bioinformatics-toolkit 0.1.1 → 0.2.0
raw patch · 31 files changed
+6982/−1304 lines, 31 filesdep +conduit-combinatorsdep +optparse-applicativedep −bbidep ~IntervalMapdep ~basedep ~bytestringnew-component:exe:mergeMotifs
Dependencies added: conduit-combinators, optparse-applicative
Dependencies removed: bbi
Dependency ranges changed: IntervalMap, base, bytestring
Files
- app/mergeMotifs.hs +153/−0
- app/mkindex.hs +11/−0
- app/viewSeq.hs +15/−0
- bioinformatics-toolkit.cabal +28/−25
- data/1.fasta +30/−0
- data/motifs.fasta +0/−1000
- data/universal_motifs.fasta +6260/−0
- exe/mkindex.hs +0/−11
- exe/viewSeq.hs +0/−15
- src/Bio/ChIPSeq.hs +33/−29
- src/Bio/Data/Bam.hs +3/−4
- src/Bio/Data/Bed.hs +8/−9
- src/Bio/Data/BigWig.hs +0/−32
- src/Bio/Data/Fasta.hs +3/−4
- src/Bio/GO.hs +0/−1
- src/Bio/GO/GREAT.hs +10/−8
- src/Bio/GO/Parser.hs +0/−1
- src/Bio/Motif.hs +3/−3
- src/Bio/Motif/Alignment.hs +26/−43
- src/Bio/Motif/Merge.hs +185/−0
- src/Bio/Motif/Search.hs +138/−59
- src/Bio/RealWorld/BioGRID.hs +2/−1
- src/Bio/RealWorld/ENCODE.hs +11/−12
- src/Bio/RealWorld/Ensembl.hs +3/−2
- src/Bio/RealWorld/UCSC.hs +2/−4
- src/Bio/Seq.hs +3/−4
- src/Bio/Seq/IO.hs +0/−1
- src/Bio/Utils/Functions.hs +20/−22
- src/Bio/Utils/Overlap.hs +12/−14
- tests/Tests/Bam.hs +21/−0
- tests/test.hs +2/−0
+ app/mergeMotifs.hs view
@@ -0,0 +1,153 @@+{-# LANGUAGE OverloadedStrings #-}++import AI.Clustering.Hierarchical hiding (drawDendrogram)+import Control.Monad (forM)+import qualified Data.ByteString.Char8 as B+import Data.Default.Class+import Data.List+import Data.List.Split (splitOn)+import Data.Ord+{-+import Diagrams.Backend.Cairo+import Diagrams.Plots.Dendrogram+import Diagrams.Prelude (dims2D, strutX, (|||))+-}+import Options.Applicative+import System.IO+import Text.Printf++import Bio.Data.Fasta+import Bio.Motif+import Bio.Motif.Alignment+import Bio.Motif.Merge+import Bio.Seq (toBS)+import Bio.Utils.Functions++data Options = Options+ { input :: FilePath+ , output :: FilePath+ , prefix :: String+ , thres :: Double+ , mode :: String+ , svg :: Maybe FilePath+ , dumpDist :: Bool+ , gap :: Double+ } deriving (Show)++parser :: Parser Options+parser = Options+ <$> argument str (metavar "INPUT")+ <*> strOption+ ( long "output"+ <> short 'o'+ <> value "merged_output.meme"+ <> metavar "OUTPUT" )+ <*> strOption+ ( long "prefix"+ <> short 'p'+ <> value "merged"+ <> metavar "PREFIX"+ <> help "PREFIX that being add to the name of the merged motif" )+ <*> option auto+ ( long "thres"+ <> short 't'+ <> value 0.2+ <> metavar "THRESHOLD"+ <> help "two motifs that have distance belowing threshold would be merged, default is 0.2" )+ <*> strOption+ ( long "mode"+ <> short 'm'+ <> value "iter"+ <> metavar "MODE"+ <> help "merging algorithm, could be iter or tree, default is iter" )+ <*> (optional . strOption)+ ( long "svg"+ <> metavar "SVG"+ <> help "draw merging tree in svg format, only available in tree mode" )+ <*> switch+ ( long "dump-dist"+ <> help "output pairwise distances of original motifs without performing any merging" )+ <*> option auto+ ( long "gap"+ <> short 'g'+ <> value 0.15+ <> metavar "GAP_PENALTY"+ <> help "gap penalty" )++-- | Return pairwise distances+pairDistance :: [Motif] -> [(B.ByteString, B.ByteString, Double)]+pairDistance ms = map (\(a,b) -> (_name a, _name b, fst $ alignment (_pwm a) (_pwm b))) $ comb ms++treeMerge :: Double -> String -> [Motif] -> Double -> ([Motif], Dendrogram Motif)+treeMerge th pre ms gap = (zipWith f [0::Int ..] $ map merge $ tree `cutAt` th, tree)+ where+ f i (suffix, pwm) = Motif ((B.pack $ pre ++ "_" ++ show i ++ "_" ++ show (toIUPAC pwm))+ `B.append` "("+ `B.append` suffix+ `B.append` ")" ) pwm+ merge tr = ( B.intercalate "+" $ map _name $ flatten tr+ , dilute $ mergeTreeWeighted align tr)+ tree = buildTree align ms+ align = alignmentBy jsd $ quadPenal gap+{-# INLINE treeMerge #-}++getSuffix :: String -> String+getSuffix = last . splitOn "."++defaultMain :: Options -> IO ()+defaultMain (Options inFl outFl pre th m svg dump gap) = do+ let readMotif = case getSuffix inFl of+ "fasta" -> readFasta'+ _ -> readMEME+ writeMotif = case getSuffix outFl of+ "fasta" -> writeFasta+ _ -> \fl x -> writeMEME fl x def+ motifs <- readMotif inFl++ if dump+ then+ mapM_ (\(a,b,c) -> B.putStrLn $ B.intercalate "\t" [a, b, B.pack $ show c]) $ pairDistance motifs+ else do+ let motifNumber = length motifs++ hPutStrLn stderr $ printf "Merging Mode: %s" m+ hPutStrLn stderr $ printf "Read %d motifs" motifNumber++ motifs' <- case m of+ "tree" -> do+ let (newMotifs, tree) = treeMerge th pre motifs gap+ fn x = B.unpack (_name x) ++ ": " ++ B.unpack (toBS $ toIUPAC $ _pwm x)++ case svg of+ Just fl -> do+ {-+ let w = 80+ h = 5 * fromIntegral motifNumber+ renderCairo fl (dims2D (10*w) (10*h)) $ drawDendrogram w h th tree fn ||| strutX 40+ -}+ return newMotifs+ _ -> return newMotifs+ "iter" -> do+ let rs = iterativeMerge (alignmentBy jsd (quadPenal gap)) th motifs+ forM rs $ \(nm, pwm, ws) -> do+ let pwm' = dilute (pwm, ws)+ return $ Motif (B.intercalate "+" nm) pwm+ -- _ -> error "Unkown mode!"++ hPutStrLn stderr $ printf "Write %d motifs" (length motifs')++ writeMotif outFl motifs'+{-# INLINE defaultMain #-}++comb :: [a] -> [(a,a)]+comb (y:ys) = zip (repeat y) ys ++ comb ys+comb _ = []+{-# INLINE comb #-}++main :: IO ()+main = execParser opts >>= defaultMain+ where+ opts = info (helper <*> parser)+ ( fullDesc+ <> header (printf "Merge similar PWMs, version %s" v))+ v = "0.2.0" :: String
+ app/mkindex.hs view
@@ -0,0 +1,11 @@+module Main where++import Bio.Seq.IO (mkIndex)+import Shelly+import qualified Data.Text as T+import System.Environment++main :: IO ()+main = do [inDir, outF] <- getArgs+ fls <- shelly . lsT . fromText . T.pack $ inDir+ mkIndex (map T.unpack fls) outF
+ app/viewSeq.hs view
@@ -0,0 +1,15 @@+module Main where++import qualified Data.ByteString.Char8 as B+import Bio.Seq+import Bio.Seq.IO+import System.Environment++main :: IO ()+main = do+ [fl, chr, start, end] <- getArgs+ g <- pack fl+ s <- getSeqs g [(B.pack chr, read start, read end)] :: IO [Either String (DNA IUPAC)]+ case head s of+ Left err -> error err+ Right x -> B.putStrLn . toBS $ x
bioinformatics-toolkit.cabal view
@@ -2,7 +2,7 @@ -- further documentation, see http://haskell.org/cabal/users-guide/ name: bioinformatics-toolkit-version: 0.1.1+version: 0.2.0 synopsis: A collection of bioinformatics tools description: A collection of bioinformatics tools license: MIT@@ -13,7 +13,7 @@ category: Bio build-type: Simple extra-source-files: README.md-cabal-version: >=1.10+cabal-version: >=1.18 data-files: data/*.fasta @@ -26,13 +26,14 @@ Bio.ChIPSeq.FragLen Bio.Data.Bam Bio.Data.Bed- Bio.Data.BigWig+-- Bio.Data.BigWig Bio.Data.Fasta Bio.GO Bio.GO.Parser Bio.GO.GREAT Bio.Motif Bio.Motif.Alignment+ Bio.Motif.Merge Bio.Motif.Search Bio.RealWorld.BioGRID Bio.RealWorld.ENCODE@@ -49,19 +50,19 @@ -- other-modules: -- other-extensions: build-depends:- base >=4.0 && <5.0+ base >=4.8 && <5.0 , aeson , aeson-pretty- , bbi+-- , bbi , binary , bytestring >=0.10 , bytestring-lexing >=0.5+ , clustering , colour- , conduit+ , conduit-combinators , containers >=0.5 , data-default-class , double-conversion- , clustering , http-conduit , hexpat , matrices >=0.4.3@@ -78,51 +79,51 @@ , vector , vector-algorithms , word8- , IntervalMap >=0.3+ , IntervalMap >=0.5.0.0 default-language: Haskell2010 executable mkindex- hs-source-dirs: exe+ hs-source-dirs: app main-is: mkindex.hs build-depends:- base >=4.6 && <5.0+ base >=4.8 && <5.0 , bioinformatics-toolkit , shelly , text default-language: Haskell2010 executable viewSeq- hs-source-dirs: exe+ hs-source-dirs: app main-is: viewSeq.hs build-depends:- base >=4.6 && <5.0+ base >=4.8 && <5.0 , bioinformatics-toolkit , bytestring default-language: Haskell2010 ---executable mergeMotifs--- hs-source-dirs: exe--- main-is: mergeMotifs.hs--- build-depends:--- base >=4.6 && <5.0--- , bioinformatics-toolkit--- , bytestring--- , clustering--- , data-default-class--- , split--- , optparse-applicative+executable mergeMotifs+ hs-source-dirs: app+ main-is: mergeMotifs.hs+ build-depends:+ base >=4.6 && <5.0+ , bioinformatics-toolkit+ , bytestring+ , clustering+ , data-default-class+ , split+ , optparse-applicative -- , haskell-plot >=0.2.0.0 -- , diagrams-cairo >=1.3 -- , diagrams-lib >=1.3--- default-language: Haskell2010+ default-language: Haskell2010 benchmark bench type: exitcode-stdio-1.0 main-is: benchmarks/bench.hs default-language: Haskell2010 build-depends:- base >=4.6 && <5.0+ base >=4.8 && <5.0 , bioinformatics-toolkit , random , criterion@@ -139,6 +140,7 @@ main-is: test.hs other-modules: Tests.Bed+ , Tests.Bam , Tests.ChIPSeq , Tests.Motif , Tests.Seq@@ -155,6 +157,7 @@ , tasty-hunit , bioinformatics-toolkit , conduit+ , conduit-combinators , unordered-containers , mtl
+ data/1.fasta view
@@ -0,0 +1,30 @@+MEME version 4++ALPHABET= ACGT++strands: + -++Background letter frequencies+A 0.25 C 0.25 G 0.25 T 0.25++MOTIF tree0.2_0_GGAKATWATMTC+letter-probability matrix: alength= 4 w= 12 nsites= 1 E= 0+ 0.001 0.001 0.997 0.001+ 0.001 0.003 0.995 0.001+ 0.997 0.001 0.001 0.001+ 0.001 0.001 0.474 0.524+ 0.997 0.001 0.001 0.001+ 0.997 0.001 0.001 0.001+ 0.25 0.25 0.25 0.25+ 0.25 0.25 0.25 0.25++MOTIF tree0.2_1_CTCCCTAAAATG+letter-probability matrix: alength= 4 w= 12 nsites= 1 E= 0+ 0.25 0.25 0.25 0.25+ 0.25 0.25 0.25 0.25+ 0.001 0.001 0.997 0.001+ 0.001 0.003 0.995 0.001+ 0.997 0.001 0.001 0.001+ 0.001 0.001 0.474 0.524+ 0.997 0.001 0.001 0.001+ 0.997 0.001 0.001 0.001
− data/motifs.fasta
