find-clumpiness (empty) → 0.2.0.1
raw patch · 8 files changed
+1084/−0 lines, 8 filesdep +aesondep +basedep +bytestringsetup-changed
Dependencies added: aeson, base, bytestring, clumpiness, containers, find-clumpiness, optparse-applicative, text, text-show, tree-fun, unordered-containers, vector
Files
- LICENSE +674/−0
- Setup.hs +2/−0
- app/Main.hs +130/−0
- find-clumpiness.cabal +51/−0
- src/LineageConvert.hs +72/−0
- src/Print.hs +31/−0
- src/TreeTransform.hs +90/−0
- src/Types.hs +34/−0
+ LICENSE view
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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ app/Main.hs view
@@ -0,0 +1,130 @@+{- find-clumpiness+By Gregory W. Schwartz++Takes a Haskell or JSON tree and finds the relationship between labels+using the clumpiness metric+-}++-- Standard+import Data.Maybe+import Data.Tree+import qualified Data.HashMap.Strict as Hash++-- Cabal+import Options.Applicative+import Math.TreeFun.Tree+import Math.TreeFun.Types+import qualified Math.Clumpiness.Algorithms as Clump+import qualified Data.Text as T+import qualified Data.Text.IO as T+import qualified Data.ByteString.Lazy.Char8 as C+import Data.Aeson+import qualified Data.Aeson.Types as AT++-- Local+import Types+import LineageConvert+import TreeTransform+import Print++-- Command line arguments+data Options = Options { input :: Maybe String+ , inputFormat :: Format+ , inputExclusivity :: Exclusivity+ , output :: Maybe String+ }++-- Command line options+options :: Parser Options+options = Options+ <$> optional ( strOption+ ( long "input"+ <> short 'i'+ <> metavar "FILE"+ <> help "The input file containing the tree with labels"+ )+ )+ <*> option auto+ ( long "format"+ <> short 'f'+ <> metavar "[Haskell] | JSON | Lineage LABEL"+ <> value Haskell+ <> help "Whether the input tree is in Haskell, JSON, or Lineage format\+ \, where the Lineage format needs an additional field to\+ \ specify what to use as the label\+ \ (for instance, Lineage tissues). The format for JSON is\+ \ [{ \"nodeID\": \"ID\", \"nodeLabels\" [ \"Label\" ] },\+ \ [RECURSION]]"+ )+ <*> option auto+ ( long "exclusivity"+ <> short 'e'+ <> metavar "[Exclusive] | AllExclusive | Majority"+ <> value Exclusive+ <> help "Whether to only look at exclusive nodes (nodes with one label\+ \ only), all nodes, or majority nodes (makes nodes exclusive\+ \ by choosing the most abundant label. If a tie, then\+ \ alphabetical)."+ )+ <*> optional ( strOption+ ( long "output"+ <> short 'o'+ <> metavar "FILE"+ <> help "The output file containing the heatmap of clumpiness"+ )+ )++-- | Get the generic AST from the file+decodeLineageTree :: C.ByteString -> Object+decodeLineageTree contents = fromMaybe+ (error "JSON is not an object")+ (decode contents :: Maybe Object)++-- | Get the lineage tree from a generic AST+getLineageTree :: Label -> Object -> Tree NodeLabel+getLineageTree label object = either error (lineageToTree label)+ . flip AT.parseEither object $ \obj -> do+ germTree <- obj .: T.pack "tree"+ tree <- germTree .: T.pack "children"+ return . rootCheck tree $ germTree+ where+ -- Get the first branch point (sometimes there are additional nodes+ -- right after the root for lineages that bypass the no root rule).