diff --git a/BioHMM.cabal b/BioHMM.cabal new file mode 100644 --- /dev/null +++ b/BioHMM.cabal @@ -0,0 +1,39 @@ +name: BioHMM +version: 1.0.0 +synopsis: Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format. +-- description: +license: GPL-3 +license-file: LICENSE +author: Florian Eggenhofer +maintainer: egg@tbi.univie.ac.at +-- copyright: +category: Bioinformatics +build-type: Simple +cabal-version: >=1.8 + +extra-source-files: + README.md changelog + +source-repository head + type: git + location: https://github.com/eggzilla/HMM + +source-repository this + type: git + location: https://github.com/eggzilla/HMM/tree/1.0.0 + tag: 1.0.0 + +library + -- Modules exported by the library. + exposed-modules: Bio.HMMData + Bio.HMMParser + Bio.HMMDraw + + -- compiler-options: + ghc-options: -Wall -O2 -fno-warn-unused-do-bind + + -- Other library packages from which modules are imported. + build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib, text, vector, ParsecTools, diagrams-cairo, filepath, colour, directory, either-unwrap, SVGFonts >= 1.6, StockholmAlignment + + -- Directories containing source files. + hs-source-dirs: src 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. 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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/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,4 @@ +HMM +==== + +Libary containing parsing and visualisation functions, as well as datastructures for Hidden Markov Models in HMMER3 format. 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 @@ +-*-change-log-*- +1.0.0 Florian Eggenhofer 22. December 2016 + * Initial release diff --git a/src/Bio/HMMData.hs b/src/Bio/HMMData.hs new file mode 100644 --- /dev/null +++ b/src/Bio/HMMData.hs @@ -0,0 +1,107 @@ +-- | Datastructures for nHMMER hidden Markov models, representing RNA families +-- For more information on nHMMER consult + +module Bio.HMMData where + +import qualified Data.Vector as V + +-- | Data structure for HMMER +data HMMER3 = HMMER3 + { + -- File format version; mandatory + version :: String, + -- Model name; mandatory + name :: String, + -- Accession number; optional + acc :: String, + -- Description; optional + desc :: Maybe String, + -- Model length; mandatory + leng :: Int, + -- Maximum instance length; optional + maxl :: Maybe Int, + -- Symbol alphabet type either amino, RNA or DNA; mandatory + alpha :: String, + -- Reference annotation; optional + rf :: Bool, + -- Model masked; optional + mm :: Bool, + -- Consensus residue annotation flag; Mandatory + cons :: Bool, + -- Consensus structure; optional + cs :: Bool, + -- Map annotation; optional + map :: Bool, + -- Date; optional + date :: String, + -- Command line log; optional + com :: Maybe String, + -- Sequence number; optional + nseq :: Int, + -- Effective sequence number; optional + effn :: Double, + -- Training alignment checksum; optional + cksum :: Int, + -- Pfam gathering treshold; optional + ga :: Maybe (Double, Double), + -- Pfam trusted cutoff; optional + tc :: Maybe (Double, Double), + -- Pfam noise cutoff; optional + nc :: Maybe (Double, Double), + -- Pfam model construction; optional + bm :: Maybe String, + -- Pfam full alignment search parameters; optional + sm :: Maybe String, + -- stats for E-value calculation describing location and slope of distribution; optional + -- MSV - Gumpel distribution; optional + localmsv :: (Double,Double), + -- Viterbi - Gumpel distribution; optional + localviterbi :: (Double,Double), + -- Forward - exponential tail fitting; optional + localforward :: (Double,Double), + -- Symbol characters for this alphabet; mandatory + hmm :: String, + -- Models overall (composite) match state emission probabilities, optional + compo :: HMMER3Composite, + -- HMMER3 nodes + begin :: HMMER3Node, + nodes :: V.Vector HMMER3Node + } + deriving (Show, Eq) + +-- | Data structure for the HMMER3 node +data HMMER3Node = HMMER3Node + { + nodeId :: Int, + -- Match emission score, one per symbol in the alphabet + matchEmissions :: V.Vector Double, + -- map annotation - number of the alignment column + nma :: Maybe Int, + -- consensus residue + ncr :: Maybe Char, + -- reference annotation + nra :: Maybe Char, + -- mask value - indicating if this position was masked during model construction + nmv :: Bool, + -- consensus structure + ncs :: Maybe Char, + -- insert emission score, one per symbol in the alphabet + insertEmissions :: V.Vector Double, + -- Transistion scores, m->m m->i m->d i->m i->i d->m d->d + m2m :: Maybe Double, + m2i :: Maybe Double, + m2d :: Maybe Double, + i2m :: Maybe Double, + i2i :: Maybe Double, + d2m :: Maybe Double, + d2d :: Maybe Double + } + deriving (Show, Eq) + +-- | Data structure for the HMMER3 overall probabilities +data HMMER3Composite = HMMER3Composite + { + -- Match emission score, one per symbol in the alphabet + compositeMatchEmissions :: V.Vector Double + } + deriving (Show, Eq) diff --git a/src/Bio/HMMDraw.hs b/src/Bio/HMMDraw.hs new file mode 100644 --- /dev/null +++ b/src/Bio/HMMDraw.hs @@ -0,0 +1,415 @@ +-- | +{-# LANGUAGE NoMonomorphismRestriction #-} +{-# LANGUAGE FlexibleContexts #-} +{-# LANGUAGE TypeFamilies #-} +{-# LANGUAGE RankNTypes #-} + +module Bio.HMMDraw + ( + drawHMMER3s, + drawHMMER3, + drawSingleHMMER3s, + svgsize, + diagramName, + printHMM, + getComparisonsHighlightParameters, + drawHMMComparison, + drawSingleHMMComparison + ) where + +import Diagrams.Prelude +import Diagrams.Backend.Cairo +import qualified Bio.HMMParser as HM +import Text.Printf +import Prelude +import qualified Bio.StockholmData as S +import Data.Maybe +import qualified Data.Vector as V +import Bio.HMMCompareResult +import Bio.StockholmDraw +import qualified Data.Colour.SRGB.Linear as R +import Data.List +import Graphics.SVGFonts +import Bio.StockholmFont + +drawHMMComparison :: String -> Int -> String -> Double -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [HMMCompareResult] -> QDiagram Cairo V2 Double Any +drawHMMComparison modelDetail entryNumberCutoff emissiontype maxWidth hmms alns comparisons + | modelDetail == "flat" = alignTL (vcat' with { _sep = 8 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | modelDetail == "simple" = alignTL (vcat' with { _sep = 8 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | modelDetail == "detailed" = alignTL (vcat' with { _sep = 40 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | otherwise = alignTL (vcat' with { _sep = 40 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + where zippedInput = zip4 hmms alns comparisonNodeLabels (V.toList colorVector) + colorVector = makeColorVector modelNumber + modelNumber = length hmms + modelNames = V.fromList (map HM.name hmms) + nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector + comparisonNodeLabels = map (getComparisonNodeLabels comparisons nameColorVector) hmms + +drawSingleHMMComparison :: String -> Int -> String -> Double -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [HMMCompareResult] -> [QDiagram Cairo V2 Double Any] +drawSingleHMMComparison modelDetail entryNumberCutoff emissiontype maxWidth hmms alns comparisons + | modelDetail == "flat" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | modelDetail == "simple" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | modelDetail == "detailed" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | otherwise = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + where zippedInput = zip4 hmms alns comparisonNodeLabels (V.toList colorVector) + colorVector = makeColorVector modelNumber + modelNumber = length hmms + modelNames = V.fromList (map HM.name hmms) + nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector + comparisonNodeLabels = map (getComparisonNodeLabels comparisons nameColorVector) hmms + +-- | +drawHMMER3s :: String -> Int -> Double -> String -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> QDiagram Cairo V2 Double Any +drawHMMER3s modelDetail entryNumberCutoff maxWidth emissiontype hmms alns + | modelDetail == "flat" = alignTL (vcat' with { _sep = 8 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | modelDetail == "simple" = alignTL (vcat' with { _sep = 8 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | modelDetail == "detailed" = alignTL (vcat' with { _sep = 40 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + | otherwise = alignTL (vcat' with { _sep = 40 } (map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput)) + where zippedInput = zip4 hmms alns blankComparisonNodeLabels colorList + blankComparisonNodeLabels = map getBlankComparisonNodeLabels hmms + colorList = replicate (length hmms) white + +drawSingleHMMER3s :: String -> Int -> Double -> String -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [QDiagram Cairo V2 Double Any] +drawSingleHMMER3s modelDetail entryNumberCutoff maxWidth emissiontype hmms alns + | modelDetail == "flat" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | modelDetail == "simple" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | modelDetail == "detailed" = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + | otherwise = map (drawHMMER3 modelDetail entryNumberCutoff maxWidth emissiontype) zippedInput + where zippedInput = zip4 hmms alns blankComparisonNodeLabels colorList + blankComparisonNodeLabels = map getBlankComparisonNodeLabels hmms + colorList = replicate (length hmms) white + + +-- | +drawHMMER3 :: String -> Int -> Double -> String -> (HM.HMMER3,Maybe S.StockholmAlignment, V.Vector (Int,V.Vector (Colour Double)), Colour Double) -> QDiagram Cairo V2 Double Any +drawHMMER3 modelDetail entriesNumberCutoff