@@ -1,1000 +0,0 @@->H3k27me3_1-0.606774 0.016294 0.13288 0.244052-0.036584 0.220797 0.734391 0.008228-0.007188 0.022713 0.970099 0-0.880368 0.00655 0 0.113082-0.022933 0.370323 0.588998 0.017746-0.03691 0.064294 0.898796 0-0.036733 0.847295 0.05167 0.064303-0.035226 0.936624 0.009752 0.018398-0.038192 0 0.961808 0-0.86875 0.034126 0 0.097123-->H3k27me3_2-0.027569 0.836023 0.098072 0.038336-0.066084 0.796257 0.084066 0.053593-0.053722 0.101794 0.788767 0.055717-0.027115 0.851343 0.096392 0.02515-0.057722 0.783978 0.10818 0.05012-0.036805 0.14198 0.733304 0.087911-0.015704 0.891019 0.070288 0.022988-0.053043 0.784949 0.107395 0.054612-0.050031 0.135567 0.737444 0.076958-->H3k27me3_3-0.057438 0.817772 0.062863 0.061926-0.106073 0.731281 0.120311 0.042334-0.030535 0.018387 0.88613 0.064948-0.030741 0.879362 0.049584 0.040314-0.015252 0.788258 0.137458 0.059032-0.10851 0.817518 0.033884 0.040088-0.036468 0.01862 0.816303 0.128608-0.009933 0.730805 0.207425 0.051837-0.03466 0.800567 0.091489 0.073284-->H3k27me3_4-0.282 0.275 0.302 0.141-0.278 0.207 0.301 0.215-0.646 0.04 0.091 0.223-0.053 0.707 0.062 0.178-0.09 0.09 0.693 0.127-0.224 0.462 0.078 0.236-0.178 0.053 0.57 0.199-0.128 0.646 0.086 0.14-0.04 0.186 0.608 0.166-0.165 0.16 0.535 0.14-0.228 0.24 0.279 0.253-0.242 0.293 0.287 0.179-->H3k27me3_5-0 0 0.951071 0.048929-0 0 0 1-0.627359 0.095216 0.049576 0.227849-0 0.024042 0.580115 0.395842-0.028143 0.971857 0 0-0 0.014661 0 0.985339-0.005613 0.019322 0.975064 0-->H3k27me3_6-0.057628 0.768463 0.028808 0.145102-0.004678 0.995322 0 0-0.84383 0.054519 0.070009 0.031642-0.013305 0.045173 0.836304 0.105218-0.380657 0.550477 0.068865 0-0.020839 0.91739 0.061771 0-0.112091 0.040031 0.815495 0.032383-0 0.682259 0.274559 0.043182-0 0.058162 0.941838 0-->H3k27me3_7-0.065186 0.381721 0.450664 0.102429-0.177422 0.633336 0.1695 0.019743-0.022156 0.928003 0.020696 0.029145-0.00933 0.028055 0.914386 0.048229-0.851568 0.036666 0.030642 0.081124-0.195895 0.028873 0.743155 0.032077-0.030455 0.668012 0.089362 0.212171-0.05471 0.033974 0.90287 0.008447-0 0.97092 0.018842 0.010238-0.00204 0.035057 0.82321 0.139693-0.189764 0.229928 0.536579 0.043729-->H3k27me3_8-0.221868 0.141908 0 0.636224-0.20352 0.751002 0.020317 0.025161-0.201842 0.316531 0.384956 0.096671-0.048677 0.037684 0.872111 0.041527-0.165474 0.038256 0.665057 0.131213-0.072201 0.842767 0.019817 0.065215-0.146093 0.028365 0.825541 0-0.058821 0.802287 0.041842 0.09705-0.144684 0.067184 0.750231 0.037901-0.08984 0.805021 0.040715 0.064423-0.839481 0.054112 0.059255 0.047152-0 0.934819 0.03832 0.026862-->H3k27me3_9-0.167882 0.520832 0.275958 0.035328-0.186393 0.813607 0 0-0.314604 0 0.670072 0.015324-0 0.926258 0.069624 0.004118-0 0.920505 0.079495 0-0 0.770725 0.040069 0.189206-0.009384 0.020025 0.970591 0-0.861156 0.05519 0 0.083654-0 0.035565 0.964435 0-->H3k27me3_10-0 0 1 0-0.887436 0.050346 0.010708 0.05151-0.045451 0.004784 0.935866 0.013899-0.026369 0.089881 0.88375 0-0.983318 0.016682 0 0-0 0.25089 0 0.74911-0 0.675374 0.324626 0-0 0 0.932479 0.067521-0 0.932663 0 0.067337-->H3k27me3_11-0.224457 0.725389 0.036157 0.013997-0.046447 0 0.953553 0-0.063569 0.918074 0.016276 0.002081-0.812151 0 0.15863 0.029219-0 0.842258 0 0.157742-0.022002 0.020292 0.957706 0-0.081601 0.82946 0.049243 0.039696-0.044825 0.029444 0.819662 0.10607-0 0.64916 0.03712 0.31372-->H3k27me3_12-0.001305 0.985088 0.006533 0.007073-0.030098 0.137468 0.031795 0.800639-0.000641 0.947329 0.050635 0.001395-0.708868 0.138382 0.048309 0.104441-0.01663 0.177837 0.764505 0.041027-0.019051 0.285605 0.03219 0.663153-0.018078 0.053027 0.222331 0.706565-0.009817 0.183174 0.02938 0.77763-0.003817 0.963035 0.008029 0.025119-0.008196 0.944821 0.003097 0.043885-0.190656 0.284665 0.035054 0.489625-0.007074 0.235282 0.708158 0.049486-->H3k27me3_13-0.201553 0.786786 0.011662 0-0.056087 0.822486 0.109843 0.011584-0.025109 0.017029 0.957862 0-0.048154 0.648583 0.029026 0.274237-0 0.034838 0.955107 0.010055-0.887569 0 0 0.112431-0.00911 0.869571 0.116133 0.005186-0.224225 0.524249 0.027113 0.224412-0.100124 0.825883 0.056214 0.017778-->H3k27me3_14-0.041 0.778533 0.042471 0.137996-0.123524 0.756722 0.072554 0.0472-0.000288 0.917455 0.082257 0-0.775207 0.042638 0.03771 0.144445-0.006508 0.054321 0.897 0.042171-0.070115 0.848451 0.062052 0.019382-0.013144 0.870986 0.107971 0.007899-0.147341 0.025824 0.057405 0.76943-0.008468 0.74943 0.196232 0.04587-0.078526 0.383205 0.380263 0.158006-0.210026 0.546259 0.16247 0.081245-0.13618 0.285236 0.265129 0.313454-->H3k27me3_15-0 0.923859 0.049081 0.027059-0.030773 0.054177 0.89204 0.02301-0.03561 0.710155 0 0.254236-0.028979 0.845767 0.059673 0.06558-0.01451 0.083137 0.902353 0-0.016964 0.039033 0.495903 0.448099-0.153442 0 0.821859 0.024698-0.003027 0.016753 0.895212 0.085008-0.827733 0.10104 0.033935 0.037292-->H3k27me3_16-0.102 0.672 0.131 0.095-0.093 0.096 0.679 0.132-0.077 0.744 0.095 0.084-0.097 0.13 0.118 0.655-0.061 0.728 0.117 0.094-0.097 0.696 0.095 0.112-0.096 0.117 0.694 0.093-0.111 0.091 0.713 0.085-0.109 0.087 0.725 0.079-0.113 0.091 0.694 0.102-->H3k27me3_17-0.001 0.898 0.1 0.001-0.001 0.001 0.997 0.001-0.219 0.001 0.543 0.237-0.164 0.001 0.674 0.161-0.098 0.001 0.9 0.001-0.116 0.001 0.882 0.001-0.001 0.097 0.901 0.001-0.001 0.001 0.997 0.001-->H3k27me3_18-0.030606 0.828389 0.056442 0.084563-0.111882 0.773152 0.089181 0.025784-0.094575 0.059243 0.746942 0.09924-0 0.954034 0.025967 0.019999-0.043145 0.011024 0.74285 0.202981-0.042381 0.028283 0.791169 0.138166-0.05721 0.033757 0.878238 0.030795-0.727749 0.098964 0 0.173287-0.125497 0.038022 0.795772 0.040709-->H3k27me3_19-0.102 0.084 0.712 0.102-0.104 0.675 0.115 0.106-0.095 0.097 0.705 0.103-0.107 0.111 0.672 0.11-0.105 0.09 0.102 0.703-0.089 0.105 0.111 0.695-0.11 0.108 0.105 0.677-0.711 0.088 0.105 0.096-0.713 0.108 0.107 0.072-0.738 0.082 0.094 0.086-->H3k27me3_20-0.051681 0.823102 0.058038 0.06718-0.04667 0.806892 0.04487 0.101568-0.086563 0.079983 0.716515 0.116939-0.003699 0.809887 0.142735 0.04368-0.038984 0.031869 0.817261 0.111886-0.049845 0.892505 0.051869 0.005781-0.11927 0.072643 0.0486 0.759487-0.010058 0.048014 0.901099 0.040829-0.064414 0.721648 0.116811 0.097128-->H3k27me3_21-0.012404 0.145428 0.788559 0.05361-0 0.987277 0 0.012723-0.020786 0.03082 0.877875 0.070519-0.004679 0.016532 0.812235 0.166554-0.052582 0.039503 0.671561 0.236354-0.163953 0.656069 0.01867 0.161309-0.059608 0.148713 0.084866 0.706813-0 0.985746 0.010521 0.003733-0 0.859543 0.092123 0.048335-->H3k27me3_22-0 0 0 1-0.012876 0 0.980217 0.006906-0.03792 0.004296 0.957784 0-0.053699 0 0.946301 0-0.94609 0.013517 0 0.040393-0.128065 0.022685 0.84925 0-0.111168 0.053925 0.043403 0.791504-0.473428 0.497362 0.019718 0.009492-->H3k27me3_23-0.035442 0.762288 0.041676 0.160594-0.109849 0.043451 0.732698 0.114002-0.077134 0.893037 0.008684 0.021145-0.185442 0.038754 0.747105 0.028699-0.06961 0.026831 0.817424 0.086134-0.019668 0.030807 0.911916 0.037608-0.097454 0.082235 0.705757 0.114554-0.8089 0.044458 0.086125 0.060517-0.13045 0.857966 0.011584 0-->H3k27me3_24-0.037785 0.189216 0 0.772999-0 1 0 0-0 1 0 0-0.036078 0 0.886905 0.077017-0 0.124555 0.83069 0.044755-0.015533 0 0.984467 0-0.121058 0 0.067534 0.811408-0 0.058872 0.879147 0.06198-0.009905 0.87634 0 0.113755-->H3k27me3_25-0.761215 0.084224 0 0.154562-0 0.095532 0.904468 0-0.091023 0.047337 0.83473 0.02691-0.136245 0.016155 0.726058 0.121543-0.02227 0.026057 0.859822 0.091851-0.206104 0.269121 0.521486 0.003288-0.029464 0.841482 0.031084 0.097971-0.026948 0 0.952093 0.020958-0.016535 0.907432 0.049712 0.026321-->H3k27me3_26-0.049624 0.873643 0.028015 0.048718-0.252582 0.665923 0.025361 0.056133-0.045616 0.891054 0.018 0.04533-0.030306 0.009068 0.941617 0.019009-0.008131 0.031025 0.950739 0.010106-0.849258 0.045227 0.042674 0.062842-0.03959 0.891805 0.053673 0.014932-0.323839 0.048021 0.609607 0.018533-0.006592 0.972602 0.005527 0.015279-->H3k27me3_27-0.088867 0.8221 0.044076 0.044957-0.042556 0.797011 0.143696 0.016737-0.009207 0.88788 0.087999 0.014914-0.781947 0.038703 0.126388 0.052963-0.012945 0.030843 0.855373 0.100839-0.034445 0.812728 0.144246 0.008581-0.131431 0.047159 0.066305 0.755105-0.00705 0.819166 0.161102 0.012682-0.094177 0.720151 0.081899 0.103773-0.184854 0.39469 0.329478 0.090978-0.058616 0.370292 0.535453 0.035639-0.006249 0.262678 0.726294 0.004778-->H3k27me3_28-0.237059 0.085644 0 0.677297-0.036429 0 0.74756 0.216011-0 0.685895 0 0.314105-0 0.990671 0.009329 0-0.822357 0.086003 0.09164 0-0 0.938432 0.061568 0-0 0.557102 0 0.442898-0 0.961506 0.038494 0-0.916383 0 0.083617 0-->H3k36me3_1-0.412511 0.030259 0.427783 0.129446-0.916679 0.062226 0.01331 0.007785-0.004271 0.008974 0.001146 0.985609-0.00015 0.88472 0.003421 0.111709-0.642004 0.002774 0.3484 0.006822-0 0.983702 0 0.016298-0.002246 0.232527 0.025492 0.739734-0.001817 0.047181 0.00822 0.942782-0.018288 0.012159 0.969052 0.000501-0.972232 0.005142 0.012633 0.009994-->H3k36me3_2-0.003553 0.962184 0.021214 0.013049-0.010587 0.007471 0.007149 0.974793-0.056903 0.002065 0.940403 0.00063-0.029341 0.127911 0.012368 0.83038-0.785189 0.080043 0.121928 0.01284-0.714592 0.118011 0.145336 0.022061-0.004274 0.118391 0.008479 0.868856-0.008939 0.958376 0.01189 0.020794-0.008619 0.934744 0.005097 0.05154-0.164029 0.677445 0.093925 0.064601-->H3k36me3_3-0.06728 0.003463 0.928563 0.000695-0.042745 0.00829 0.002542 0.946423-0.7652 0.083152 0.151537 0.000111-0.752591 0.056491 0.174836 0.016082-0.037203 0.041632 0.061134 0.860031-0.009265 0.953082 0.018104 0.019549-0.012137 0.928617 0.003188 0.056058-0 0.953697 0.002099 0.044204-0.988637 0.00156 0.008536 0.001267-->H3k36me3_4-0.002921 0.975182 0.019283 