf/ViennaRNA/DotPlot/Export.hs +175/−0
• BioInf/ViennaRNA/DotPlot/Import.hs +39/−0
• LICENSE +675/−0
• RNAdotplot.hs +59/−0
• RNAdraw.cabal +64/−0
• Setup.hs +2/−0
• changelog +3/−0

@@ -0,0 +1,93 @@+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE TupleSections #-}++-- | Several methods to draw ascii dot-bracket figures onto the screen. The+-- result will be one sequence line, a dot-bracket string, and possibly a list+-- of annotated basepairs. The dot-bracket string can handle base triplets.++module BioInf.Secondary.Draw.DotBracket where++import Data.ByteString.Char8 (ByteString)+import qualified Data.ByteString.Char8 as BS+import qualified Data.Vector.Unboxed as V+import Text.Printf+import Prelude hiding (sequence)++import Biobase.Secondary++++-- | The class of dot-bracket drawable structures.++class DotBracketDraw a where+  -- | Draw a secondary structure. It is assumed that the structure is+  -- pseudoknot-free.+  draw :: PairAnno -> SequenceNumbering -> a -> String+  -- | As 'draw' but returns the different strings as parts. These can then be+  -- further altered by the receiving end.+  drawParts :: PairAnno -> SequenceNumbering -> a -> Parts+  -- | Draw a pseudoknotted secondary structures.+  drawPK :: PairAnno -> SequenceNumbering -> a -> String++data Parts = Parts+  { numbers :: Maybe String+  , sequence :: String+  , structure :: String+  , extended :: [String]+  }++-- | ++instance DotBracketDraw (String,[ExtPairIdx]) where+  draw pa sn (seq,xs) = unlines $+    maybe [] (:[]) numbers +++    [ sequence+    , structure+    ] ++ extended+    where+      Parts{..} = drawParts pa sn (seq,xs)+  drawParts pa sn (seq,xs) = Parts+    { numbers = if sn==Numbered then Just . take l . concat $ repeat ['0'..'9'] else Nothing+    , sequence = seq+    , structure = V.toList $ V.accum updateStructure (V.fromList $ replicate l '.') (map ((,'(').baseL) xs ++ map ((,')').baseR) xs)+    , extended = [ printf "  %4d %4d   %c-%c   %s" (baseL x) (baseR x) (seq!!baseL x) (seq!!baseR x) (show $ baseT x)+                 | x <- xs, pa == Always || pa == Required && baseT x /= cWW+                 ]+    } where+      l = length seq+      updateStructure cur new+        | cur == '.' = new+        | cur == new && cur == '(' = '<'+        | cur == new && cur == ')' = '>'+        | cur `elem` "()" && new `elem` "()" = 'X'+        | otherwise = '3' -- three outgoing edges...++instance DotBracketDraw (String,[PairIdx]) where+  draw pa sn (seq,xs) = draw pa sn (seq,map (\x -> ((baseL x, baseR x), baseT x)) xs)+  drawParts pa sn (seq,xs) = drawParts pa sn (seq, map (\x -> ((baseL x, baseR x), baseT x)) xs)++instance DotBracketDraw (ByteString,[PairIdx]) where+  draw pa sn (seq,xs) = draw pa sn (BS.unpack seq,xs)+  drawParts pa sn (seq,xs) = drawParts pa sn (BS.unpack seq, xs)++instance DotBracketDraw (ByteString,[ExtPairIdx]) where+  draw pa sn (seq,xs) = draw pa sn (BS.unpack seq,xs)+  drawParts pa sn (seq,xs) = drawParts pa sn (BS.unpack seq, xs)++-- | How to handle the list of annotated pairs.++data PairAnno+  -- | Never write out the pair list with pair-type information.+  = Never+  -- | Only write out those pairs that are non-canonical, or the required list+  -- of pairs to get all information on the secondary structure.+  | Required+  -- | Always write out all pairs.+  | Always+  deriving (Show,Read,Eq)++data SequenceNumbering+  = Numbered+  | NotNumbered+  deriving (Show,Read,Eq)