+ rootCheck [tree] _ = tree+ rootCheck _ tree = tree++findClumpiness :: Options -> IO ()+findClumpiness opts = do+ contents <- case input opts of+ Nothing -> C.getContents+ (Just x) -> C.readFile x++ let inputTree = case inputFormat opts of+ Haskell -> read . C.unpack $ contents+ JSON -> either error id+ $ eitherDecode contents :: Tree NodeLabel+ Lineage x -> getLineageTree x+ . decodeLineageTree+ $ contents+ inputSuperTree = convertToSuperTree+ . filterExclusiveTree (inputExclusivity opts)+ . innerToLeaves+ $ inputTree+ propertyMap = getPropertyMap inputSuperTree+ clumpResult = Clump.generateClumpMap+ (const True)+ propertyMap+ inputSuperTree++ case output opts of+ Nothing -> T.putStrLn . printClumpList $ clumpResult+ (Just x) -> T.writeFile x . printClumpList $ clumpResult++main :: IO ()+main = execParser opts >>= findClumpiness+ where+ opts = info (helper <*> options)+ ( fullDesc+ <> progDesc "Find the clumpiness of different pairs of labels in a\+ \ tree"+ <> header "find-clumpiness, Gregory W. Schwartz" )
+ find-clumpiness.cabal view
@@ -0,0 +1,51 @@+name: find-clumpiness+version: 0.2.0.1+synopsis: Find the clumpiness of labels in a tree+description: Please see README.md+homepage: http://github.com/GregorySchwartz/find-clumpiness#readme+license: GPL-2+license-file: LICENSE+author: Gregory W. Schwartz+maintainer: gregory.schwartz@drexel.edu+copyright: Copyright 2015 Gregory W. Schwartz+category: Math+build-type: Simple+-- extra-source-files:+cabal-version: >=1.10++library+ hs-source-dirs: src+ exposed-modules: Types+ , LineageConvert+ , TreeTransform+ , Print+ build-depends: base >= 4.7 && < 5+ , clumpiness+ , tree-fun+ , containers+ , unordered-containers+ , vector+ , text+ , text-show+ , aeson+ default-language: Haskell2010++executable find-clumpiness+ hs-source-dirs: app+ main-is: Main.hs+ ghc-options: -threaded -rtsopts -with-rtsopts=-N -O2+ build-depends: base+ , find-clumpiness+ , clumpiness+ , tree-fun+ , containers+ , unordered-containers+ , aeson+ , text+ , bytestring+ , optparse-applicative+ default-language: Haskell2010++source-repository head+ type: git+ location: https://github.com/GregorySchwartz/find-clumpiness
+ src/LineageConvert.hs view
@@ -0,0 +1,72 @@+{- LineageConvert+By Gregory W. Schwartz++Collects functions pertaining to converting the lineage format from the+clash database to the workable tree+-}++{-# LANGUAGE OverloadedStrings #-}++module LineageConvert+ ( lineageToTree+ ) where++-- Standard+import Data.Maybe+import qualified Data.Sequence as Seq+import Data.Tree+import qualified Data.HashMap.Strict as Hash+import Debug.Trace++-- Cabal+import qualified Data.Vector as V+import qualified Data.Text as T+import Math.TreeFun.Types+import Math.TreeFun.Tree+import Data.Aeson+import Data.Aeson.Types++-- Local+import Types++-- | Convert a lineage format into the workable tree format+lineageToTree :: Label -> Object -> Tree NodeLabel+lineageToTree label object = Node { rootLabel = getNodeLabel label object+ , subForest = map+ (lineageToTree label)+ . getChildren+ $ object+ }++-- | Get the NodeLabel of a node+getNodeLabel :: Label -> Object -> NodeLabel+getNodeLabel label object = NodeLabel { nodeID = getNodeID object+ , nodeLabels = getLabel label object+ }++-- | Get the NodeLabel of a node+getNodeID :: Object -> T.Text+getNodeID object = T.intercalate "_"+ . (\(Object x) -> Hash.keys x)+ . either error id+ . flip parseEither object $ \obj -> do+ info <- obj .: "data"+ seqIDs <- info .: "seq_ids"+ return seqIDs++-- | Get the label of the node+getLabel :: Label -> Object -> Labels+getLabel label object = Seq.fromList+ . V.toList+ . either error id+ . flip parseEither object $ \obj -> do+ info <- obj .: "data"+ labels <- info .: label+ return labels++-- | Get the children of a node+getChildren :: Object -> [Object]+getChildren object = either error id+ . flip parseEither object $ \obj -> do+ children <- obj .: "children"+ return children
+ src/Print.hs view