0.002614-0.389395 0.000673 0.019729 0.590203-0.009176 0.003798 0.9865 0.000525-0.0083 0.017494 0.966122 0.008083-0.860109 0.077394 0.019347 0.04315-0.024896 0.006935 0.96517 0.002999-0.02811 0.022893 0.022859 0.926139-0.031456 0.018898 0.528436 0.42121-0.023575 0.914853 0.018795 0.042778-0.456293 0 0.543707 0-->H3k36me3_5-0.040974 0.015834 0.806165 0.137026-0.000482 0.951344 0.005066 0.043108-0.003276 0.952792 0.001466 0.042467-0.015066 0.000847 0.008931 0.975156-0.001057 0.962622 0.011316 0.025005-0.008398 0.962897 0.007132 0.021573-0.012183 0.890617 0.008478 0.088722-0.732122 0.079602 0.16567 0.022606-0.720023 0.13387 0.126859 0.019248-->H3k36me3_6-0.000676 0.978498 0.018077 0.002749-0.007447 0.021657 0.001438 0.969458-0.02526 0.005255 0.963432 0.006053-0.07272 0.003095 0.908564 0.015622-0.024316 0.245887 0.724174 0.005622-0.023618 0.808526 0.050988 0.116868-0.780085 0.03254 0.176005 0.01137-0.838104 0.073281 0.055882 0.032733-0.018699 0.895298 0.064705 0.021298-0.882149 0.01584 0.017592 0.084419-->H3k36me3_7-0.932231 0.007543 0.057018 0.003208-0.033304 0.038088 0.898609 0.029999-0.020811 0.019055 0.953415 0.00672-0.972527 0.020669 0.004139 0.002664-0.020958 0.000775 0.978098 0.000169-0.720805 0.014303 0.264037 0.000855-0.974348 0.006919 0.010349 0.008383-0.03354 0.013051 0.120669 0.832741-0.006406 0.879915 0.00736 0.10632-0.309651 0.049391 0.629367 0.01159-0.038361 0.93892 0 0.022719-0 0.004613 0.003955 0.991433-->H3k36me3_8-0.008194 0.049311 0.015898 0.926597-0.090861 0.564763 0.035339 0.309037-0.178644 0.025419 0.794867 0.001069-0.952999 0.030655 0.002213 0.014134-0.006241 0.038922 0.951929 0.002908-0.870211 0.060451 0.062974 0.006364-0.01117 0.937917 0.005864 0.045049-0.124574 0.853348 0.009747 0.012331-0.925735 0.044778 0.020247 0.00924-->H3k36me3_9-0.904352 0.033657 0.020888 0.041103-0.025522 0.316953 0.654973 0.002552-0.60872 0.051391 0.110131 0.229758-0.02877 0.868779 0.089199 0.013253-0.011526 0.964667 0.011639 0.012168-0.933367 0.006451 0.006633 0.053549-0.008692 0.020278 0.96526 0.00577-0.008984 0.884634 0.094607 0.011775-0.018634 0.916658 0.007392 0.057316-0.172494 0.135223 0.23282 0.459462-->H3k36me3_10-0.919685 0.012377 0.043492 0.024446-0.07339 0.006966 0.901569 0.018075-0.02117 0.041673 0.927641 0.009516-0.039129 0.872396 0.042334 0.046141-0.106186 0.120244 0.071998 0.701573-0.038702 0.053091 0.907428 0.00078-0.686984 0.061773 0.191688 0.059555-0.212205 0.012475 0.759124 0.016196-0.052953 0.044408 0.887356 0.015283-->H3k36me3_11-0.919696 0.003455 0.049962 0.026887-0.694257 0.264183 0.018576 0.022983-0.009563 0.960945 0.002416 0.027076-0.024854 0.004572 0.001935 0.968639-0.01113 0.925409 0.014847 0.048614-0.000416 0.958359 0.033243 0.007983-0.046887 0.036202 0.008047 0.908863-0.025582 0.00419 0.968692 0.001536-0.813344 0.020974 0.142688 0.022994-->H3k36me3_12-0.000105 0.991402 0.007214 0.001279-0.00254 0.001259 0.000272 0.995929-0.001064 0.992408 0.004293 0.002235-0 0.010284 0.002637 0.987079-0.949042 0.024663 0.017051 0.009244-0.006653 0.987799 0.000557 0.00499-0.230691 0.031043 0.008711 0.729555-0.944702 0.008495 0.037851 0.008953-0.90633 0.089644 0.001487 0.002539-0.854696 0.130088 0.009795 0.005422-->H3k36me3_13-0.00307 0.670061 0.000684 0.326185-0.248509 0.001502 0.728177 0.021812-0 0.985736 0 0.014264-0 0 0.050282 0.949718-0.000754 0.003429 0.011552 0.984265-0.019913 0 0.979321 0.000766-0.989083 0.004283 0.004944 0.00169-0.992549 0.000812 0.005428 0.001212-0 0.989639 0 0.010361-0.004247 0.932986 0.048163 0.014604-->H3k36me3_14-0.81174 0.019665 0.140907 0.027687-0.080253 0.047986 0.097927 0.773834-0.019734 0.914965 0.03224 0.033061-0.045194 0.878126 0.026402 0.050277-0.008454 0.956647 0.005975 0.028924-0.928903 0.015369 0.02804 0.027687-0.031443 0.073964 0.883553 0.01104-0.006821 0.844347 0.128921 0.019911-0.685602 0.075362 0.010203 0.228833-0.162236 0.589332 0.228093 0.020339-->H3k36me3_15-0.882402 0.033396 0.068885 0.015316-0.830804 0.119149 0.04082 0.009227-0.831424 0.037807 0.111478 0.019291-0.048734 0.195949 0.754178 0.001138-0.035274 0.016171 0.019563 0.928992-0.037379 0.136887 0.820595 0.005138-0.01301 0.923482 0.038584 0.024925-0.046365 0.003483 0.001277 0.948875-0.031845 0.001009 0.959658 0.007488-->H3k36me3_16-0.22142 0.661973 0.052298 0.064309-0.065963 0.723622 0.168499 0.041916-0.672261 0.085026 0.135066 0.107646-0.047246 0.166603 0.767594 0.018557-0.016197 0.846993 0.012173 0.124637-0.058715 0.772271 0.146818 0.022196-0.062856 0.034337 0.136185 0.766622-0.079586 0.143703 0.67515 0.101561-0.047924 0.130594 0.775836 0.045647-->H3k36me3_17-0.05465 0.033561 0.893461 0.018328-0.084497 0.018699 0.88612 0.010684-0.006624 0.016727 0.958797 0.017852-0.007727 0.018333 0.002741 0.971199-0.02039 0.170582 0.042949 0.76608-0.003044 0.009809 0.00288 0.984266-0.000433 0.920931 0.000922 0.077714-0.673304 0.014996 0.159279 0.152421-0.001107 0.990042 0.004468 0.004383-0.019357 0.577936 0.006314 0.396393-->H3k36me3_18-0 0.973926 0.007321 0.018753-0.950074 0.005704 0.007072 0.03715-0.010533 0.040159 0.928987 0.020321-0.028786 0.880034 0.034524 0.056655-0.017522 0.033617 0.016692 0.932169-0.796171 0.092793 0.062744 0.048293-0.069759 0.915717 0.001579 0.012946-0.064312 0.01818 0.006552 0.910956-0.013023 0.635436 0.094048 0.257493-0.506109 0.152271 0.317617 0.024004-->H3k36me3_19-0.009099 0.768966 0.174896 0.04704-0.005736 0.949914 0.009358 0.034992-0.008481 0.699832 0.004802 0.286885-0.637203 0.048626 0.304202 0.00997-0.700166 0.085486 0.129955 0.084392-0.005993 0 0.994007 0-0.022416 0.026348 0.030887 0.920349-0.899538 0.006936 0.040875 0.052651-0.034571 0.027553 0.922674 0.015202-0.012281 0.974302 0.003413 0.010005-->H3k36me3_20-0 0.954634 0.020821 0.024545-0.959916 0.010502 0.01948 0.010102-0 0.964407 0.004213 0.031381-0.006762 0.006861 0.034083 0.952295-0.001316 0.022362 0.188212 0.78811-0.004588 0.039112 0.052845 0.903455-0.097028 0.008342 0.887728 0.006902-0.035378 0.005466 0.920855 0.038301-0.062433 0.039808 0.892798 0.004961-->H3k36me3_21-0.859214 0.02391 0.093131 0.023745-0.011283 0.67469 0.030872 0.283154-0.222336 0.011084 0.646888 0.119693-0.018063 0.914944 0.018984 0.048009-0.005282 0.966931 0.012938 0.01485-0.018928 0.00973 0.005204 0.966138-0.042841 0.025086 0.931121 0.000953-0.078391 0.025731 0.053763 0.842115-0.868978 0.057046 0.069564 0.004412-->H3k36me3_22-0.60841 0.005091 0.2906 0.095899-0.003456 0.99488 0.001023 0.00064-0.004149 0.698563 0.081454 0.215835-0.873008 0.0357 0.090623 0.00067-0.138171 0.03005 0.009922 0.821856-0.001478 0.068544 0.92731 0.002668-0.025352 0 0.005404 0.969244-0.16004 0.005446 0.031354 0.803159-0.002049 0.037332 0.957441 0.003178-->H3k36me3_23-0.016215 0.899832 0.033387 0.050566-0.894176 0.061417 0.013931 0.030477-0.000727 0.981877 0.014869 0.002526-0.093005 0.057132 0.09865 0.751213-0.026234 0.644096 0.256871 0.072798-0.007867 0.906725 0.066711 0.018698-0.755779 0.044818 0.031628 0.167774-0.11542 0.054551 0.724506 0.105524-0.014303 0.901416 0.055745 0.028536-->H3k36me3_24-0.101078 0.638138 0.230415 0.03037-0.04837 0.189042 0.164568 0.598021-0.003459 0.929466 0.046241 0.020833-0.909886 0.040184 0.017452 0.032478-0 0.985452 0.010825 0.003723-0.02308 0.035562 0.017328 0.924031-0.026869 0.195428 0.681141 0.096562-0.013393 0.791357 0.110883 0.084367-0.852359 0.066776 0.030189 0.050677-->H3k36me3_25-1 0 0 0-0.997517 0 0.001911 0.000572-0.989396 0.010604 0 0-0.997988 0 0.002012 0-0 0.004599 0.009508 0.985893-0.002489 0.022044 0.007222 0.968244-1 0 0 0-0 0 1 0-->H3k36me3_26-0 0.050941 0.9481 0.000958-0.917975 0.004396 0.04399 0.033638-0.080107 0.01739 0.009995 0.892508-0.003122 0.910747 0.071006 0.015124-0.856541 0.004123 0.092481 0.046855-0 0.954192 0.021677 0.024131-0.324062 0.003366 0.672572 0-0.007931 0.891422 0.022519 0.078128-0.019644 0.947779 0.008891 0.023686-0.801951 0.055033 0.13526 0.007756-0.064093 0.803326 0.002803 0.129778-->H3k36me3_27-0.977359 0.010318 0.003964 0.008359-0.003647 0.0648 0.922837 0.008716-0.02984 0.134662 0.678923 0.156574-0.057661 0.09916 0.035379 0.8078-0.068183 0.827109 0.101843 0.002865-0.944543 0.002283 0.03896 0.014213-0.2072 0.0287 0.760046 0.004054-0.072374 0.025213 0.887926 0.014487-0.871529 0.014581 0.070648 0.043242-->H3k36me3_28-0.001057 0.012283 0.98666 0-0.080845 0.003927 0.914187 0.001042-0.053964 0.89972 0.009015 0.037301-0.584604 0.017961 0.397435 0-0.000917 0.011319 0.987138 0.000625-0.968632 0.013738 0.008291 0.009339-0.006691 0 0.111601 0.881708-0.001018 0.961972 0.025565 0.011445-0.944747 0 0.055253 0-->H3k36me3_29-0.919554 0.010718 0.050146 0.019582-0.026146 0.922507 0.035952 0.015394-0.038863 0.669532 0.038846 0.252759-0.089452 0.798815 0.071686 0.040047-0.003881 0.209842 0.009636 0.776641-0.163106 0.038113 0.792181 0.0066-0.008861 0.069439 0.010575 0.911125-0.008895 0.891756 0.073583 0.025765-0.042975 0.048174 0.02657 0.882281-->H3k36me3_30-0.005893 0.014907 0.9792 0-0.70184 0.008031 0 0.290129-0.045003 0.012658 0.940072 0.002267-0.015291 0.001339 0.983371 0-0.023043 0.009685 0.004654 0.962617-0.001328 0.011501 0.584003 0.403169-0.009777 0.004999 0.978982 0.006243-0.014365 0.929085 0.045343 0.011207-0.965775 0.006529 0.009204 0.018492-0 0.480552 0.457615 0.061833-->H3k36me3_31-0.00587 0.212446 0.771873 0.009811-0.013448 0.024481 0 0.962071-0.018008 0.085861 0.223536 0.672595-0.001198 0.066174 0.029182 0.903447-0 0.928497 0.015111 0.056392-0.685426 0.032575 0.123895 0.158104-0.00504 0.949661 0.010899 0.0344-0.000889 0.93481 0.004957 0.059345-0.938088 0.016945 0.018351 0.026615-0.002431 0.058992 0.241834 0.696743-->H3k36me3_32-0.027825 0.835602 0.030067 0.106506-0.147398 0.016565 0.015743 0.820294-0.01865 0.017184 