@@ -0,0 +1,57 @@+{-# LANGUAGE PatternGuards #-}+{-# LANGUAGE TupleSections #-}+{-# LANGUAGE ScopedTypeVariables #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE TypeOperators #-}++-- | Handles ViennaRNA dot-plots.++module BioInf.ViennaRNA.DotPlot where++import qualified Data.Array.IArray as A+import qualified Data.Text as T+import qualified Data.Vector.Unboxed as VU+import qualified Data.Map as M+import Data.List+import Control.Arrow++import Biobase.Secondary+import Biobase.Secondary.Diagrams++++type Color = (Double,Double,Double)++data DotPlot = DotPlot+  { dotplot     :: A.Array (Int,Int) (Maybe (Double,Maybe Color))+  , isPartition :: Bool   -- are we doing a partition function plot+  , rnaSequence :: T.Text+  }+  deriving (Eq,Show)++++clearMFE :: DotPlot -> DotPlot+clearMFE dp@DotPlot{..} = dp { dotplot = dotplot A.// (os) } where+  os = [ (ij,Nothing) | ij@(i,j) <- A.indices dotplot, j<i ]++addStructure :: [(String,Color)] -> String -> [([Int],String)] -> DotPlot -> [String] -> DotPlot+addStructure cs dc cm dp@DotPlot{..} xs+  | Nothing <- dc `lookup` cs = error "default color not in list of current colors"+  | any ((/=) (snd . snd . A.bounds $ dotplot) . length) xs = error $ "structure(s) with wrong length detected:\n" ++ unlines xs+  | otherwise = dp { dotplot = dotplot A.// cells }+  where+    Just defC = dc `lookup` cs+    lps :: [(Int,[PairIdx])]+    lps = map (fromD1S . mkD1S) xs+    ms  = zipWith mkMap [(1::Int) ..] (map snd lps)+    mkMap k ps = M.fromList $ map (,[k]) $ map ((+1) *** (+1)) ps+    unn = M.unionsWith (++) ms+    cells = [ ((j,i), mkEntry i j zs) | ((i,j),zs) <- M.assocs unn ]+    mkEntry i j zs+      | Just clr <- lookupColor zs = Just (0.95, Just clr)+      | otherwise                  = Just (0.95, Nothing)+    lookupColor zs = do+      cmJ <- (sort zs) `lookup` cm+      cmJ `lookup` cs+