maxWidth emissiontype (model,aln,comparisonNodeLabels,modelColor) + | modelDetail == "flat" = hcat $ V.toList (V.map drawHMMNodeFlat currentNodes) + | modelDetail == "simple" = hcat $ V.toList (V.map drawHMMNodeSimple currentNodes) + | modelDetail == "detailed" = applyAll ([bg white]) verboseNodesAlignment + | otherwise = hcat $ V.toList (V.map drawHMMNodeSimple currentNodes) + where nodeNumber = fromIntegral $ length currentNodes + --nodes with begin node + currentNodes = HM.begin model `V.cons` HM.nodes model + nodeAlignmentColIndices = V.map (fromJust . HM.nma) currentNodes + alphabet = HM.alpha model + alphabetSymbols = HM.alphabetToSymbols alphabet + boxlength = (fromIntegral (length alphabetSymbols)) + 1 + nodeWidth = (6.0 :: Double) + nodeNumberPerRow = floor (maxWidth / nodeWidth - 2) + nodesIntervals = makeNodeIntervals nodeNumberPerRow nodeNumber + verboseNodes = vcat' with { _sep = 3 } (V.toList (V.map (drawDetailedNodeRow alphabetSymbols emissiontype boxlength nodeNumber currentNodes comparisonNodeLabels) nodesIntervals)) + verboseNodesAlignment = alignTL (vcat' with { _sep = 5 } [modelHeader,verboseNodes,alignmentDiagram]) + modelHeader = makeModelHeader (HM.name model) modelColor + alignmentDiagram = if isJust aln then drawStockholmLines entriesNumberCutoff maxWidth nodeAlignmentColIndices comparisonNodeLabels (fromJust aln) else mempty + --connectedNodes = makeConnections boxlength currentNodes + --selfconnectedNodes = makeSelfConnections boxlength currentNodes + --arrowList = map makeArrow connectedNodes ++ map makeSelfArrow selfconnectedNodes + --labelList = map makeLabel connectedNodes ++ map makeSelfLabel selfconnectedNodes + +makeModelHeader :: String -> Colour Double -> QDiagram Cairo V2 Double Any +makeModelHeader mName modelColor = strutX 2 ||| setTitelLetter mName ||| strutX 1 ||| rect 4 4 # lw 0.1 # fc modelColor + +makeNodeIntervals :: Int -> Int -> V.Vector (Int,Int) +makeNodeIntervals nodeNumberPerRow nodeNumber = rowIntervals + where rowVector = V.iterateN rowNumber (1+) 0 + rowNumber = ceiling $ (fromIntegral nodeNumber :: Double) / (fromIntegral nodeNumberPerRow :: Double) + rowIntervals = V.map (setRowInterval nodeNumberPerRow nodeNumber) rowVector + + + +setRowInterval :: Int -> Int -> Int -> (Int,Int) +setRowInterval nodeNumberPerRow nodeNumber nodeIndex = (rowStart,safeLength) + where rowStart = nodeIndex*nodeNumberPerRow + rowLength = nodeNumberPerRow + safeLength = if rowStart + rowLength >= nodeNumber then (nodeNumber - rowStart) else rowLength + +drawDetailedNodeRow :: [Char] -> String -> Double -> Int -> V.Vector HM.HMMER3Node -> V.Vector (Int,V.Vector (Colour Double)) -> (Int, Int) -> QDiagram Cairo V2 Double Any +drawDetailedNodeRow alphabetSymbols emissiontype boxLength lastIndex allNodes comparisonNodeLabels (currentIndex,nodeSliceLength) = detailedRow + where currentNodes = V.slice currentIndex nodeSliceLength allNodes + --withLastRowNodes = V.slice (currentIndex -1) (nodeSliceLength +1) allNodes + detailedRow = applyAll (lastRowList ++ arrowList ++ labelList) detailedNodes + nextIndex = currentIndex + nodeSliceLength + detailedNodes = hcat (V.toList (V.map (drawHMMNodeVerbose alphabetSymbols emissiontype boxLength currentIndex nextIndex lastIndex comparisonNodeLabels) currentNodes)) + arrowNodes = if currentIndex > 1 then currentNodes else currentNodes + connectedNodes = makeConnections boxLength arrowNodes + selfConnectedNodes = makeSelfConnections boxLength arrowNodes + arrowList = V.toList (V.map makeArrow connectedNodes V.++ V.map makeSelfArrow selfConnectedNodes) + labelList = V.toList (V.map makeLabel connectedNodes V.++ V.map makeSelfLabel selfConnectedNodes) + --add arrows and labels for transitions from previous row + lastNode = if currentIndex > 1 then V.slice (currentIndex -1) 1 allNodes else V.empty + lastRowConnections = makeLastRowConnections boxLength lastNode + lastRowList = V.toList (V.map makeArrow lastRowConnections V.++ V.map makeLabel lastRowConnections) + +--setLetter :: String -> QDiagram Cairo V2 Double Any +--setLetter echar = alignedText 0.5 0.5 [echar] # fontSize 2 <> rect 1.0 1.0 # lw 0 -- # translate (r2 (negate 0.5, 0)) +--setLetter t = textWithSize' t 2.0 +setLabelLetter :: String -> QDiagram Cairo V2 Double Any +--setLabelLetter echar = alignedText 0.5 0.5 [echar] # fontSize 0.75 <> rect 0.4 0.5 # lw 0 +setLabelLetter t = textWithSize' t 2.0 +setTitelLetter :: String -> QDiagram Cairo V2 Double Any +--setTitelLetter echar = alignedText 0.5 0.5 [echar] # fontSize 4.0 <> rect 4.0 4.0 # lw 0 +setTitelLetter t = textWithSize' t 4.0 + +makeLastRowConnections :: Double -> V.Vector HM.HMMER3Node -> V.Vector ([Char], [Char], Double, (Double, Double)) +makeLastRowConnections boxlength currentnodes = mm1A V.++ md1A V.++ im1A V.++ dm1A V.