0.96346 0.000705-0.811514 0.017567 0.103109 0.06781-0.058709 0.010857 0.923336 0.007097-0.22332 0.067862 0.702356 0.006463-0.077166 0.812135 0.020988 0.08971-0.794925 0.063402 0.106321 0.035352-0.076781 0.017228 0.896096 0.009896-->H3k36me3_33-0.28239 0.00308 0.66605 0.04848-0.006395 0.980825 0.005253 0.007527-0.943723 0.019739 0.007425 0.029113-0.023457 0.026908 0.949635 0-0.024511 0.045941 0.040224 0.889324-0.087171 0.001414 0.90956 0.001856-0.032953 0.086727 0.858562 0.021758-0.043944 0.756823 0.004067 0.195166-0.530697 0.017996 0.373231 0.078076-->H3k36me3_34-1 0 0 0-0.899924 0.012201 0.077813 0.010061-0.983382 0.003567 0.010553 0.002498-0.054735 0.942875 0.00239 0-0.020183 0.708769 0.085405 0.185643-0.010158 0.836989 0.004265 0.148587-0.015848 0.933207 0.000393 0.050552-0.834088 0.002349 0.160635 0.002928-0 0.130753 0.006978 0.862269-->H3k36me3_35-0.010712 0.847385 0.035623 0.10628-0.003611 0.856391 0.005876 0.134122-0.705357 0.008514 0.215873 0.070257-0 0.076906 0.003708 0.919386-0.010812 0.940153 0.010889 0.038146-0.019558 0.011158 0.009881 0.959402-0 0.912582 0.069699 0.017719-0.205869 0.167232 0.034953 0.591946-0.809279 0.042703 0.116952 0.031065-->H3k36me3_36-0.774845 0.020892 0.188444 0.015819-0.046869 0.046224 0.892087 0.014819-0.038936 0.093175 0.711246 0.156643-0.024784 0.926375 0.019708 0.029133-0.845001 0.013071 0.106818 0.03511-0.02403 0.044879 0.742407 0.188685-0.021144 0.070082 0.903262 0.005513-0.789184 0.064255 0.013028 0.133533-0.057027 0.015332 0.894381 0.03326-->H3k36me3_37-0.892006 0.050529 0.004518 0.052947-0.929454 0.004419 0.02214 0.043986-0.026154 0.889842 0.073229 0.010774-0.916297 0.001224 0.062965 0.019515-0.006583 0.293303 0.153373 0.546741-0.794208 0.068959 0.115636 0.021197-0.002683 0.179151 0.809093 0.009073-0.053853 0.165226 0.049169 0.731753-0.025423 0.002331 0.961049 0.011197-->H3k36me3_38-0.611015 0.381214 0.004009 0.003763-0.952794 0.025639 0.009368 0.012199-0.153521 0.82543 0.012908 0.008141-0.069069 0.848914 0.062295 0.019722-0.021454 0.009984 0.010235 0.958328-0.003052 0.943686 0.009798 0.043464-0.015209 0.766826 0.152517 0.065448-0.029932 0.046145 0.858404 0.065519-0.006437 0.773855 0.007769 0.21194-->H3k36me3_39-0 0.997159 0.001235 0.001606-0.070598 0.018906 0 0.910496-0.080071 0.670981 0.016896 0.232052-0.847996 0.086118 0.004285 0.061601-0.941722 0 0.058278 0-0.945067 0 0.054022 0.000911-0.947439 0.042437 0.006122 0.004001-0.950897 0.042896 0.004833 0.001374-0.972425 0.027575 0 0-0.808207 0.189053 0.00274 0-->H3k36me3_40-0 0.488302 0 0.511698-0.326084 0.045974 0.555576 0.072367-0 0.902679 0.003992 0.093329-0.048088 0.945195 0.002591 0.004127-0 0.948647 0.00164 0.049713-0.930135 0.00143 0.056366 0.012069-0 0.014649 0.981362 0.003989-0.006494 0.989833 0.003673 0-0 0.104576 0.001271 0.894152-0.96452 0.0203 0.015181 0-->H3k36me3_41-0.001894 0.950087 0.025304 0.022715-0.921449 0.018594 0.03558 0.024377-0.005648 0.941668 0.008425 0.044259-0.00218 0.914476 0.023949 0.059394-0.846917 0.039877 0.093493 0.019713-0.02074 0.313675 0.06233 0.603255-0.090929 0.028919 0.87049 0.009662-0.020382 0.76811 0.015853 0.195655-0.003603 0.882984 0.0047 0.108713-0.11662 0.479464 0.102319 0.301596-->H3k36me3_42-0.810977 0.004871 0.159193 0.024959-0.011096 0.955056 0.019831 0.014016-0.015746 0.961809 0.005249 0.017197-0.076484 0.013566 0.007299 0.902651-0 0.989289 0.010711 0-0.886521 0.031408 0.079126 0.002945-0.255718 0.06 0.597657 0.086624-0.097263 0.042865 0.77098 0.088892-0.026254 0.006217 0.021618 0.945911-->H3k36me3_43-0.006143 0.003397 0.963095 0.027365-0.064462 0.848995 0 0.086543-0.274996 0.004109 0.202708 0.518186-0.00106 0.965502 0.015939 0.017499-0.834139 0.036895 0.126006 0.00296-0.01903 0.222489 0.011339 0.747143-0.196842 0.013587 0.781826 0.007745-0.001173 0.95275 0.011071 0.035006-0.006254 0.985028 0.004546 0.004172-->H3k36me3_44-0.10144 0.56942 0.095451 0.233689-0.11475 0.008777 0.699136 0.177337-0.009882 0.005122 0.015821 0.969174-0.013055 0.004043 0.972658 0.010244-0.88118 0.040719 0.010247 0.067853-0.063349 0.016347 0.798433 0.121871-0.016712 0.94582 0.019492 0.017976-0.009032 0.91158 0.004368 0.07502-0.850769 0.129613 0.005472 0.014146-->H3k36me3_45-0.025097 0.879699 0.024053 0.071151-0.108123 0.03167 0.04076 0.819447-0.01298 0.878373 0.090374 0.018274-0.027724 0.038849 0.007367 0.92606-0.013234 0.007289 0.965278 0.014199-0.021564 0.046201 0.01581 0.916424-0.042964 0.639999 0.120265 0.196773-0.595976 0.200519 0.160376 0.043129-0.008453 0.940496 0.012248 0.038804-0.061462 0.542457 0.137743 0.258339-->H3k36me3_46-0.114206 0.108627 0.775148 0.00202-0.040201 0.849107 0.075996 0.034697-0.891444 0.020683 0.048754 0.039119-0.053378 0.047139 0.897656 0.001827-0.091474 0.040686 0.866214 0.001626-0.674014 0.107546 0.008192 0.210248-0.166723 0.022014 0.806289 0.004974-0.067126 0.021483 0.904298 0.007093-0.804812 0.136065 0.020322 0.0388-->H3k36me3_47-0.024889 0.105094 0.767292 0.102726-0.912153 0.006795 0.081053 0-0.013073 0.009563 0.940711 0.036653-0.010903 0.935927 0.05317 0-0 0.159601 0.006981 0.833418-0.293496 0.120075 0.586429 0-0.007238 0.023724 0.002171 0.966867-0 0.021055 0.971398 0.007547-0.589138 0.04026 0.035987 0.334615-0.006491 0.013307 0 0.980203-->H3k36me3_48-0.934702 0 0.062228 0.00307-0.003373 0.970668 0.001714 0.024245-0.356315 0.39856 0.245125 0-0 0.003698 0 0.996302-0.000898 0.003489 0.995613 0-0.003142 0.029837 0.937759 0.029262-0.014567 0.971985 0.007442 0.006006-0.147584 0.026321 0.163884 0.66221-0.655472 0.018438 0.083972 0.242118-->H3k36me3_49-0.759851 0.087607 0.048312 0.10423-0.024825 0.934356 0.030984 0.009836-0.003299 0.980731 0.010745 0.005226-0.842888 0.080928 0.066673 0.009511-0.00237 0.978292 0.008187 0.011152-0.85562 0.068684 0.020269 0.055427-0.038686 0.766025 0.064353 0.130936-0.136724 0.652591 0.163121 0.047564-0.020079 0.82756 0.106334 0.046027-0.339958 0.044072 0.449717 0.166253-0.002456 0.023074 0.87749 0.096979-0.003583 0.779471 0.203144 0.013801-->H3k36me3_50-0.128161 0.129664 0.713792 0.028383-0.004565 0.9862 0.001003 0.008232-0.798998 0.081084 0.042152 0.077766-0.004875 0.778633 0.205189 0.011303-0.019553 0.939324 0.020115 0.021008-0.868394 0.018873 0.066862 0.045871-0.003594 0.874075 0.063006 0.059324-0.008774 0.86022 0.035407 0.095598-0.811466 0.007365 0.141121 0.040049-->H3k36me3_51-0.737976 0.018171 0.130776 0.113077-0.011037 0.085834 0.898712 0.004417-0.028514 0.031026 0.073368 0.867093-0.011541 0.027051 0.951167 0.010241-0.842861 0.009248 0.085301 0.06259-0.027145 0.063794 0.689289 0.219772-0.020781 0.880483 0.088308 0.010428-0.12984 0.012688 0.024012 0.83346-0 0.012803 0.971691 0.015507-->H3k36me3_52-0.015139 0.34128 0.00703 0.636552-0.705418 0.180077 0.07348 0.041025-0 0.978434 0.014328 0.007238-0.176047 0.203605 0.000578 0.619769-0.003157 0.895704 0.097982 0.003157-0.879347 0.005983 0.037696 0.076973-0.054011 0.024876 0.919087 0.002026-0.082555 0.068701 0.827464 0.02128-0.782412 0.02585 0.008528 0.18321-->H3k36me3_53-0.101 0.587 0.141 0.171-0.073 0.1 0.678 0.149-0.348 0.2 0.102 0.35-0.178 0.476 0.055 0.291-0.042 0.226 0.705 0.027-0.85 0.034 0.065 0.051-0.025 0.65 0.115 0.21-0.184 0.081 0.705 0.03-->H3k36me3_54-0.135136 0.697312 0.074937 0.092615-0 0.947702 0.044472 0.007827-0.029985 0.931444 0.029358 0.009212-0.628134 0.001826 0.01032 0.359719-0 0.938682 0.030387 0.030932-0.078092 0.814343 0.022242 0.085322-0.014109 0.045762 0.005665 0.934464-0 0.943892 0.056108 0-0.010588 0.148248 0.784909 0.056254-0.320235 0.016901 0.521988 0.140877-->H3k36me3_55-0.706908 0.042083 0.075769 0.17524-0.013156 0.001979 0.950923 0.033942-0.00974 0.851683 0.135991 0.002586-0.035698 0.955895 0.008407 0-0.726227 0.007418 0.245694 0.020661-0 0.067194 0.922738 0.010068-0.081936 0.063635 0.834154 0.020275-0.014378 0.785319 0.011176 0.189127-0.944722 0.01517 0.010148 0.02996-->H3k36me3_56-0.923371 0.040613 0.035004 0.001011-0.834497 0.090343 0.04551 0.029651-0.007527 0.030823 0.959929 0.001721-0.125878 0 0.870903 0.003219-0.007889 0.832338 0 0.159773-0.025808 0.084089 0.857356 0.032747-0.029025 0.001524 0.962293 0.007158-0.014345 0.238691 0.738412 0.008552-0.018055 0.714245 0.101775 0.165925-->H3k4me1_1-0.021 0.018 0.002 0.959-0.041 0.136 0.015 0.808-0.245 0.001 0.014 0.74-0.243 0.078 0.666 0.013-0.142 0.835 0.002 0.021-0.878 0.04 0.001 0.081-0.256 0.026 0.021 0.697-0.34 0.116 0.217 0.327-0.452 0.062 0.114 0.373-0.085 0.464 0.321 0.13-0.863 0.072 0.002 0.063-0.805 0.071 0.091 0.033-->H3k4me1_2-0.126221 0.096725 0.652362 0.124692-0.157713 0.76706 0.074905 0.000322-0.123264 0.011594 0.004509 0.860634-0.006538 0.043494 0.947226 0.002742-0.850792 0.026025 0.048173 0.07501-0.029324 0.225233 0.739268 0.006175-0.048641 0.103353 0.059443 0.788562-0.091813 0.767385 0.096649 0.044154-0.823017 0.070473 0.006845 0.099666-->H3k4me1_3-0.142656 0.046092 0.628207 0.183044-0.077532 0.721399 0.068271 0.132798-0.862808 0.039974 0.036854 0.060365-0.01964 0.009924 0.018916 0.95152-0.053006 0 0.025394 0.9216-0.033778 0.023827 0.012824 0.929571-0.123322 0.106461 0.047877 0.72234-0.764536 0.032298 0.029472 0.173695-0.754843 0.118183 0.056065 0.070909
+ data/universal_motifs.fasta view
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− exe/mkindex.hs
@@ -1,11 +0,0 @@-module Main where--import Bio.Seq.IO (mkIndex)-import Shelly-import qualified Data.Text as T-import System.Environment--main :: IO ()-main = do [inDir, outF] <- getArgs- fls <- shelly . lsT . fromText . T.pack $ inDir- mkIndex (map T.unpack fls) outF
− exe/viewSeq.hs
