diff --git a/BioInf/Secondary/Draw/DotBracket.hs b/BioInf/Secondary/Draw/DotBracket.hs new file mode 100644 --- /dev/null +++ b/BioInf/Secondary/Draw/DotBracket.hs @@ -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) diff --git a/BioInf/ViennaRNA/DotPlot.hs b/BioInf/ViennaRNA/DotPlot.hs new file mode 100644 --- /dev/null +++ b/BioInf/ViennaRNA/DotPlot.hs @@ -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 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 + diff --git a/BioInf/ViennaRNA/DotPlot/Export.hs b/BioInf/ViennaRNA/DotPlot/Export.hs new file mode 100644 --- /dev/null +++ b/BioInf/ViennaRNA/DotPlot/Export.hs @@ -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 + | ij, 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 +|] diff --git a/BioInf/ViennaRNA/DotPlot/Import.hs b/BioInf/ViennaRNA/DotPlot/Import.hs new file mode 100644 --- /dev/null +++ b/BioInf/ViennaRNA/DotPlot/Import.hs @@ -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 + diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,675 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + 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. 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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 +. + diff --git a/RNAdotplot.hs b/RNAdotplot.hs new file mode 100644 --- /dev/null +++ b/RNAdotplot.hs @@ -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)) + ] + diff --git a/RNAdraw.cabal b/RNAdraw.cabal new file mode 100644 --- /dev/null +++ b/RNAdraw.cabal @@ -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 + diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/changelog b/changelog new file mode 100644 --- /dev/null +++ b/changelog @@ -0,0 +1,3 @@ +0.2.0.1 + +- updated minimal library dependencies