++ dd1A + where mm1A = V.map makemm1A currentnodes + md1A = V.map (makemd1A boxlength) currentnodes + im1A = V.map makeim1A currentnodes + dm1A = V.map (makedm1A boxlength) currentnodes + dd1A = V.map makedd1A currentnodes + +makeConnections :: Double -> V.Vector HM.HMMER3Node -> V.Vector ([Char], [Char], Double, (Double, Double)) +makeConnections boxlength currentnodes = mm1A V.++ miA V.++ md1A V.++ im1A V.++ dm1A V.++ dd1A + where mm1A = V.map makemm1A currentnodes + miA = V.map (makemiA boxlength) currentnodes + md1A = V.map (makemd1A boxlength) currentnodes + im1A = V.map makeim1A currentnodes + dm1A = V.map (makedm1A boxlength) currentnodes + dd1A = V.map makedd1A currentnodes + +makeSelfConnections :: Double -> V.Vector HM.HMMER3Node -> V.Vector ([Char], [Char], Double, (Double, Double)) +makeSelfConnections boxlength currentnodes = V.map (makeiiA boxlength) currentnodes + +makemm1A :: HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makemm1A currentNode = (show ((HM.nodeId) currentNode) ++ "m", show ((HM.nodeId currentNode) + 1) ++ "m", maybe 0 ((roundPos 2) . exp . negate) (HM.m2m currentNode),(0,0.5)) +makemiA :: Double -> HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makemiA boxlength currentNode = (show ((HM.nodeId) currentNode) ++ "m", show ((HM.nodeId currentNode)) ++ "i", maybe 0 ((roundPos 2) . exp . negate) (HM.m2i currentNode),(0,setiayOffset boxlength)) +makemd1A :: Double -> HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makemd1A _ currentNode = (show ((HM.nodeId) currentNode) ++ "m", show ((HM.nodeId currentNode) + 1) ++ "d", maybe 0 ((roundPos 2) . exp . negate) (HM.m2d currentNode),(1.5,2.0)) +makeim1A :: HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makeim1A currentNode = (show ((HM.nodeId) currentNode) ++ "i", show ((HM.nodeId currentNode) + 1) ++ "m", maybe 0 ((roundPos 2) . exp . negate) (HM.i2m currentNode),(0,negate 0.5)) +makeiiA :: Double -> HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makeiiA _ currentNode = (show ((HM.nodeId) currentNode) ++ "i", show ((HM.nodeId currentNode)) ++ "i", maybe 0 ((roundPos 2) . exp . negate) (HM.i2i currentNode),(0,4.7)) +makedm1A :: Double -> HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makedm1A _ currentNode = (show ((HM.nodeId) currentNode) ++ "d", show ((HM.nodeId currentNode) + 1) ++ "m", maybe 0 ((roundPos 2) . exp . negate) (HM.d2m currentNode),(negate 1.5,3.0)) +makedd1A :: HM.HMMER3Node -> (String, String, Double, (Double, Double)) +makedd1A currentNode = (show ((HM.nodeId) currentNode) ++ "d", show ((HM.nodeId currentNode) + 1) ++ "d", maybe 0 ((roundPos 2) . exp . negate) (HM.d2d currentNode),(negate 1,1)) + +setiayOffset :: Double -> Double +setiayOffset boxlength + | boxlength <= 10 = 0.6 + | otherwise = 3.5 + +makeArrow :: (String,String,Double,(Double,Double)) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any +makeArrow (lab1,lab2,weight,_) = connectOutside' arrowStyle1 (lab1) (lab2) + where arrowStyle1 = with & arrowHead .~ spike & shaftStyle %~ lw (local (0.1)) & headLength .~ local 0.001 & shaftStyle %~ dashingG [weight, 0.1] 0 & headStyle %~ fc black . opacity (weight * 2) + +makeSelfArrow :: (String,String,Double,(Double,Double)) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any +makeSelfArrow (lab1,_,weight,_) = connectPerim' arrowStyle lab1 lab1 (4/12 @@ turn) (2/12 @@ turn) + where arrowStyle = with & arrowHead .~ spike & arrowShaft .~ shaft' & arrowTail .~ lineTail & tailTexture .~ solid black & shaftStyle %~ lw (local (0.1)) & headLength .~ local 0.001 & tailLength .~ 0.9 & shaftStyle %~ dashingG [weight, 0.1] 0 & headStyle %~ fc black . opacity (weight * 2) + shaft' = arc xDir (-2.7/5 @@ turn) + +-- %~ lw (local (0.1 * weight)) + +makeLabel :: (String, String,Double,(Double,Double)) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any +makeLabel (n1,n2,weight,(xOffset,yOffset))= + withName n1 $ \b1 -> + withName n2 $ \b2 -> + let v = location b2 .-. location b1 + midpoint = location b1 .+^ (v ^/ 2) + in + atop (position [((midpoint # translateX (negate 0.25 + xOffset) # translateY (0 + yOffset)), setLabelLetter (show weight)) ]) + +makeSelfLabel :: (String, String,Double,(Double,Double)) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any +makeSelfLabel (n1,n2,weight,(xOffset,yOffset))= + withName n1 $ \b1 -> + withName n2 $ \b2 -> + let v = location b2 .-. location b1 + midpoint = location b1 .