@@ -1,15 +0,0 @@-module Main where--import qualified Data.ByteString.Char8 as B-import Bio.Seq-import Bio.Seq.IO-import System.Environment--main :: IO ()-main = do- [fl, chr, start, end] <- getArgs- g <- pack fl- s <- getSeqs g [(B.pack chr, read start, read end)] :: IO [Either String (DNA IUPAC)]- case head s of- Left err -> error err- Right x -> B.putStrLn . toBS $ x
src/Bio/ChIPSeq.hs view
@@ -2,12 +2,12 @@ {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE BangPatterns #-} module Bio.ChIPSeq- ( rpkmBed+ ( monoColonalize+ , rpkmBed , rpkmSortedBed- , monoColonalize- , profiling- , profilingCoverage+ , rpkmBinBed , rpkmBam+ , rpgcBinBed , tagCountDistr , peakCluster ) where@@ -16,9 +16,7 @@ import qualified Bio.SamTools.BamIndex as BI import Control.Monad (liftM, forM_, forM) import Control.Monad.Primitive (PrimMonad)-import Control.Monad.Trans.Class (lift)-import Data.Conduit-import qualified Data.Conduit.List as CL+import Conduit import Data.Function (on) import qualified Data.Foldable as F import qualified Data.HashMap.Strict as M@@ -79,7 +77,7 @@ => Sorted (V.Vector b) -> Sink BED m (v Double) rpkmSortedBed (Sorted regions) = do vec <- lift $ GM.replicate l 0- n <- CL.foldM (count vec) (0 :: Int)+ n <- foldMC (count vec) (0 :: Int) let factor = fromIntegral n / 1e9 lift $ liftM (G.imap (\i x -> x / factor / (fromIntegral . size) (regions V.! i))) $ G.unsafeFreeze vec@@ -89,7 +87,7 @@ p | _strand tag == Just True = chromStart tag | _strand tag == Just False = chromEnd tag - 1 | otherwise = error "Unkown strand"- xs = concat . snd . unzip $+ xs = concat $ IM.elems $ IM.containing (M.lookupDefault IM.empty chr intervalMap) p addOne v xs return $ succ nTags@@ -102,11 +100,11 @@ -- | divide each region into consecutive bins, and count tags for each bin. The -- total number of tags is also returned-profiling :: (PrimMonad m, G.Vector v Int, BEDLike b)- => Int -- ^ bin size- -> [b] -- ^ regions- -> Sink BED m ([v Int], Int)-profiling k beds = do+rpkmBinBed :: (Num a, PrimMonad m, G.Vector v a, BEDLike b)+ => Int -- ^ bin size+ -> [b] -- ^ regions+ -> Sink BED m ([v a], Int)+rpkmBinBed k beds = do initRC <- lift $ forM beds $ \bed -> do let start = chromStart bed end = chromEnd bed@@ -124,11 +122,13 @@ let p | strand == Just True = start | strand == Just False = end - 1 | otherwise = error "profiling: unkown strand"- overlaps = concat . snd . unzip $+ overlaps = concat $ IM.elems $ IM.containing (M.lookupDefault IM.empty chr intervalMap) p lift $ forM_ overlaps $ \x -> do let (v, idxFn) = vs `G.unsafeIndex` x- i = idxFn p+ i = let i' = idxFn p+ l = GM.length v+ in if i' >= l then l - 1 else i' GM.unsafeRead v i >>= GM.unsafeWrite v i . (+1) sink (nTags+1) vs @@ -136,15 +136,16 @@ return (rc, nTags) intervalMap = bedToTree (++) $ zip beds $ map return [0..]-{-# INLINE profiling #-}+{-# INLINE rpkmBinBed #-} --- | divide each region into consecutive bins, and count tags for each bin. The--- total number of tags is also returned-profilingCoverage :: (PrimMonad m, G.Vector v Int, BEDLike b1, BEDLike b2)+-- | divide each region into consecutive bins, and compute+-- reads per genome coverage (RPGC) for each bin. The+-- total number of tags is also returned.+rpgcBinBed :: (Num a, PrimMonad m, G.Vector v a, BEDLike b1, BEDLike b2) => Int -- ^ bin size -> [b1] -- ^ regions- -> Sink b2 m ([v Int], Int)-profilingCoverage k beds = do+ -> Sink b2 m ([v a], Int)+rpgcBinBed k beds = do initRC <- lift $ forM beds $ \bed -> do let start = chromStart bed end = chromEnd bed@@ -162,12 +163,15 @@ let chr = chrom bed start = chromStart bed end = chromEnd bed- overlaps = concat . snd . unzip $ IM.intersecting+ overlaps = concat $ IM.elems $ IM.intersecting (M.lookupDefault IM.empty chr intervalMap) $ IM.IntervalCO start end lift $ forM_ overlaps $ \x -> do let (v, idxFn) = vs `G.unsafeIndex` x- lo = idxFn start- hi = idxFn end+ lo = let i = idxFn start+ in if i < 0 then 0 else i+ hi = let i = idxFn end+ l = GM.length v+ in if i >= l then l - 1 else i forM_ [lo..hi] $ \i -> GM.unsafeRead v i >>= GM.unsafeWrite v i . (+1) sink (nTags+1) vs@@ -176,14 +180,14 @@ return (rc, nTags) intervalMap = bedToTree (++) $ zip beds $ map return [0..]-{-# INLINE profilingCoverage #-}+{-# INLINE rpgcBinBed #-} -- | calculate RPKM using BAM file (*.bam) and its index file (*.bam.bai), using -- constant space rpkmBam :: BEDLike b => FilePath -> Conduit b IO Double rpkmBam fl = do- nTags <- lift $ readBam fl $$ CL.foldM (\acc bam -> return $+ nTags <- lift $ readBam fl $$ foldMC (\acc bam -> return $ if isUnmap bam then acc else acc + 1) 0.0 handle <- lift $ BI.open fl conduit nTags handle@@ -198,7 +202,7 @@ rc <- lift $ viewBam h (chr, s, e) $$ readCount s e yield $ rc * 1e9 / n / fromIntegral (e-s) conduit n h- readCount l u = CL.foldM f 0.0+ readCount l u = foldMC f 0.0 where f acc bam = do let p1 = fromIntegral . fromJust . position $ bam rl = fromIntegral . fromJust . queryLength $ bam@@ -237,7 +241,7 @@ -> Int -- ^ radius -> Int -- ^ cutoff -> Source m BED-peakCluster peaks r th = mergeBedWith mergeFn peaks' $= CL.filter g+peakCluster peaks r th = mergeBedWith mergeFn peaks' $= filterC g where peaks' = map f peaks f b = let chr = chrom b
src/Bio/Data/Bam.hs view
@@ -21,8 +21,7 @@ import Bio.SamTools.BamIndex import Control.Monad.Trans.Class (lift) import qualified Data.ByteString.Char8 as B-import Data.Conduit (Source, Conduit, yield)-import qualified Data.Conduit.List as CL+import Conduit (Source, Conduit, yield, concatMapC) import Data.Maybe (fromJust) import Bio.Data.Bed @@ -37,7 +36,7 @@ {-# INLINE readBam #-} bamToBed :: Monad m => Conduit Bam1 m BED-bamToBed = CL.mapMaybe f+bamToBed = concatMapC f where f bam =case targetName bam of Just chr ->@@ -52,7 +51,7 @@ viewBam :: IdxHandle -> (B.ByteString, Int, Int) -> Source IO Bam1 viewBam handle (chr, s, e) = case lookupTarget (idxHeader handle) chr of Nothing -> return ()- Just chrId -> do + Just chrId -> do q <- lift $ query handle chrId (fromIntegral s,fromIntegral e) go q where
src/Bio/Data/Bed.hs view
@@ -46,8 +46,7 @@ import Control.Arrow ((***)) import Control.Monad.State.Strict import qualified Data.ByteString.Char8 as B-import Data.Conduit-import qualified Data.Conduit.List as CL+import Conduit import Data.Default.Class (Default(..)) import Data.Function (on) import qualified Data.Foldable as F@@ -98,7 +97,7 @@ -- | non-streaming version hReadBed' :: MonadIO m => Handle -> m [b]- hReadBed' h = hReadBed h $$ CL.consume+ hReadBed' h = hReadBed h $$ sinkList {-# INLINE hReadBed' #-} readBed :: MonadIO m => FilePath -> Source m b@@ -109,7 +108,7 @@ -- | non-streaming version readBed' :: MonadIO m => FilePath -> m [b]- readBed' fl = readBed fl $$ CL.consume+ readBed' fl = readBed fl $$ sinkList {-# INLINE readBed' #-} hWriteBed :: MonadIO m => Handle -> Sink b m ()@@ -121,7 +120,7 @@ {-# INLINE hWriteBed #-} hWriteBed' :: MonadIO m => Handle -> [b] -> m ()- hWriteBed' handle beds = CL.sourceList beds $$ hWriteBed handle+ hWriteBed' handle beds = yieldMany beds $$ hWriteBed handle {-# INLINE hWriteBed' #-} writeBed :: MonadIO m => FilePath -> Sink b m ()@@ -131,7 +130,7 @@ {-# INLINE writeBed #-} writeBed' :: MonadIO m => FilePath -> [b] -> m ()- writeBed' fl beds = CL.sourceList beds $$ writeBed fl+ writeBed' fl beds = yieldMany beds $$ writeBed fl {-# INLINE writeBed' #-} {-# MINIMAL asBed, fromLine, toLine, chrom, chromStart, chromEnd #-}@@ -238,7 +237,7 @@ -- | return records in A that are overlapped with records in B intersectSortedBed :: (BEDLike b1, BEDLike b2) => [b1] -> Sorted (V.Vector b2) -> [b1]-intersectSortedBed a (Sorted b) = filter (not . null . f) a+intersectSortedBed a (Sorted b) = filter (not . IM.null . f) a where f bed = let chr = chrom bed interval = IM.IntervalCO (chromStart bed) $ chromEnd bed@@ -263,7 +262,7 @@ where f bed = let chr = chrom bed interval = IM.IntervalCO (chromStart bed) $ chromEnd bed- in (bed, fn $ map snd $ IM.intersecting (M.lookupDefault IM.empty chr tree) interval)+ in (bed, fn $ IM.elems $ IM.intersecting (M.lookupDefault IM.empty chr tree) interval) tree = sortedBedToTree const . Sorted . V.toList . V.zip b $ b {-# INLINE intersectSortedBedWith #-} @@ -407,7 +406,7 @@ {-# INLINE fetchSeq #-} fetchSeq' :: (BioSeq DNA a, MonadIO m) => Genome -> [BED] -> m [Either String (DNA a)]-fetchSeq' g beds = CL.sourceList beds $= fetchSeq g $$ CL.consume+fetchSeq' g beds = yieldMany beds $= fetchSeq g $$ sinkList {-# INLINE fetchSeq' #-} -- * BED3 format
− src/Bio/Data/BigWig.hs
@@ -1,32 +0,0 @@-module Bio.Data.BigWig- ( module Data.BBI.BigWig- , accumScores- , normalizedScores- ) where--import Data.BBI.BigWig-import Data.Conduit-import qualified Data.Conduit.List as CL-import Bio.Data.Bed---- | for each BED region, return total scores of all wig records overlapped with it-accumScores :: BEDLike b => BWFile -> Conduit b IO Double-accumScores bwF = CL.mapM (helper bwF)-{-# INLINE accumScores #-}---- | for each BED region, return normalized scores (divided by the length) of--- all wig records overlapped with it-normalizedScores :: BEDLike b => BWFile -> Conduit b IO Double-normalizedScores bwF = CL.mapM $ \bed -> do- x <- helper bwF bed- return $ x / (fromIntegral . size) bed-{-# INLINE normalizedScores #-}--helper :: BEDLike b => BWFile -> b -> IO Double-helper bwF bed = queryBWFile bwF (chr, start, end) $$ CL.fold f 0.0- where- f acc (_, s, e, v) = acc + fromIntegral (e - s) * v- chr = chrom bed- start = chromStart bed- end = chromEnd bed-{-# INLINE helper #-}
src/Bio/Data/Fasta.hs view
