-- Hoogle documentation, generated by Haddock -- See Hoogle, http://www.haskell.org/hoogle/ -- | Library for reading Meme XML output -- @package memexml @version 0.0.3 -- | This module contains a hierarchical data structure for Multiple EM for -- Motif Elicitation (MEME) results For more information on MEME consult: -- http://meme.nbcr.net/meme/ module Bio.MemeData -- | Document Root of Meme xml output data MemeResult MemeResult :: String -> String -> TrainingSet -> Model -> [Motif] -> ScannedSiteSummary -> MemeResult memeversion :: MemeResult -> String memerelease :: MemeResult -> String trainingset :: MemeResult -> TrainingSet model :: MemeResult -> Model motifs :: MemeResult -> [Motif] scannedSiteSummary :: MemeResult -> ScannedSiteSummary -- | Training set defines the data used for the motif search data TrainingSet TrainingSet :: String -> Int -> MemeAlphabet -> MemeAmbigs -> [Sequence] -> LetterFrequencies -> TrainingSet trainingsetDatafile :: TrainingSet -> String trainingsetLength :: TrainingSet -> Int trainingsetAlphabet :: TrainingSet -> MemeAlphabet trainingsetAmbigs :: TrainingSet -> MemeAmbigs trainingsetSequences :: TrainingSet -> [Sequence] trainingsetLetterFrequencies :: TrainingSet -> LetterFrequencies data MemeAlphabet MemeAlphabet :: String -> Int -> [MemeLetter] -> MemeAlphabet memeAlphabetId :: MemeAlphabet -> String memeAlphabetLength :: MemeAlphabet -> Int memeAlphabetLetters :: MemeAlphabet -> [MemeLetter] data MemeLetter MemeLetter :: String -> Char -> MemeLetter memeLetterId :: MemeLetter -> String memeLetterSymbol :: MemeLetter -> Char data MemeAmbigs MemeAmbigs :: [MemeLetter] -> MemeAmbigs memeAmbigLetters :: MemeAmbigs -> [MemeLetter] data Sequence Sequence :: String -> String -> Int -> Double -> Sequence sequenceId :: Sequence -> String sequenceName :: Sequence -> String sequenceLength :: Sequence -> Int sequenceWeight :: Sequence -> Double data LetterFrequencies LetterFrequencies :: AlphabetArray -> LetterFrequencies letterFrequenciesAlphabetArray :: LetterFrequencies -> AlphabetArray data Model Model :: String -> String -> String -> Int -> String -> String -> Int -> Int -> Double -> Int -> Int -> String -> Int -> Int -> Double -> Int -> String -> Double -> String -> Double -> Int -> Double -> Int -> Int -> Int -> String -> String -> String -> String -> BackgroundFrequencies -> Model commandLine :: Model -> String host :: Model -> String modelType :: Model -> String nmotifs :: Model -> Int evalueThreshold :: Model -> String objectFunction :: Model -> String minWidth :: Model -> Int maxWidth :: Model -> Int minic :: Model -> Double wg :: Model -> Int ws :: Model -> Int endGaps :: Model -> String minSites :: Model -> Int maxSites :: Model -> Int wnSites :: Model -> Double prob :: Model -> Int spMap :: Model -> String spFuzz :: Model -> Double prior :: Model -> String beta :: Model -> Double maxiter :: Model -> Int distance :: Model -> Double numSequences :: Model -> Int numPositions :: Model -> Int seed :: Model -> Int seqfrac :: Model -> String strands :: Model -> String priorsFile :: Model -> String reasonForStopping :: Model -> String backgroundFrequencies :: Model -> BackgroundFrequencies data BackgroundFrequencies BackgroundFrequencies :: String -> AlphabetArray -> BackgroundFrequencies source :: BackgroundFrequencies -> String backgroundFrequenciesAlphabetArray :: BackgroundFrequencies -> AlphabetArray data AlphabetArray AlphabetArray :: [AlphabetArrayValue] -> AlphabetArray alphabetArrayValues :: AlphabetArray -> [AlphabetArrayValue] data AlphabetArrayValue AlphabetArrayValue :: String -> Double -> AlphabetArrayValue letterId :: AlphabetArrayValue -> String frequency :: AlphabetArrayValue -> Double -- | The motifs are predicted by appying the model to the trainingset data Motif Motif :: String -> String -> Int -> Int -> Double -> Double -> Int -> Double -> Double -> Double -> String -> Scores -> Propabilities -> [ContributingSite] -> Motif motifId :: Motif -> String motifName :: Motif -> String motifWidth :: Motif -> Int motifSites :: Motif -> Int motifIc :: Motif -> Double motifRe :: Motif -> Double motifLlr :: Motif -> Int motifEvalue :: Motif -> Double motifBayesTreshold :: Motif -> Double motifElapsedTime :: Motif -> Double motifRegularexpression :: Motif -> String motifScores :: Motif -> Scores motifProbabilites :: Motif -> Propabilities motifContributingsites :: Motif -> [ContributingSite] data Scores Scores :: AlphabetMatrix -> Scores scoreAlphabetMatrix :: Scores -> AlphabetMatrix data Propabilities Propabilities :: AlphabetMatrix -> Propabilities propabilitiesAlphabetMatrix :: Propabilities -> AlphabetMatrix data AlphabetMatrix AlphabetMatrix :: [AlphabetArray] -> AlphabetMatrix alphabetMatrixArrays :: AlphabetMatrix -> [AlphabetArray] data ContributingSite ContributingSite :: String -> Int -> String -> Double -> String -> String -> Site -> ContributingSite contributingSiteId :: ContributingSite -> String contributingSitePosition :: ContributingSite -> Int contributingSiteStrand :: ContributingSite -> String contributingSitePvalue :: ContributingSite -> Double contributingSiteLeftFlank :: ContributingSite -> String contributingSiteRightFlank :: ContributingSite -> String contributingSite :: ContributingSite -> Site data Site Site :: [LetterReference] -> Site siteLetterReferences :: Site -> [LetterReference] data LetterReference LetterReference :: String -> LetterReference letterReference :: LetterReference -> String -- | Scanned sites contain all sites evaluated for possible motifs data ScannedSiteSummary ScannedSiteSummary :: Double -> [ScannedSites] -> ScannedSiteSummary pThresh :: ScannedSiteSummary -> Double scannedSites :: ScannedSiteSummary -> [ScannedSites] data ScannedSites ScannedSites :: String -> Double -> Int -> [ScannedSite] -> ScannedSites scannedsitesSequenceId :: ScannedSites -> String scannedSitesPvalue :: ScannedSites -> Double numSites :: ScannedSites -> Int scannedSiteArray :: ScannedSites -> [ScannedSite] data ScannedSite ScannedSite :: String -> String -> Int -> Double -> ScannedSite scannedsiteMotifId :: ScannedSite -> String strand :: ScannedSite -> String position :: ScannedSite -> Int scannedSitePvalue :: ScannedSite -> Double instance Show MemeLetter instance Eq MemeLetter instance Show MemeAlphabet instance Eq MemeAlphabet instance Show MemeAmbigs instance Eq MemeAmbigs instance Show Sequence instance Eq Sequence instance Show AlphabetArrayValue instance Eq AlphabetArrayValue instance Show AlphabetArray instance Eq AlphabetArray instance Show BackgroundFrequencies instance Eq BackgroundFrequencies instance Show Model instance Eq Model instance Show LetterFrequencies instance Eq LetterFrequencies instance Show TrainingSet instance Eq TrainingSet instance Show AlphabetMatrix instance Eq AlphabetMatrix instance Show Propabilities instance Eq Propabilities instance Show Scores instance Eq Scores instance Show LetterReference instance Eq LetterReference instance Show Site instance Eq Site instance Show ContributingSite instance Eq ContributingSite instance Show Motif instance Eq Motif instance Show ScannedSite instance Eq ScannedSite instance Show ScannedSites instance Eq ScannedSites instance Show ScannedSiteSummary instance Eq ScannedSiteSummary instance Show MemeResult instance Eq MemeResult -- | Parse Multiple EM for Motif Elicitation (MEME) XML output. xml parsing -- is done with the HXT libary. For more information on MEME consult: -- http://meme.nbcr.net/meme/ module Bio.MemeXML -- | Parse XML results in XML format parseXML :: String -> IOStateArrow s b XmlTree -- | gets all subtrees with the specified tag name atTag :: ArrowXml a => String -> a XmlTree XmlTree -- | gets all subtrees with the specified id attribute atId :: ArrowXml a => String -> a XmlTree XmlTree -- | removes whitespace characters rstrip :: String -> String -- | gets the whole memexml document tree getMemeResult :: ArrowXml a => a XmlTree MemeResult -- | get the Training set subtree getTrainingSet :: ArrowXml a => a XmlTree TrainingSet getMemeAlphabet :: ArrowXml a => a XmlTree MemeAlphabet getLetter :: ArrowXml a => a XmlTree MemeLetter getAmbigs :: ArrowXml a => a XmlTree MemeAmbigs getLetterFrequencies :: ArrowXml a => a XmlTree LetterFrequencies -- | get the model subtree getModel :: ArrowXml a => a XmlTree Model getBackgroundFrequencies :: ArrowXml a => a XmlTree BackgroundFrequencies getScannedSiteSummary :: ArrowXml a => a XmlTree ScannedSiteSummary getScannedSites :: ArrowXml a => a XmlTree ScannedSites getScannedSite :: ArrowXml a => a XmlTree ScannedSite getSequence :: ArrowXml a => a XmlTree Sequence -- | get a result motif getMotif :: ArrowXml a => a XmlTree Motif getContributingSite :: ArrowXml a => a XmlTree ContributingSite