+^ (v ^/ 2) + in + atop (position [(midpoint # translateX (negate 0.25 + xOffset) # translateY (0 + yOffset), setLabelLetter (show weight))]) + +-- | +drawHMMNodeFlat :: HM.HMMER3Node -> QDiagram Cairo V2 Double Any +drawHMMNodeFlat _ = rect 2 2 # lw 0.1 + +-- | +drawHMMNodeSimple :: HM.HMMER3Node -> QDiagram Cairo V2 Double Any +drawHMMNodeSimple _ = rect 2 2 # lw 0.1 + +-- | +drawHMMNodeVerbose :: String -> String -> Double -> Int -> Int -> Int -> V.Vector (Int, V.Vector (Colour Double))-> HM.HMMER3Node -> QDiagram Cairo V2 Double Any +drawHMMNodeVerbose alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex comparisonNodeLabels node + | idNumber == 0 = beginBox + | idNumber == (lastIndex - 1) = nodeBox ||| endBox + | idNumber == rowStart = rowStartBox idNumber boxlength ||| nodeBox + | idNumber == rowEnd - 1 = nodeBox ||| rowEndBox idNumber boxlength + | otherwise = nodeBox + where idNumber = HM.nodeId node + nodeLabels = V.toList (snd (comparisonNodeLabels V.! idNumber)) + nid = show idNumber + beginBox = strutX 7 ||| (idBox nid nodeLabels === strutY 0.5 === emptyDeletions === strutY 1.5 === insertions nid === strutY 1.5 === beginState boxlength nid) ||| (strutX 4) + nodeBox = idBox nid nodeLabels === strutY 0.5 === deletions nid === strutY 2.5 === insertions nid === strutY 1.5 === matches alphabetSymbols emissiontype boxlength node ||| (strutX 4) + endBox = emptyIdBox === strutY 0.5 === emptyDeletions === strutY 1.5 === emptyInsertions === strutY 1.5 === endState boxlength idNumber ||| strutX 4 + +-- | idBox associates the node with its index and a tupel of a list of modelidentifiers and the total model number +--idBox nid nodeLabels = alignedText 0 0 nid # fontSize 2 # translate (r2 ((negate ((fromIntegral ((length nid) * 2))/2)), negate 1.25)) +idBox :: String -> [Colour Double] -> QDiagram Cairo V2 Double Any +idBox nid nodeLabels = text' nid # translate (r2 ((negate ((fromIntegral ((length nid) * 2))/2)), negate 1.25)) <> wheel nodeLabels <> rect 1.5 3 # lw 0 + +emptyIdBox :: QDiagram Cairo V2 Double Any +emptyIdBox = rect 1.5 1.5 # lw 0 + +rowStartBox :: Int -> Double -> QDiagram Cairo V2 Double Any +rowStartBox idNumber boxlength = rect 0 1.5 #lw 0.0 === rect 0 6 # lw 0.1 # named (nid ++ "d") === rect 0 6 # lw 0.1 #named (nid ++ "i") === rect 0 (boxlength + 2) # lw 0.1 # named (nid ++ "m") ||| strutX 2.5 + where nid = show (idNumber - 1) + +rowEndBox :: Int -> Double -> QDiagram Cairo V2 Double Any +rowEndBox idNumber boxlength = rect 0.1 1.5 #lw 0.0 === rect 0.1 6 # lw 0.1 # named (nid ++ "d") === rect 0.1 6 # lw 0.1 #named (nid ++ "i") === rect 0.1 (boxlength + 2) #lw 0.1 #named (nid ++ "m") + where nid = show (idNumber + 1) + +deletions :: String -> QDiagram Cairo V2 Double Any +deletions nid = alignedText 0 0 "D" # translate (r2 (negate 0.25,0.25)) <> circle 3 # lw 0.1 # fc white # named (nid ++ "d") +emptyDeletions :: QDiagram Cairo V2 Double Any +emptyDeletions = circle 3 # lw 0.0 # fc white +insertions :: String -> QDiagram Cairo V2 Double Any +insertions nid = alignedText 0 0 "I" # translate (r2 (0,0.25)) <> rect 4.2426 4.2426 # lw 0.1 # rotateBy (1/8) # fc white # named (nid ++ "i") + +emptyInsertions :: QDiagram Cairo V2 Double Any +emptyInsertions = rect 4.2426 4.2426 # lw 0 # rotateBy (1/8) # fc white + +matches :: [Char] -> String -> Double -> HM.HMMER3Node -> QDiagram Cairo V2 Double Any +matches alphabetSymbols emissiontype boxlength node = entries # translate (r2 (negate 2.5,boxlength/2 -1)) <> outerbox # named (nid ++ "m") + where outerbox = rect 6 boxlength # lw 0.1 # fc white + entries = vcat (map (emissionEntry emissiontype) symbolsAndEmissions) + symbolsAndEmissions = zip (map wrap alphabetSymbols) (V.toList emissionEntries) + emissionEntries = setEmissions emissiontype (HM.matchEmissions node) + nid = show $ HM.nodeId node + +wheel :: [Colour Double] -> QDiagram Cairo V2 Double Any +wheel colors = wheel' # rotate r + where + wheel' = mconcat $ zipWith fc colors (iterateN n (rotate a) w) + n = length colors + a = 1 / (fromIntegral n) @@ turn + w = wedge 3 xDir a # lwG 0 + r = (1/4 @@ turn) ^-^ (1/(2*(fromIntegral n)) @@ turn) + +-- B → M 1 , B → I 0 , B → D 1 ; I 0 → M 1 , I 0 → I 0 +beginState :: Double -> String -> QDiagram Cairo V2 Double Any +beginState boxlength nid = alignedText 0.5 0.5 "BEGIN" <> outerbox # named (nid ++ "m") <> rect 6 boxlength # named (nid ++ "d") # lw 0.1 + where outerbox = rect 6 boxlength # lw 0.1 # fc white + +endState :: Double -> Int -> QDiagram Cairo V2 Double Any +endState boxlength idNumber = alignedText 0.5 0.5 "END" <> outerbox # named (nid ++ "m") <> rect 6 boxlength # named (nid ++ "d") # lw 0.1 <> rect 6 boxlength # named (nid ++ "i") # lw 0.1 + where outerbox = rect 6 boxlength # lw 0.1 # fc white + nid = show (idNumber + 1) + +--transitions boxlength node = rect 6 h # lw 0 # translate (r2(0,negate (height/2))) +-- where h = (boxlength + 1 + 1 + 6 + 6) + +setEmissions :: String -> V.Vector Double -> V.Vector Double +setEmissions emissiontype emissions + | emissiontype == "score" = scoreentries + | emissiontype == "probability" = propentries + | emissiontype == "bar" = barentries + | otherwise = barentries + where scoreentries = emissions + propentries = V.map (exp . negate) emissions + barentries = V.map (exp . negate) emissions + +wrap :: t -> [t] +wrap x = [x] + +emissionEntry :: String -> (String,Double) -> QDiagram Cairo V2 Double Any +emissionEntry emissiontype (symbol,emission) + | emissiontype == "probability" = textentry + | emissiontype == "score" = textentry + | emissiontype == "bar" = barentry + | otherwise = barentry + where textentry = alignedText 0 0.1 (symbol ++ " " ++ printf "%.3f" emission) # translate (r2 (negate 0.5,0)) <> (rect 2 1 # lw 0 ) + --barentry = stroke (textSVG symbol 2) ||| bar emission + barentry = (alignedText 0 0.01 symbol # translate (r2 (negate 0.25,negate 0.3)) <> (rect 2 1 # lw 0 )) ||| bar emission + +bar :: Double -> QDiagram Cairo V2 Double Any +bar emission = (rect (4 * emission) 1 # lw 0 # fc black # translate (r2 (negate (2 - (4 * emission/2)),0)) <> rect 4 1 # lw 0.03 ) + +svgsize :: SizeSpec V2 Double +svgsize = mkSizeSpec2D Nothing Nothing + +-- | Check for available cairo output formats +diagramName :: String -> String -> Either String String +diagramName filename fileformat + | fileformat == "pdf" = Right (filename ++ "." ++ fileformat ) + | fileformat == "svg" = Right (filename ++ "." ++ fileformat ) + | fileformat == "png" = Right (filename ++ "." ++ fileformat ) + | fileformat == "ps" = Right (filename ++ "." ++ fileformat ) + | otherwise = Left "Unsupported output format requested (use svg, pdf, ps, png)" + +printHMM :: String -> SizeSpec V2 Double -> QDiagram Cairo V2 Double Any -> IO () +printHMM outputName = renderCairo outputName + +roundPos :: (RealFrac a) => Int -> a -> a +roundPos positions number = (fromInteger $ round $ number * (10^positions)) / (10.0^^positions) + +getComparisonsHighlightParameters :: [HM.HMMER3] -> [HMMCompareResult] -> [(Int,Int,Int,Int,Int,Int,Int,Int)] +getComparisonsHighlightParameters sortedmodels comp = map (getComparisonHighlightParameters sortedmodels) comp + +getComparisonHighlightParameters :: [HM.HMMER3] -> HMMCompareResult -> (Int,Int,Int,Int,Int,Int,Int,Int) +getComparisonHighlightParameters _ comp = (a,b,c,d,a,f,c,e) + where a = 1 + b = head (model1matchednodes comp) + c = 2 + d = head (model2matchednodes comp) + e = last (model2matchednodes comp) + f = last (model1matchednodes comp) + + +getComparisonNodeLabels :: [HMMCompareResult] -> V.Vector (String, Colour Double) -> HM.HMMER3 -> V.Vector (Int, V.Vector (Colour Double)) +getComparisonNodeLabels comparsionResults colorVector model = comparisonNodeLabels + where modelName = HM.name model + relevantComparisons1 = filter ((modelName==) . model1Name) comparsionResults + modelNodeInterval1 = map (\a -> (model2Name a,model2matchednodes a)) relevantComparisons1 + relevantComparisons2 = filter ((modelName==) . model2Name) comparsionResults + modelNodeInterval2 = map (\a -> (model1Name a,model1matchednodes a)) relevantComparisons2 + modelNodeIntervals = V.fromList (modelNodeInterval1 ++ modelNodeInterval2) + colorNodeIntervals = V.map (modelToColor colorVector) modelNodeIntervals + nodeNumber = length (HM.nodes model) + comparisonNodeLabels = V.generate (nodeNumber +1) (makeComparisonNodeLabel colorNodeIntervals) + --nodeColorLabels = map model colorNodeIntervals + +getBlankComparisonNodeLabels :: HM.HMMER3 -> V.Vector (Int, V.Vector (Colour Double)) +getBlankComparisonNodeLabels model = comparisonNodeLabels + where comparisonNodeLabels = V.generate (nodeNumber +1 ) makeBlankComparisonNodeLabel + nodeNumber = length (HM.nodes model) + +modelToColor :: V.Vector (String,Colour Double) -> (String,[Int]) -> (Colour Double,[Int]) +modelToColor colorVector (mName,nInterval) = nColorInterval + where nColorInterval = (snd (fromJust entry),nInterval) + --nColorInterval = maybe Nothing (\a -> Just (snd a,nInterval)) entry + entry = V.find (\(a,_)-> mName == a) colorVector + +makeComparisonNodeLabel :: V.Vector (Colour Double,[Int]) -> Int -> (Int,(V.Vector (Colour Double))) +makeComparisonNodeLabel colorNodeIntervals nodeNumber = comparisonNodeLabel + where relevantColorNodeIntervals = V.filter (\(_,b) -> elem nodeNumber b) colorNodeIntervals + modelColors = V.map fst relevantColorNodeIntervals + comparisonNodeLabel = if (null modelColors) then (nodeNumber,V.singleton white) else (nodeNumber,modelColors) + +makeBlankComparisonNodeLabel :: Int -> (Int,(V.Vector (Colour Double))) +makeBlankComparisonNodeLabel nodeNumber = (nodeNumber,V.singleton white) + +makeColorVector :: Int -> V.Vector (Colour Double) +makeColorVector modelNumber = V.map (\(a,b,c) -> R.rgb a b c) modelRGBTupel + where indexVector = V.iterateN (modelNumber) (1+) 0 + stepSize = (765 :: Double) / (fromIntegral modelNumber) + modelRGBTupel = V.map (makeRGBTupel stepSize) indexVector + +makeRGBTupel :: Double -> Int -> (Double,Double,Double) +makeRGBTupel