@@ -22,8 +22,7 @@ import Bio.Seq import Control.Monad.State.Lazy import qualified Data.ByteString.Char8 as B-import Data.Conduit-import qualified Data.Conduit.List as CL+import Conduit import System.IO class FastaLike f where@@ -37,7 +36,7 @@ -- | non-stream version, read whole file in memory readFasta' :: FilePath -> IO [f]- readFasta' fl = readFasta fl $$ CL.consume+ readFasta' fl = readFasta fl $$ sinkList -- writeFasta :: FilePath -> [f] -> IO () {-# MINIMAL fromFastaRecord #-} @@ -54,7 +53,7 @@ loop [] handle where loop :: [B.ByteString] -> Handle -> Source IO (B.ByteString, [B.ByteString])- loop acc h = do + loop acc h = do eof <- liftIO $ hIsEOF h if eof then liftIO (hClose h) >> output acc else do l <- liftIO $ B.hGetLine h
src/Bio/GO.hs view
@@ -9,7 +9,6 @@ import qualified Data.Text as T import Data.Text.Encoding (decodeUtf8) import qualified Data.ByteString.Char8 as B-import Data.Foldable (foldl') import qualified Data.HashMap.Strict as M import Data.Maybe
src/Bio/GO/GREAT.hs view
@@ -7,7 +7,7 @@ import Control.Monad.Primitive import qualified Data.ByteString.Char8 as B-import Data.Conduit+import Conduit import Data.Default.Class import qualified Data.HashMap.Strict as M import qualified Data.IntervalMap as IM@@ -41,12 +41,14 @@ getRegulatoryDomains (BasalPlusExtension up dw ext) gs = bedToTree undefined $ flip map basal $ \(BED3 chr s e, go) -> let intervals = fromJust . M.lookup chr $ basalTree- s' = case IM.intersecting intervals (IM.OpenInterval (s - ext) s) of- [] -> s - ext- x -> min s (maximum $ map (upperBound . fst) x)- e' = case IM.intersecting intervals (IM.OpenInterval e (e + ext)) of- [] -> e + ext- x -> max e (minimum $ map (lowerBound . fst) x)+ s' = let im = IM.intersecting intervals $ IM.OpenInterval (s-ext) s+ in if IM.null im+ then s - ext+ else min s $ maximum $ map upperBound $ IM.keys im+ e' = let im = IM.intersecting intervals $ IM.OpenInterval e (e+ext)+ in if IM.null im+ then e + ext+ else max e $ minimum $ map lowerBound $ IM.keys im in (BED3 chr s' e', go) where basalTree = bedToTree (error "encounter redundant regions") basal@@ -69,7 +71,7 @@ let chr = chrom bed s = chromStart bed e = chromEnd bed- terms = nub' . concatMap snd . IM.intersecting+ terms = nub' . concat . IM.elems . IM.intersecting (M.lookupDefault IM.empty chr tree) $ IM.IntervalCO s e go (n+1) $ foldl (\acc t -> M.insertWith (+) t 1 acc) termCount terms _ -> return (n, termCount)
src/Bio/GO/Parser.hs view
@@ -5,7 +5,6 @@ ) where import Control.Arrow ((&&&))-import Control.Applicative ((<$>)) import qualified Data.ByteString.Lazy.Char8 as L import qualified Data.HashMap.Strict as M import Data.Maybe
src/Bio/Motif.hs view
@@ -14,7 +14,7 @@ , scores' , score , optimalScore- , CDF+ , CDF(..) , cdf , cdf' , scoreCDF@@ -35,7 +35,7 @@ import Control.Arrow ((&&&)) import Control.Monad.State.Lazy import qualified Data.ByteString.Char8 as B-import Data.Conduit+import Conduit import Data.Double.Conversion.ByteString (toShortest) import Data.Default.Class import Data.List (sortBy, foldl')@@ -224,7 +224,7 @@ pValueToScore :: Double -> Bkgd -> PWM -> Double pValueToScore p bg pwm = cdf' (scoreCDF bg pwm) $ 1 - p -newtype CDF = CDF (V.Vector (Double, Double))+newtype CDF = CDF (V.Vector (Double, Double)) deriving (Read, Show) -- P(X <= x) cdf :: CDF -> Double -> Double
src/Bio/Motif/Alignment.hs view
@@ -1,21 +1,18 @@ {-# LANGUAGE Rank2Types #-}+{-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE BangPatterns #-}- module Bio.Motif.Alignment ( alignment , alignmentBy , linPenal , quadPenal , cubePenal- , mergePWM- , buildTree- , progressiveMerging+ , expPenal+ , AlignFn ) where -import AI.Clustering.Hierarchical import qualified Data.Vector.Generic as G-import qualified Data.Vector as V import qualified Data.Vector.Unboxed as U import qualified Data.Matrix.Unboxed as M @@ -25,32 +22,41 @@ -- | penalty function takes the gaps number as input, return penalty value type PenalFn = Int -> Double -type DistanceFn = (G.Vector v Double, G.Vector v (Double, Double)) => v Double -> v Double -> Double+type DistanceFn = forall v. (G.Vector v Double, G.Vector v (Double, Double))+ => v Double -> v Double -> Double -alignment :: PWM -> PWM -> (Double, (PWM, PWM, Int))-alignment = alignmentBy jsd quadPenal+type AlignFn = PWM+ -> PWM+ -> (Double, (Bool, Int)) -- ^ (distance, (on same direction,+ -- position w.r.t. the first pwm)) +alignment :: AlignFn+alignment = alignmentBy jsd $ quadPenal 0.15+ -- | linear penalty-linPenal :: PenalFn-linPenal n = fromIntegral n * 0.3+linPenal :: Double -> PenalFn+linPenal x n = fromIntegral n * x -- | quadratic penalty-quadPenal :: PenalFn-quadPenal n = fromIntegral (n ^ (2 :: Int)) * 0.15+quadPenal :: Double -> PenalFn+quadPenal x n = fromIntegral (n ^ (2 :: Int)) * x -- | cubic penalty-cubePenal :: PenalFn-cubePenal n = fromIntegral (n ^ (3 :: Int)) * 0.01+cubePenal :: Double -> PenalFn+cubePenal x n = fromIntegral (n ^ (3 :: Int)) * x -- | exponentail penalty-expPenal :: PenalFn-expPenal n = fromIntegral (2^n :: Int) * 0.01+expPenal :: Double -> PenalFn+expPenal x n = fromIntegral (2^n :: Int) * x -- internal gaps are not allowed, larger score means larger distance, so the smaller the better-alignmentBy :: DistanceFn -> PenalFn -> PWM -> PWM -> (Double, (PWM, PWM, Int))+alignmentBy :: DistanceFn -- ^ compute the distance between two aligned pwms+ -> PenalFn -- ^ gap penalty+ -> AlignFn alignmentBy fn pFn m1 m2- | fst forwardAlign <= fst reverseAlign = (fst forwardAlign, (m1, m2, snd forwardAlign))- | otherwise = (fst reverseAlign, (m1, m2', snd reverseAlign))+ | fst forwardAlign <= fst reverseAlign =+ (fst forwardAlign, (True, snd forwardAlign))+ | otherwise = (fst reverseAlign, (False, snd reverseAlign)) where forwardAlign | d1 < d2 = (d1,i1) | otherwise = (d2,-i2)@@ -94,26 +100,3 @@ n1 = length s1 n2 = length s2 {-# INLINE alignmentBy #-}--mergePWM :: (PWM, PWM, Int) -> PWM-mergePWM (m1, m2, i) | i >= 0 = PWM Nothing (M.fromRows $ take i s1 ++ zipWith f (drop i s1) s2 ++ drop (n1 - i) s2)- | otherwise = PWM Nothing (M.fromRows $ take (-i) s2 ++ zipWith f (drop (-i) s2) s1 ++ drop (n2 + i) s1)- where- f = G.zipWith (\x y -> (x+y)/2)- s1 = M.toRows . _mat $ m1- s2 = M.toRows . _mat $ m2- n1 = length s1- n2 = length s2--progressiveMerging :: Dendrogram Motif -> PWM-progressiveMerging t = case t of- Branch _ _ left right -> f (progressiveMerging left) $ progressiveMerging right- Leaf a -> _pwm a- where- f a b = mergePWM $! snd $ alignment a b---- | build a guide tree from a set of motifs-buildTree :: [Motif] -> Dendrogram Motif-buildTree motifs = hclust Average (V.fromList motifs) δ- where- δ (Motif _ x) (Motif _ y) = fst $ alignment x y
+ src/Bio/Motif/Merge.hs view
@@ -0,0 +1,185 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE FlexibleContexts #-}+module Bio.Motif.Merge+ ( mergePWM+ , mergePWMWeighted+ , dilute+ , trim+ , mergeTree+ , mergeTreeWeighted+ , iterativeMerge+ , buildTree+ )where++import AI.Clustering.Hierarchical hiding (size)+import Control.Arrow (first)+import Control.Monad (forM_, when)+import Control.Monad.ST (runST, ST)+import qualified Data.ByteString.Char8 as B+import Data.List (dropWhileEnd)+import qualified Data.Matrix.Symmetric.Mutable as MSU+import qualified Data.Matrix.Unboxed as MU+import Data.Maybe+import qualified Data.Vector as V+import qualified Data.Vector.Mutable as VM+import qualified Data.Vector.Unboxed as U++import Bio.Motif+import Bio.Motif.Alignment+import Bio.Utils.Functions (kld)++mergePWM :: (PWM, PWM, Int) -> PWM+mergePWM (m1, m2, shift) | shift >= 0 = merge shift (_mat m1) $ _mat m2+ | otherwise = merge (-shift) (_mat m2) $ _mat m1+ where+ merge s a b = PWM Nothing $ MU.fromRows $ loop 0+ where+ n1 = MU.rows a+ n2 = MU.rows b+ loop i | i' < 0 || (i < n1 && i' >= n2) = MU.takeRow a i : loop (i+1)+ | i < n1 && i' < n2 = f (MU.takeRow a i) (MU.takeRow b i') : loop (i+1)+ | i >= n1 && i' < n2 = MU.takeRow b i' : loop (i+1)+ | otherwise = []+ where+ i' = i - s+ f = U.zipWith (\x y -> (x+y)/2)++mergePWMWeighted :: (PWM, [Int]) -- ^ pwm and weights at each position+ -> (PWM, [Int])+ -> Int -- ^ shift+ -> (PWM, [Int])+mergePWMWeighted m1 m2 shift+ | shift >= 0 = merge shift (first _mat m1) $ first _mat m2+ | otherwise = merge (-shift) (first _mat m2) $ first _mat m1++ where+ merge s (p1,w1) (p2,w2) = first (PWM Nothing . MU.fromRows) $ unzip $ loop 0+ where+ a = V.fromList $ zip (MU.toRows p1) w1+ b = V.fromList $ zip (MU.toRows p2) w2+ n1 = V.length a+ n2 = V.length b+ loop i | i' < 0 || (i < n1 && i' >= n2) = a V.! i : loop (i+1)+ | i < n1 && i' < n2 = f (a V.! i) (b V.! i') : loop (i+1)+ | i >= n1 && i' < n2 = b V.! i' : loop (i+1)+ | otherwise = []+ where+ i' = i - s+ f (xs, wx) (ys, wy) = (U.zipWith (\x y ->+ (fromIntegral wx * x + fromIntegral wy * y) /+ fromIntegral (wx + wy)) xs ys, wx + wy)++-- | dilute positions in a PWM that are associated with low weights+dilute :: (PWM, [Int]) -> PWM+dilute (pwm, ws) = PWM Nothing $ MU.fromRows $ zipWith f ws $ MU.toRows $ _mat pwm+ where+ f w r | w < n = let d = fromIntegral $ n - w+ in U.map (\x -> (fromIntegral w * x + 0.25 * d) / fromIntegral n) r+ | otherwise = r+ n = maximum ws+{-# INLINE dilute #-}++trim :: Bkgd -> Double -> PWM -> PWM+trim (BG (a,c,g,t)) cutoff pwm = PWM Nothing $ MU.fromRows $ dropWhileEnd f $+ dropWhile f rs+ where+ f x = kld x bg < cutoff+ rs = MU.toRows $ _mat pwm+ bg = U.fromList [a,c,g,t]+{-# INLINE trim #-}++mergeTree :: AlignFn -> Dendrogram Motif -> PWM+mergeTree align t = case t of+ Branch _ _ left right -> f (mergeTree align left) $ mergeTree align right+ Leaf a -> _pwm a+ where+ f a b | isSame = mergePWM (a, b, i)+ | otherwise = mergePWM (a, rcPWM b, i)+ where (_, (isSame, i)) = align a b++mergeTreeWeighted :: AlignFn -> Dendrogram Motif -> (PWM, [Int])+mergeTreeWeighted align t = case t of+ Branch _ _ left right -> f (mergeTreeWeighted align left) $+ mergeTreeWeighted align right+ Leaf a -> (_pwm a, replicate (size $ _pwm a) 1)+ where+ f (a,w1) (b,w2)+ | isSame = mergePWMWeighted (a,w1) (b,w2) i+ | otherwise = mergePWMWeighted (a,w1) (rcPWM b, reverse w2) i+ where (_, (isSame, i)) = align a b+{-# INLINE mergeTreeWeighted #-}++iterativeMerge :: AlignFn+ -> Double -- cutoff+ -> [Motif] -- ^ Motifs to be merged. Motifs must have unique name.