@@ -0,0 +1,175 @@+{-# LANGUAGE PatternGuards #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}+{-# LANGUAGE QuasiQuotes #-}++module BioInf.ViennaRNA.DotPlot.Export where++import Data.Text (Text)+import qualified Data.Array.IArray as A+import qualified Data.Text as T+import Text.Printf+import Text.QuasiText+import Data.List (sortBy)+import Data.Ord+import Data.Function++import BioInf.ViennaRNA.DotPlot++++dotPlotToText :: DotPlot -> Text+dotPlotToText DotPlot{..} = qqDotPlot rnaSequence cs where+  cs = [ T.pack (conv i j p mc) | ((i,j),Just (p,mc)) <- (sortBy (comparing snd) $ A.assocs dotplot) ]+  conv i j p mc+    | i<j                     = printf "%5d %5d %10.8f ubox" i j p+    | i>j, Nothing      <- mc = printf "%5d %5d %10.8f lbox" j i z+    | i>j, Just (r,g,b) <- mc = printf "%5d %5d %10.8f %f %f %f cbox" j i z r g b+    where z = 0.95 :: Double++++-- * QQ stuff++qqDotPlot :: Text -> [Text] -> Text+qqDotPlot s xs' = let xs = T.unlines xs' in [embed|+%!PS-Adobe-3.0 EPSF-3.0+%%Title: RNA Dot Plot+%%Creator: BioInf.ViennaRNA.DotPlot.Export+%%CreationDate:+%%BoundingBox: 66 211 518 662+%%DocumentFonts: Helvetica+%%Pages: 1+%%EndComments++%Options: -d2 +% +%This file contains the square roots of the base pair probabilities in the form+% i  j  sqrt(p(i,j)) ubox++%%BeginProlog+/DPdict 100 dict def+DPdict begin+/logscale false def+/lpmin 1e-05 log def++/box { %size x y box - draws box centered on x,y+   2 index 0.5 mul sub            % x -= 0.5+   exch 2 index 0.5 mul sub exch  % y -= 0.5+   3 -1 roll dup rectfill+} bind def++/ubox {+   logscale {+      log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if+   } if+   3 1 roll+   exch len exch sub 1 add box+} bind def++/lbox {+   3 1 roll+   len exch sub 1 add box+} bind def++/cbox {+   setrgbcolor+   3 1 roll+   len exch sub 1 add box+   0 0 0 setrgbcolor+} bind def++/drawseq {+% print sequence along all 4 sides+[ [0.7 -0.3 0 ]+  [0.7 0.7 len add 0]+  [-0.3 len sub -0.4 -90]+  [-0.3 len sub 0.7 len add -90]+] {+   gsave+    aload pop rotate translate+    0 1 len 1 sub {+     dup 0 moveto+     sequence exch 1 getinterval+     show+    } for+   grestore+  } forall+} bind def++/drawgrid{+  0.01 setlinewidth+  len log 0.9 sub cvi 10 exch exp  % grid spacing+  dup 1 gt {+     dup dup 20 div dup 2 array astore exch 40 div setdash+  } { [0.3 0.7] 0.1 setdash } ifelse+  0 exch len {+     dup dup+     0 moveto+     len lineto +     dup+     len exch sub 0 exch moveto+     len exch len exch sub lineto+     stroke+  } for+  [] 0 setdash+  0.04 setlinewidth +  currentdict /cutpoint known {+    cutpoint 1 sub+    dup dup -1 moveto len 1 add lineto+    len exch sub dup+    -1 exch moveto len 1 add exch lineto+    stroke+  } if+  0.5 neg dup translate+} bind def++end+%%EndProlog+DPdict begin+%delete next line to get rid of title+270 665 moveto /Helvetica findfont 14 scalefont setfont (dot.ps) show++/sequence { (\+$s\+) } def+/len { sequence length } bind def++72 216 translate+72 6 mul len 1 add div dup scale+/Helvetica findfont 0.95 scalefont setfont++drawseq+0.5 dup translate+% draw diagonal+0.04 setlinewidth+0 len moveto len 0 lineto stroke ++/min { 2 copy gt { exch } if pop } bind def++/utri{ % i j prob utri+  gsave+  1 min 2 div+  0.85 mul 0.15 add 0.95  0.33+  3 1 roll % prepare hsb color+  sethsbcolor+  % now produce the coordinates for lines+  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub+  moveto lineto lineto closepath fill+  grestore+} bind def++%data starts here++%start of quadruplex data++%draw the grid+drawgrid++%start of base pair probability data+$xs+showpage+end+%%EOF+|]

@@ -0,0 +1,39 @@+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE OverloadedStrings #-}++module BioInf.ViennaRNA.DotPlot.Import where++import Data.Text (Text(..))+import qualified Data.Array.IArray as A+import qualified Data.Text as T+import qualified Data.Text.Read as R++import BioInf.ViennaRNA.DotPlot++++textToDotPlot :: Text -> DotPlot+textToDotPlot t = DotPlot (A.accumArray (const id) Nothing ((1,1),(l,l)) (map f ps)) True sq where+  l  = T.length sq+  ls = T.lines t+  sq = case (drop 1 . dropWhile (not . T.isPrefixOf "/sequence") $ ls) of+         (x:_)     -> T.init x+         otherwise -> error $ "lines do not contain sequence part: " ++ show ls+  ps = filter (T.isSuffixOf "box")+     . filter (not . T.isPrefixOf "%")+     . takeWhile (not . T.isPrefixOf "showpage")+     . drop 1+     . dropWhile (not . T.isPrefixOf "%start of base pair probability data")+     $ ls+  f p'+    | last p == "cbox" = ( (rdI $ p!!1, rdI $ p!!0), (Just (rdP $ p!!2, Just (rdP $ p!!3, rdP $ p!!4, rdP $ p!!5))) )+    | last p == "ubox" = ( (rdI $ p!!0, rdI $ p!!1), (Just (rdP $ p!!2, Nothing)) )+    | last p == "lbox" = ( (rdI $ p!!1, rdI $ p!!0), (Just (rdP $ p!!2, Nothing)) )+    where p = T.words p'+          rdI :: Text -> Int+          rdI = chk . R.decimal+          rdP :: Text -> Double+          rdP = chk . R.rational+          chk (Left e)      = error $ "dotplot/import read error: " ++ e ++ " in " ++ T.unpack p' ++ show p+          chk (Right (k,_)) = k+