@@ -0,0 +1,31 @@+{- Print+By Gregory W. Schwartz++Collects functions pertaining to the printing of results+-}++{-# LANGUAGE BangPatterns, OverloadedStrings #-}++module Print+ ( printClumpList+ ) where++-- Cabal+import qualified Data.Text as T+import qualified Math.Clumpiness.Types as ClumpType+import TextShow++-- Local+import Types++printClumpList :: ClumpType.ClumpList Label -> T.Text+printClumpList clumpList = T.append header body+ where+ header = "property1,property2,value\n"+ body = T.unlines+ . map ( \(!p1, !p2, !v) -> T.intercalate "," [ p1+ , p2+ , showt v+ ]+ )+ $ clumpList
+ src/TreeTransform.hs view
@@ -0,0 +1,90 @@+{- TreeTransform+By Gregory W. Schwartz++Collects functions pertaining to taking a Haskell tree of (Tree Label) and+converting it to a usable SuperNodeTree+-}++{-# LANGUAGE BangPatterns, ViewPatterns #-}++module TreeTransform+ ( convertToSuperTree+ , getPropertyMap+ , innerToLeaves+ , filterExclusiveTree+ ) where++-- Standard+import qualified Data.Map.Strict as Map+import qualified Data.Sequence as Seq+import qualified Data.Set as Set+import Data.Tree+import qualified Data.Foldable as F+import Data.Function (on)++-- Cabal+import qualified Data.Text as T+import Math.TreeFun.Types+import Math.TreeFun.Tree++-- Local+import Types++-- | Convert the input tree to a SuperNodeTree+convertToSuperTree :: Tree NodeLabel -> Tree (SuperNode NodeLabel)+convertToSuperTree = toSuperNodeTree SuperRoot++-- | Convert inner nodes with labels to leaves+innerToLeaves :: Tree NodeLabel -> Tree NodeLabel+innerToLeaves n@(Node { subForest = [] }) = n+innerToLeaves n@( Node { rootLabel = NodeLabel { nodeLabels = (Seq.null -> True)+ }+ }+ ) = n { subForest = map innerToLeaves . subForest $ n }+innerToLeaves n@( Node { rootLabel = NodeLabel { nodeID = x }+ , subForest = xs+ }+ ) =+ Node { rootLabel = NodeLabel {nodeID = T.cons 'S' x, nodeLabels = Seq.empty}+ , subForest = (n { subForest = [] }) : map innerToLeaves xs+ }++-- | Get the PropertyMap of a SuperNodeTree, ignoring nodes that have no+-- labels+getPropertyMap :: Tree (SuperNode NodeLabel) -> PropertyMap NodeLabel Label+getPropertyMap = Map.fromList+ . map (\ !x -> (myRootLabel x, nodeLabels . myRootLabel $ x))+ . filter (not . Seq.null . nodeLabels . myRootLabel)+ . leaves++-- | Change labels to be exclusive or not+filterExclusiveTree :: Exclusivity+ -> Tree NodeLabel+ -> Tree NodeLabel+filterExclusiveTree ex n =+ n { rootLabel = (rootLabel n) { nodeLabels = exclusiveLabel ex+ . nodeLabels+ . rootLabel+ $ n+ }+ , subForest = map (filterExclusiveTree ex) . subForest $ n+ }++-- | Transform the labels to be exclusive, non exclusive, or majority ruled+exclusiveLabel :: Exclusivity -> Labels -> Labels+exclusiveLabel _ (Seq.null -> True) = Seq.empty+exclusiveLabel AllExclusive xs =+ Seq.fromList . Set.toList . Set.fromList . F.toList $ xs+exclusiveLabel Exclusive xs =+ if Seq.length uniqueSeq > 1+ then Seq.empty+ else uniqueSeq+ where+ uniqueSeq = Seq.fromList . Set.toList . Set.fromList . F.toList $ xs+exclusiveLabel Majority xs = Seq.singleton+ . fst+ . F.maximumBy (compare `on` snd)+ . Map.toList+ . Map.fromListWith (+)+ . flip zip [1,1..]+ . F.toList $ xs
+ src/Types.hs view
@@ -0,0 +1,34 @@+-- Types module+-- By Gregory W. Schwartz+--+-- Collects all application specific types++{-# LANGUAGE DeriveGeneric #-}++module Types where++-- Standard+import GHC.Generics+import qualified Data.Sequence as Seq+import Data.Tree++-- Cabal+import qualified Data.Text as T+import Data.Aeson++-- Algebraic+data NodeLabel = NodeLabel { nodeID :: !T.Text+ , nodeLabels :: !Labels+ } deriving (Generic, Eq, Ord, Read, Show)++data Format = Haskell | JSON | Lineage T.Text deriving (Read)++data Exclusivity = Exclusive | AllExclusive | Majority deriving (Read)++-- Simple+type Label = T.Text++-- Advanced+type Labels = Seq.Seq Label++instance FromJSON NodeLabel