+ -> [([B.ByteString], PWM, [Int])]+iterativeMerge align th motifs = runST $ do+ motifs' <- V.unsafeThaw $ V.fromList $ flip map motifs $ \x ->+ Just ([_name x], _pwm x, replicate (size $ _pwm x) 1)++ let n = VM.length motifs'+ iter mat = do+ -- retrieve the minimum value+ ((i, j), (d, (isSame, pos))) <- loop ((-1,-1), (1/0, undefined)) 0 1+ if d < th+ then do+ Just (nm1, pwm1, w1) <- VM.unsafeRead motifs' i+ Just (nm2, pwm2, w2) <- VM.unsafeRead motifs' j+ let merged = (nm1 ++ nm2, pwm', w')+ (pwm',w') | isSame = mergePWMWeighted (pwm1, w1) (pwm2, w2) pos+ | otherwise = mergePWMWeighted (pwm1, w1)+ (rcPWM $ pwm2, reverse w2) pos++ -- update+ forM_ [0..n-1] $ \i' -> MSU.unsafeWrite mat (i',j) Nothing+ VM.unsafeWrite motifs' i $ Just merged+ VM.unsafeWrite motifs' j Nothing+ forM_ [0..n-1] $ \j' -> when (i /= j') $ do+ x <- VM.unsafeRead motifs' j'+ case x of+ Just (_, pwm2',_) -> do+ let ali | i < j' = Just $ align pwm' pwm2'+ | otherwise = Just $ align pwm2' pwm'+ MSU.unsafeWrite mat (i,j') ali+ _ -> return ()+ iter mat+ else return ()+ where+ loop ((i_min, j_min), d_min) i j+ | i >= n = return ((i_min, j_min), d_min)+ | j >= n = loop ((i_min, j_min), d_min) (i+1) (i+2)+ | otherwise = do+ x <- MSU.unsafeRead mat (i,j)+ case x of+ Just d -> if fst d < fst d_min+ then loop ((i,j), d) i (j+1)+ else loop ((i_min, j_min), d_min) i (j+1)+ _ -> loop ((i_min, j_min), d_min) i (j+1)++ -- initialization+ mat <- MSU.replicate (n,n) Nothing :: ST s (MSU.SymMMatrix VM.MVector s (Maybe (Double, (Bool, Int))))+ forM_ [0..n-1] $ \i -> forM_ [i+1 .. n-1] $ \j -> do+ Just (_, pwm1, _) <- VM.unsafeRead motifs' i+ Just (_, pwm2, _) <- VM.unsafeRead motifs' j+ MSU.unsafeWrite mat (i,j) $ Just $ align pwm1 pwm2++ iter mat+ results <- V.unsafeFreeze motifs'+ return $ V.toList $ V.map fromJust $ V.filter isJust results+{-# INLINE iterativeMerge #-}++-- | build a guide tree from a set of motifs+buildTree :: AlignFn -> [Motif] -> Dendrogram Motif+buildTree align motifs = hclust Average (V.fromList motifs) δ+ where+ δ (Motif _ x) (Motif _ y) = fst $ align x y++cutTreeBy :: Double -- ^ start+ -> Double -- ^ step+ -> ([Dendrogram a] -> Bool) -> Dendrogram a -> [Dendrogram a]+cutTreeBy start step fn tree = go start+ where+ go x | fn clusters = clusters+ | x - step > 0 = go $ x - step+ | otherwise = clusters+ where clusters = cutAt tree x
src/Bio/Motif/Search.hs view
@@ -1,50 +1,74 @@-{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE BangPatterns #-}+{-# LANGUAGE FlexibleContexts #-} module Bio.Motif.Search ( findTFBS , findTFBS' , findTFBSSlow , maxMatchSc- , MotifCompo(..)- , spacingConstraint+ , SpaceDistribution(..)+ , spaceConstraint+ , spaceConstraintHelper ) where -import Bio.Seq (DNA, toBS)-import qualified Bio.Seq as Seq (length)-import Bio.Motif-import Control.Parallel.Strategies (parMap, rdeepseq)-import Data.Conduit-import qualified Data.HashSet as S-import Data.List (foldl', intercalate)-import Data.Ord (comparing)-import qualified Data.ByteString.Char8 as B-import qualified Data.Vector.Unboxed as U-import qualified Data.Matrix.Unboxed as M+import Conduit (Source, await, mapC, sinkVector,+ yield, ($$), (=$=))+import Control.Arrow ((***))+import Control.Monad.ST (runST)+import Control.Parallel.Strategies (parMap, rdeepseq)+import qualified Data.ByteString.Char8 as B+import Data.Function (on)+import qualified Data.HashMap.Strict as HM+import qualified Data.HashSet as S+import Data.List (nubBy)+import qualified Data.Matrix.Unboxed as M+import Data.Ord (comparing)+import qualified Data.Vector.Unboxed as U +import Bio.Motif (Bkgd (..), Motif (..), PWM (..),+ pValueToScore, rcPWM, scores',+ size)+import Bio.Seq (DNA, toBS)+import qualified Bio.Seq as Seq (length)+ -- | given a user defined threshold, look for TF binding sites on a DNA -- sequence, using look ahead search. This function doesn't search for binding -- sites on the reverse strand-findTFBS :: Monad m => Bkgd -> PWM -> DNA a -> Double -> Source m Int-findTFBS bg pwm dna thres = loop 0+findTFBS :: Monad m+ => Bkgd+ -> PWM+ -> DNA a+ -> Double+ -> Bool -- ^ whether to skip ambiguous sequences. Recommend: True+ -- in most cases+ -> Source m Int+findTFBS bg pwm dna thres skip = loop 0 where loop !i | i >= l - n + 1 = return ()- | otherwise = do let (d, _) = lookAheadSearch bg pwm sigma dna i thres+ | otherwise = do let (d, _) = searchFn bg pwm sigma dna i thres if d == n - 1 then yield i >> loop (i+1) else loop (i+1) sigma = optimalScoresSuffix bg pwm l = Seq.length dna n = size pwm+ searchFn | skip = lookAheadSearch'+ | otherwise = lookAheadSearch {-# INLINE findTFBS #-} -- | a parallel version of findTFBS-findTFBS' :: Bkgd -> PWM -> DNA a -> Double -> [Int]-findTFBS' bg pwm dna th = concat $ parMap rdeepseq f [0,step..l-n+1]+findTFBS' :: Bkgd+ -> PWM+ -> DNA a+ -> Double+ -> Bool+ -> [Int]+findTFBS' bg pwm dna th skip = concat $ parMap rdeepseq f [0,step..l-n+1] where f x = loop x where loop i | i >= x+step || i >= l-n+1 = []- | otherwise = let d = fst $ lookAheadSearch bg pwm sigma dna i th+ | otherwise = let d = fst $ searchFn bg pwm sigma dna i th in if d == n-1 then i : loop (i+1) else loop (i+1)@@ -52,11 +76,13 @@ l = Seq.length dna n = size pwm step = 500000+ searchFn | skip = lookAheadSearch'+ | otherwise = lookAheadSearch {-# INLINE findTFBS' #-} -- | use naive search findTFBSSlow :: Monad m => Bkgd -> PWM -> DNA a -> Double -> Source m Int-findTFBSSlow bg pwm dna thres = scores' bg pwm dna $=+findTFBSSlow bg pwm dna thres = scores' bg pwm dna =$= loop 0 where loop i = do v <- await@@ -137,59 +163,112 @@ n = size pwm {-# INLINE lookAheadSearch #-} +-- | this version skip sequences contain ambiguous bases, like "N"+lookAheadSearch' :: Bkgd -- ^ background nucleotide distribution+ -> PWM -- ^ pwm+ -> U.Vector Double -- ^ best possible match score of suffixes+ -> DNA a -- ^ DNA sequence+ -> Int -- ^ starting location on the DNA+ -> Double -- ^ threshold+ -> (Int, Double) -- ^ (d, sc_d), the largest d such that sc_d > th_d+lookAheadSearch' (BG (a, c, g, t)) pwm sigma dna start thres = loop (0, -1) 0+ where+ loop (!acc, !th_d) !d+ | acc < th_d = (d-2, acc)+ | otherwise = if d >= n+ then (d-1, acc)+ else loop (acc + sc, thres - sigma U.! d) (d+1)+ where+ sc = case toBS dna `B.index` (start + d) of+ 'A' -> log $! matchA / a+ 'C' -> log $! matchC / c+ 'G' -> log $! matchG / g+ 'T' -> log $! matchT / t+ _ -> -1 / 0+ matchA = addSome $ M.unsafeIndex (_mat pwm) (d,0)+ matchC = addSome $ M.unsafeIndex (_mat pwm) (d,1)+ matchG = addSome $ M.unsafeIndex (_mat pwm) (d,2)+ matchT = addSome $ M.unsafeIndex (_mat pwm) (d,3)+ addSome !x | x == 0 = pseudoCount+ | otherwise = x+ pseudoCount = 0.0001+ n = size pwm+{-# INLINE lookAheadSearch' #-}++{- data MotifCompo = MotifCompo- { _motif1 :: Motif- , _motif2 :: Motif+ { _motif1 :: Motif+ , _motif2 :: Motif , _sameDirection :: Bool- , _spacing :: Int- , _score :: Double+ , _spacing :: Int+ , _score :: Double } instance Show MotifCompo where show (MotifCompo m1 m2 isSame sp sc) = intercalate "\t" [B.unpack $ _name m1, B.unpack $ _name m2, show isSame, show sp, show sc]+ -} +data SpaceDistribution = SpaceDistribution+ { _motif1 :: Motif+ , _nSites1 :: (Int, Int)+ , _motif2 :: Motif+ , _nSites2 :: (Int, Int)+ , _same :: [(Int, Int)]+ , _opposite :: [(Int, Int)]+ } deriving (Show, Read)+ -- | search for spacing constraint between two TFs-spacingConstraint :: Motif -- ^ motif 1- -> Motif -- ^ motif 2- -> Bkgd -- ^ backgroud nucleotide distribution- -> Double -- ^ p-Value for motif finding- -> Int -- ^ half window size- -> Int -- ^ max distance to search- -> DNA a -> [MotifCompo]-spacingConstraint m1@(Motif _ pwm1) m2@(Motif _ pwm2) bg th w k dna = same ++ oppose+spaceConstraint :: [(Motif, Motif)] -- ^ motifs, names must be unique+ -> Bkgd -- ^ backgroud nucleotide distribution+ -> Double -- ^ p-Value for motif finding+ -> Int -- ^ half window size, typical 5+ -> Int -- ^ max distance to search, typical 300+ -> DNA a -> [SpaceDistribution]+spaceConstraint pairs bg th w k dna = flip map pairs $ \(a, b) ->+ let (m1, site1) = HM.lookupDefault undefined (_name a) sites+ (m2, site2) = HM.lookupDefault undefined (_name b) sites+ (same, opposite) = spaceConstraintHelper site1 site2 w k+ in SpaceDistribution m1 ((U.length *** U.length) site1) m2+ ((U.length *** U.length) site2) same opposite where- rs = let rs' = [-k, -k+2*w+1 .. 