stepSize modelNumber = (a,b,c) + where totalSize = (fromIntegral modelNumber) * stepSize + a = (rgbBoundries (totalSize - 255))/255 + b = (rgbBoundries (totalSize - a - 255))/255 + c = (rgbBoundries (totalSize - a - b))/255 + +rgbBoundries :: Double -> Double +rgbBoundries rgbValue + | rgbValue>210 = 210 + | rgbValue<50 = 50 + | otherwise = rgbValue + +text' :: String -> QDiagram Cairo V2 Double Any +text' t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 3 3) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.75)) + +textWithSize' :: String -> Double -> QDiagram Cairo V2 Double Any +textWithSize' t si = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False si si) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate siOffset, negate siOffset)) + where siOffset = si/2 diff --git a/src/Bio/HMMParser.hs b/src/Bio/HMMParser.hs new file mode 100644 --- /dev/null +++ b/src/Bio/HMMParser.hs @@ -0,0 +1,277 @@ +-- | Parse HMM models +-- Currently contains a parser for HMMER3 models +-- For more information on HMMER consult: +module Bio.HMMParser ( + parseHMMER3, + readHMMER3, + alphabetToSymbols, + module Bio.HMMData + ) where + +import Bio.HMMData +import Text.ParserCombinators.Parsec +import Text.Parsec.Numbers +import qualified Control.Exception.Base as CE +import qualified Data.Vector as V + +-- | parse HMMER3 model from input string +parseHMMER3 :: [Char] -> Either ParseError [HMMER3] +parseHMMER3 input = parse genParseHMMER3s "HMMER3" input + +-- | parse HMMER3 from input filePath +readHMMER3 :: String -> IO (Either ParseError [HMMER3]) +readHMMER3 filePath = do + parsedFile <- parseFromFile genParseHMMER3s filePath + CE.evaluate parsedFile + +-- | Parse the input as HMMER3 datatype +genParseHMMER3s :: GenParser Char st [HMMER3] +genParseHMMER3s = do + hmmers <- many1 genParseHMMER3 + eof + return hmmers + +-- | Parse the input as HMMER3 datatype +genParseHMMER3 :: GenParser Char st HMMER3 +genParseHMMER3 = do + string "HMMER3/" + _version <- many1 (noneOf "\n") + newline + _name <- parseStringAttribute "NAME" + _acc <- try (parseStringAttribute "ACC") + _desc <- optionMaybe (try (parseStringAttribute "DESC")) + _leng <- parseIntAttribute "LENG" + _maxl <- optionMaybe (try (parseIntAttribute "MAXL")) + _alph <- parseStringAttribute "ALPH" + _rf <- parseSwitchAttribute "RF" + _mm <- parseSwitchAttribute "MM" + _cons <- parseSwitchAttribute "CONS" + _cs <- parseSwitchAttribute "CS" + _map <- parseSwitchAttribute "MAP" + _date <- parseStringAttribute "DATE" + _com <- many (try (parseStringAttribute "COM")) + _nseq <- parseIntAttribute "NSEQ" + _effn <- parseFloatAttribute "EFFN" + _cksum <- parseIntAttribute "CKSUM" + _ga <- optionMaybe (try (parseStatAttribute "GA")) + _tc <- optionMaybe (try (parseStatAttribute "TC")) + _nc <- optionMaybe (try (parseStatAttribute "NC")) + _bm <- optionMaybe (try (parseStringAttribute "BM")) + _sm <- optionMaybe (try (parseStringAttribute "SM")) + _localmsv <- parseStatAttribute "STATS LOCAL MSV" + _localviterbi <- parseStatAttribute "STATS LOCAL VITERBI" + _localforward <- parseStatAttribute "STATS LOCAL FORWARD" + string "HMM" + _hmm <- many1 (try parseAlphabetSymbol) + many1 (oneOf " ") + newline + many1 (noneOf "\n") + newline + (_compo,_begin) <- parseHMMER3Composite _alph + _nodes <- many1 (parseHMMER3Node _alph) + string "//" + newline + return $ HMMER3 _version _name _acc _desc _leng _maxl _alph _rf _mm _cons _cs _map _date (if null _com then Nothing else Just (concat _com)) _nseq _effn _cksum _ga _tc _nc _bm _sm _localmsv _localviterbi _localforward _hmm _compo _begin (V.fromList _nodes) + +parseSwitchAttribute :: String -> GenParser Char st Bool +parseSwitchAttribute fieldName = do + string fieldName + many1 (oneOf " ") + _switch <- try (string "yes") <|> try (string "no") + newline + return (switchToBool _switch) + +switchToBool :: String -> Bool +switchToBool switch + | switch == "yes" = True + | otherwise = False + +parseStringAttribute :: String -> GenParser Char st String +parseStringAttribute fieldName = do + string fieldName + many1 (oneOf " ") + _string <- many1 (noneOf "\n") + newline + return _string + +parseFloatAttribute :: String -> GenParser Char st Double +parseFloatAttribute fieldName = do + string fieldName + many1 (oneOf " ") + _double <- parseFloat + newline + return _double + +parseIntAttribute :: String -> GenParser Char st Int +parseIntAttribute fieldName = do + string fieldName + many1 (oneOf " ") + _int <- parseIntegral + newline + return _int + +parseStatAttribute :: String -> GenParser Char st (Double,Double) +parseStatAttribute fieldName = do + string fieldName + many1 (oneOf " ") + _stat1 <- parseFloat + --many1 (oneOf " ") + _stat2 <- parseFloat + optional (string ";") + newline + return (_stat1,_stat2) + +-- | Parse HMMER3 