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@@ -0,0 +1,59 @@+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE DeriveDataTypeable #-}++module Main where++import System.Console.CmdArgs+import qualified Data.Text.IO as T+import Data.List (nubBy,sort)+import Data.Function+import Data.List.Split (splitOn)++import BioInf.ViennaRNA.DotPlot+import BioInf.ViennaRNA.DotPlot.Export+import BioInf.ViennaRNA.DotPlot.Import++++data Options = Options+  { infile       :: String+  , outfile      :: String+  , structures   :: [String]+  , colorRGB     :: [(String,(Double,Double,Double))]+  , colorize     :: [(String,String)]+  , defaultColor :: String+  } deriving (Show,Data,Typeable)++options = Options+  { infile       = ""      &= help "file to process, stdin if empty"+  , outfile      = ""      &= help "output file, stdout if empty"+  , structures   = []      &= help "structures to put into dotplot. Both, upper and lower part for mfe plots, only lower part for partition function plots"+  , colorRGB     = cs      &= help "defines an rgb color"+  , colorize     = []      &= help "color a set of structures. define all subsets. Write the structures as 1-2-4,red to color 1,2, and 4 red. (deficiency of the optparser)"+  , defaultColor = "black" &= help "color to choose if no matching set for coloring was found"+  }++main = do+  o@Options{..} <- cmdArgs $ options+  i <- case infile of+         "" -> T.getContents+         fi -> T.readFile fi+  let cSs = map (\xs -> (sort . map read . splitOn "-" $ fst xs, snd xs)) colorize+  let dpOld = textToDotPlot i+  let dpNew = if null structures+                then dpOld+                else addStructure (nubBy ((==) `on` fst) $ reverse colorRGB) defaultColor cSs (clearMFE dpOld) structures+  case outfile of+    "" -> T.putStrLn          . dotPlotToText $ dpNew+    fo -> T.writeFile outfile . dotPlotToText $ dpNew++cs =+  [ ("black"   , (0,0,0))+  , ("red"     , (1,0,0))+  , ("green"   , (0,1,0))+  , ("blue"    , (0,0,1))+  , ("cyan"    , (0,1,1))+  , ("magenta" , (1,0,1))+  , ("yellow"  , (1,1,0))+  ]+

@@ -0,0 +1,64 @@+name:           RNAdraw+version:        0.2.0.1+author:         Christian Hoener zu Siederdissen+maintainer:     choener@tbi.univie.ac.at+homepage:       http://www.tbi.univie.ac.at/~choener/+copyright:      Christian Hoener zu Siederdissen, 2011-2014+category:       Bioinformatics+synopsis:       Draw RNA secondary structures+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.4.0+description:+                We provide a number of ways to draw RNA secondary structures.+                In particular, the following types of structures can be (more+                or less elegantly) drawn:+                .+                * Dot plots for mfe and partition function+                .+                * canonical RNA secondary structures without pseudoknots+                .+                * non-canonical extended RNA secondary structures+                .+                * pseudoknotted secondary structures+                .+                From top to bottom, the beauty of presentation degrades. Some+                emphasis is put on ASCII-drawings, especially Vienna+                dot-bracket-like notation.++extra-source-files:+  changelog++library+  build-depends:+    base >3 && <5               ,+    array                       ,+    bytestring                  ,+    containers                  ,+    repa            >= 3.2      ,+    split           >= 0.2      ,+    text                        ,+    vector          >= 0.10     ,+    QuasiText       >= 0.1.2.5  ,+    PrimitiveArray  >= 0.5.3    ,+    BiobaseXNA      >= 0.8.1++  exposed-modules:+    BioInf.Secondary.Draw.DotBracket+    BioInf.ViennaRNA.DotPlot+    BioInf.ViennaRNA.DotPlot.Export+    BioInf.ViennaRNA.DotPlot.Import++  ghc-options:+    -O2++executable RNAdotplot+  build-depends:+    cmdargs >= 0.10+  main-is:+    RNAdotplot.hs+  ghc-options:+    -O2+

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

@@ -0,0 +1,3 @@+0.2.0.1++- updated minimal library dependencies