BioHMM (empty) → 1.0.0
raw patch · 8 files changed
+1522/−0 lines, 8 filesdep +ParsecToolsdep +SVGFontsdep +StockholmAlignmentsetup-changed
Dependencies added: ParsecTools, SVGFonts, StockholmAlignment, base, colour, diagrams-cairo, diagrams-lib, directory, either-unwrap, filepath, parsec, text, vector
Files
- BioHMM.cabal +39/−0
- LICENSE +675/−0
- README.md +4/−0
- Setup.hs +2/−0
- changelog +3/−0
- src/Bio/HMMData.hs +107/−0
- src/Bio/HMMDraw.hs +415/−0
- src/Bio/HMMParser.hs +277/−0
+ BioHMM.cabal view
@@ -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
+ LICENSE view
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+ README.md view
@@ -0,0 +1,4 @@+HMM+====++Libary containing parsing and visualisation functions, as well as datastructures for Hidden Markov Models in HMMER3 format.
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ changelog view
@@ -0,0 +1,3 @@+-*-change-log-*-+1.0.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 22. December 2016+ * Initial release
+ src/Bio/HMMData.hs view
@@ -0,0 +1,107 @@+-- | Datastructures for nHMMER hidden Markov models, representing RNA families+-- For more information on nHMMER consult <http://eddylab.org/infernal/>++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)
+ src/Bio/HMMDraw.hs view
@@ -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
+ src/Bio/HMMParser.hs view
@@ -0,0 +1,277 @@+-- | Parse HMM models+-- Currently contains a parser for HMMER3 models+-- For more information on HMMER consult: <http://hmmer.org>+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)