composite +parseHMMER3Composite :: String -> GenParser Char st (HMMER3Composite,HMMER3Node) +parseHMMER3Composite alphabet = do + many1 (oneOf " ") + _nodeId <- many1 (noneOf " ") + _matchEmissions <- count (setEmissionNumber alphabet) (try parseDoubleParameter) + newline + _insertEmissions <- many1 parseDoubleParameter + newline + _bm2m <- parseOptionalFloatParameter + _bm2i <- parseOptionalFloatParameter + _bm2d <- parseOptionalFloatParameter + _bi2m <- parseOptionalFloatParameter + _bi2i <- parseOptionalFloatParameter + _bd2m <- parseOptionalFloatParameter + _bd2d <- parseOptionalFloatParameter + newline + return (HMMER3Composite (V.fromList _matchEmissions),HMMER3Node (0 :: Int) V.empty (Just (0::Int)) Nothing Nothing False Nothing (V.fromList _insertEmissions) _bm2m _bm2i _bm2d _bi2m _bi2i _bd2m _bd2d) + +-- | Parse HMMER3 node +parseHMMER3Node :: String -> GenParser Char st HMMER3Node +parseHMMER3Node alphabet = do + _nodeId <- parseIntParameter + _matchEmissions <- count (setEmissionNumber alphabet) (try parseDoubleParameter) + _nma <- parseOptionalIntParameter + _ncs <- parseOptionalCharParameter + _nrf <- parseOptionalCharParameter + _nmm <- parseMaskParameter + _ncs <- parseOptionalStructureParameter + newline + _insertEmissions <- many1 parseDoubleParameter + newline + _m2m <- parseOptionalFloatParameter + _m2i <- parseOptionalFloatParameter + _m2d <- parseOptionalFloatParameter + _i2m <- parseOptionalFloatParameter + _i2i <- parseOptionalFloatParameter + _d2m <- parseOptionalFloatParameter + _d2d <- parseOptionalFloatParameter + newline + return $ HMMER3Node _nodeId (V.fromList _matchEmissions) _nma _ncs _nrf _nmm _ncs (V.fromList _insertEmissions) _m2m _m2i _m2d _i2m _i2i _d2m _d2d + +setEmissionNumber :: String -> Int +setEmissionNumber alphabet + | alphabet == "DNA" = 4 + | alphabet == "dna" = 4 + | alphabet == "RNA" = 4 + | alphabet == "rna" = 4 + | alphabet == "AMINO" = 20 + | alphabet == "amino" = 20 + | alphabet == "COINS" = 2 + | alphabet == "coins" = 2 + | alphabet == "DICE" = 6 + | alphabet == "dice" = 6 + | otherwise = 0 + +alphabetToSymbols :: String -> String +alphabetToSymbols alphabet + | alphabet == "DNA" = "ACGT" + | alphabet == "dna" = "ACGT" + | alphabet == "RNA" = "ACGU" + | alphabet == "rna" = "ACGU" + | alphabet == "AMINO" = "ACDEFGHIKLMNPQRSTVWY" + | alphabet == "amino" = "ACDEFGHIKLMNPQRSTVWY" + | alphabet == "COINS" = "HT" + | alphabet == "coins" = "HT" + | alphabet == "DICE" = "123456" + | alphabet == "dice" = "123456" + | otherwise = "" + +parseDoubleParameter :: GenParser Char st Double +parseDoubleParameter = do + many1 (oneOf " ") + _float <- parseFloat + return _float + +parseAlphabetSymbol :: GenParser Char st Char +parseAlphabetSymbol = do + many1 (try (oneOf " ")) + _symbol <- try (oneOf ("ABCDEFGHIJKLMNOPQRSTUVWXYZ")) + return _symbol + +--parseCharParameter :: GenParser Char st Char +--parseCharParameter = do +-- many1 (oneOf " ") +-- _symbol <- upper +-- return _symbol + +parseIntParameter :: GenParser Char st Int +parseIntParameter = do + many1 (oneOf " ") + _int <- parseIntegral + return _int + +--parseStructureParameter :: GenParser Char st Char +--parseStructureParameter = do +-- many1 (oneOf " ") +-- _stru <- oneOf "<>().:[]{}~,_ABCDEFGHIJKLMNOPQRST" +-- return _stru + +parseOptionalCharParameter :: GenParser Char st (Maybe Char) +parseOptionalCharParameter = do + many1 (oneOf " ") + _symbol <- alphaNum <|> char '-' + return (optionalCharToMaybe _symbol) + +parseOptionalIntParameter :: GenParser Char st (Maybe Int) +parseOptionalIntParameter = do + many1 (oneOf " ") + _int <- many1 digit + return (optionalIntToMaybe _int) + +parseOptionalFloatParameter :: GenParser Char st (Maybe Double) +parseOptionalFloatParameter = do + many1 (oneOf " ") + _float <- many1 (oneOf "1234567890.e-*") + return (optionalFloatToMaybe _float) + +parseMaskParameter :: GenParser Char st Bool +parseMaskParameter = do + many1 (oneOf " ") + _mask <- oneOf "m-" + return (maskToBool _mask) + +maskToBool :: Char -> Bool +maskToBool mask + | mask == 'm' = True + | otherwise = False + +optionalCharToMaybe :: Char -> Maybe Char +optionalCharToMaybe c + | c == '-' = Nothing + | otherwise = Just c + +optionalIntToMaybe :: String -> Maybe Int +optionalIntToMaybe c + | c == "-" = Nothing + | otherwise = Just (read c :: Int) + +optionalStructureToMaybe :: Char -> Maybe Char +optionalStructureToMaybe c + | c == '-' = Nothing + | otherwise = Just c + +optionalFloatToMaybe :: String -> Maybe Double +optionalFloatToMaybe c + | c == "*" = Nothing + | otherwise = Just (read c :: Double) + +parseOptionalStructureParameter :: GenParser Char st (Maybe Char) +parseOptionalStructureParameter = do + many1 (oneOf " ") + _stru <- oneOf "<>().:[]{}~,_ABCDEFGHIJKLMNOPQRST-" + return (optionalStructureToMaybe _stru)