0]- in rs' ++ map (*(-1)) (reverse rs')- -- on the same orientation- same = zipWith f rs $ zipWith (+) nFF nRR- where- nFF = map (nOverlap forward1 forward2 w) rs- nRR = map (nOverlap reverse1 reverse2 w) $ reverse rs- f r c = MotifCompo m1 m2 True r $ fromIntegral c / n- oppose = zipWith f rs $ zipWith (+) nFR nRF+ motifs = nubBy ((==) `on` _name) $ concatMap (\(a,b) -> [a,b]) pairs+ findSites (Motif _ pwm) = (fwd, rev) where- nFR = map (nOverlap forward1 reverse2 w) rs- nRF = map (nOverlap reverse1 forward2 w) $ reverse rs- f r c = MotifCompo m1 m2 False r $ fromIntegral c / n- forward1 = findTFBS' bg pwm1 dna th1- forward2 = S.fromList $ findTFBS' bg pwm2 dna th2- reverse1 = map (+ (s1 - 1)) $ findTFBS' bg (rcPWM pwm1) dna th1'- reverse2 = S.fromList $ map (+ (s2 - 1)) $ findTFBS' bg (rcPWM pwm2) dna th2'- th1 = pValueToScore th bg pwm1- th1' = pValueToScore th bg $ rcPWM pwm1- th2 = pValueToScore th bg pwm2- th2' = pValueToScore th bg $ rcPWM pwm2- s1 = size pwm1- s2 = size pwm2- n = sqrt $ fromIntegral $ (length forward1 + length reverse1) * (S.size forward2 + S.size reverse2)+ fwd = runST $ findTFBS bg pwm dna cutoff True $$ sinkVector+ rev = runST $ findTFBS bg pwm' dna cutoff' True =$=+ mapC (+ (size pwm - 1)) $$ sinkVector+ cutoff = pValueToScore th bg pwm+ cutoff' = pValueToScore th bg pwm'+ pwm' = rcPWM pwm+ sites = HM.fromList $ map (\m -> (_name m, (m, findSites m))) motifs+{-# INLINE spaceConstraint #-} - nOverlap :: [Int] -> S.HashSet Int -> Int -> Int -> Int- nOverlap xs ys w' i = foldl' f 0 xs+spaceConstraintHelper :: (U.Vector Int, U.Vector Int)+ -> (U.Vector Int, U.Vector Int)+ -> Int+ -> Int+ -> ([(Int, Int)], [(Int, Int)])+spaceConstraintHelper (fw1, rv1) (fw2, rv2) w k = (same, oppose)+ where+ rs = let rs' = [-k, -k+2*w+1 .. 0]+ in rs' ++ map (*(-1)) (reverse rs')+ fw2' = S.fromList $ U.toList fw2+ rv2' = S.fromList $ U.toList rv2+ nOverlap :: U.Vector Int -> S.HashSet Int -> Int -> Int -> Int+ nOverlap xs ys w' i = U.foldl' f 0 xs where f acc x | any (`S.member` ys) [x + i - w' .. x + i + w'] = acc + 1 | otherwise = acc-{-# INLINE spacingConstraint #-}+ same = zip rs $ zipWith (+) nFF nRR+ where+ nFF = map (nOverlap fw1 fw2' w) rs+ nRR = map (nOverlap rv1 rv2' w) $ reverse rs+ oppose = zip rs $ zipWith (+) nFR nRF+ where+ nFR = map (nOverlap fw1 rv2' w) rs+ nRF = map (nOverlap rv1 fw2' w) $ reverse rs+{-# INLINE spaceConstraintHelper #-} {- computePValue :: Double -> [Int] -> [(Int, Double)]
src/Bio/RealWorld/BioGRID.hs view
@@ -82,7 +82,8 @@ let request = initReq { method = "GET" , requestHeaders = [("Content-type", "text/plain")] }- r <- withManager $ \manager -> httpLbs request manager+ manager <- newManager tlsManagerSettings+ r <- httpLbs request manager return $ map parseAsTab2 $ BL.lines $ responseBody r where url = base ++ "/interactions/?searchNames=ture&includeInteractors=false"
src/Bio/RealWorld/ENCODE.hs view
@@ -39,7 +39,6 @@ , showResult ) where -import Control.Applicative ((<$>)) import Data.Aeson import Data.Aeson.Types import Data.Aeson.Encode.Pretty (encodePretty)@@ -47,12 +46,10 @@ import qualified Data.ByteString.Lazy.Char8 as B import qualified Data.ByteString.Char8 as BS import qualified Data.Sequence as S-import qualified Data.Foldable as F import qualified Data.Text as T import qualified Data.Vector as V import Network.HTTP.Conduit import Data.Default.Class-import Data.Monoid import Bio.RealWorld.ID @@ -66,9 +63,9 @@ show (KeyWords x y) = f x ++ g y where f x' | S.null x' = ""- | otherwise = "searchTerm=" ++ F.foldr1 (\a b -> b ++ ('+':a)) x' ++ "&"+ | otherwise = "searchTerm=" ++ foldr1 (\a b -> b ++ ('+':a)) x' ++ "&" g y' | S.null y' = ""- | otherwise = F.foldr1 (\a b -> b ++ ('&':a)) y'+ | otherwise = foldr1 (\a b -> b ++ ('&':a)) y' instance Monoid KeyWords where mempty = KeyWords S.empty S.empty@@ -80,14 +77,15 @@ -- | general search using keywords and a set of constraints. Example: -- search ["chip", "sp1"] ["type=experiment"] search :: KeyWords -> IO (Either String [Value])-search kw = do +search kw = do initReq <- parseUrl url- let request = initReq { method = "GET" + let request = initReq { method = "GET" , requestHeaders = [("accept", "application/json")] }- r <- withManager $ \manager -> httpLbs request manager+ manager <- newManager tlsManagerSettings+ r <- httpLbs request manager return $ (eitherDecode . responseBody) r >>=- parseEither (withObject "ENCODE_JSON" (.: "@graph"))+ parseEither (withObject "ENCODE_JSON" (.: "@graph")) where url = base ++ "search/?" ++ show kw @@ -119,10 +117,11 @@ openUrl :: String -> String -> IO B.ByteString openUrl url datatype = do initReq <- parseUrl url- let request = initReq { method = "GET" + let request = initReq { method = "GET" , requestHeaders = [("accept", BS.pack datatype)] }- r <- withManager $ \manager -> httpLbs request manager+ manager <- newManager tlsManagerSettings+ r <- httpLbs request manager return $ responseBody r jsonFromUrl :: String -> IO (Either String Value)@@ -148,6 +147,6 @@ as :: FromJSON a => Value -> a as = getResult . fromJSON where- getResult (Error e) = error e + getResult (Error e) = error e getResult (Success x) = x {-# INLINE as #-}
src/Bio/RealWorld/Ensembl.hs view
@@ -28,11 +28,12 @@ lookupHelp :: [EnsemblID] -> IO (Either String Object) lookupHelp xs = do initReq <- parseUrl url- let request = initReq { method = "POST" + let request = initReq { method = "POST" , requestHeaders = [("Content-type", "application/json")] , requestBody = body }- r <- withManager $ \manager -> httpLbs request manager+ manager <- newManager tlsManagerSettings+ r <- httpLbs request manager return . eitherDecode . responseBody $ r where url = base ++ "/lookup/id/"
src/Bio/RealWorld/UCSC.hs view
@@ -21,10 +21,8 @@ , readUCSCGenes' ) where -import Control.Monad.IO.Class (liftIO) import qualified Data.ByteString.Char8 as B-import Data.Conduit-import qualified Data.Conduit.List as CL+import Conduit import qualified Data.Vector.Unboxed as U import System.IO @@ -69,7 +67,7 @@ {-# INLINE readUCSCGenes #-} readUCSCGenes' :: FilePath -> IO [UCSCGene]-readUCSCGenes' fl = readUCSCGenes fl $$ CL.consume+readUCSCGenes' fl = readUCSCGenes fl $$ sinkList {-# INLINE readUCSCGenes' #-} readGeneFromLine :: B.ByteString -> UCSCGene
src/Bio/Seq.hs view
@@ -1,8 +1,8 @@ {-# LANGUAGE MultiParamTypeClasses #-} {-# LANGUAGE BangPatterns #-} {-# LANGUAGE FlexibleContexts #-}-module Bio.Seq - ( +module Bio.Seq+ ( -- * Alphabet Basic , IUPAC@@ -24,7 +24,6 @@ import qualified Data.HashMap.Strict as M import qualified Data.HashSet as S import Data.Char8 (toUpper)-import Data.Monoid (Monoid(..)) -- | Alphabet defined by http://www.chem.qmul.ac.uk/iupac/ -- | Standard unambiguous alphabet@@ -77,7 +76,7 @@ class BioSeq' s => BioSeq s a where alphabet :: s a -> S.HashSet Char- fromBS :: B.ByteString -> s a + fromBS :: B.ByteString -> s a instance BioSeq DNA Basic where alphabet _ = S.fromList "ACGT"
src/Bio/Seq/IO.hs view
@@ -16,7 +16,6 @@ import Bio.Seq import Bio.Utils.Misc (readInt)-import Control.Applicative ((<$>)) import qualified Data.ByteString.Char8 as B import qualified Data.HashMap.Lazy as M import Data.List.Split
src/Bio/Utils/Functions.hs view
@@ -18,6 +18,7 @@ , ihs' , scale , filterFDR+ , slideAverage , hyperquick , kld , jsd@@ -32,7 +33,7 @@ import qualified Data.Vector as V import qualified Data.Vector.Generic as G import qualified Data.Vector.Unboxed as U-import Statistics.Sample (meanVarianceUnb)+import Statistics.Sample (meanVarianceUnb, mean) import Statistics.Function (sortBy) -- | inverse hyperbolic sine transformation@@ -55,7 +56,10 @@ {-# INLINE scale #-} -- | given the p-values, filter data by controling FDR-filterFDR :: G.Vector v (a, Double) => Double -> v (a, Double) -> v (a, Double)+filterFDR :: G.Vector v (a, Double)+ => Double -- ^ desired FDR value+ -> v (a, Double) -- ^ input data and pvalues+ -> v (a, Double) filterFDR α xs = go n . sortBy (comparing snd) $ xs where go rank v | rank <= 0 = G.empty@@ -64,6 +68,19 @@ n = G.length xs {-# INLINE filterFDR #-} +-- | Compute the sliding average for each entry in a vector+slideAverage :: (Fractional a, G.Vector v a)+ => Int -- ^ size of HALF sliding window, 2 means a total+ -- window size is 5+ -> v a+ -> v a+slideAverage k xs = G.generate n $ \i -> go xs (max 0 (i-k)) (min (n-1) (i+k))+ where+ go v i j = let l = j - i + 1+ in G.foldl' (+) 0 (G.unsafeSlice i l v) / fromIntegral l+ n = G.length xs+{-# INLINE slideAverage #-}+ hyperquick :: Int -> Int -> Int -> Int -> Double hyperquick x m _n _N = loop (m-2) s s (2*e) where@@ -82,28 +99,9 @@ ( 1 - fromIntegral (_n-1-x) / fromIntegral (_N-1-m) ) e = 1e-20 -{--hyperquick' :: Int -> Int -> Int -> Int -> Double-hyperquick' x m _n _N = loop (m-2) s s (2*e)- where- loop !k !ak !bk !epsk- | k < _N - (_n-x) - 1 && epsk > e =- let ck = ak / bk- k' = k + 1- jjm = invJm _n x _N k'- bk' = bk * jjm + 1- ak' = ak * jjm- espk' = fromIntegral (_N - (_n - x) - 1 - k') * (ck - ak' / bk')- in loop k' ak' bk' espk'- | otherwise = 1 - (ak / bk - epsk / 2)- s = foldl' (\s' k -> 1 + s' * invJm _n x _N k) 1.0 [x..m-2]- invJm _n x _N m = ( 1 - fromIntegral x / fromIntegral (m+1) ) /- ( 1 - fromIntegral (_n-1-x) / fromIntegral (_N-1-m) )- e = 1e-200- -} -- | compute the Kullback-Leibler divergence between two valid (not check) probability distributions.--- kl(X,Y) = \sum_i P(x_i) log_2(P(x_i)\/P(y_i)). +-- kl(X,Y) = \sum_i P(x_i) log_2(P(x_i)\/P(y_i)). kld :: (G.Vector v Double, G.Vector v (Double, Double)) => v Double -> v Double -> Double kld xs ys | G.length xs /= G.length ys = error "Incompitable dimensions" | otherwise = G.foldl' f 0 . G.zip xs $ ys
src/Bio/Utils/Overlap.hs view
@@ -13,9 +13,7 @@ import Data.Function import Bio.Data.Bed import Control.Monad-import Data.Conduit-import qualified Data.Conduit.List as CL-import Control.Monad.Trans.Class (lift)+import Conduit -- | convert lines of a BED file into a data structure - A hashmap of which the -- | chromosomes, and values are interval maps.@@ -45,7 +43,7 @@ intervals = case set of Just iMap -> IM.intersecting iMap.toInterval $ b _ -> []- forM_ intervals (\interval -> do + forM_ intervals (\interval -> do let i = snd interval nucl = overlap b . fst $ interval VM.write v i . (+nucl) =<< VM.read v i@@ -56,7 +54,7 @@ featMap = toMap.map (\x -> (x^.chrom, (x^.chromStart, x^.chromEnd))) $ bin featWidth = V.fromList.map (\x -> x^.chromEnd - x^.chromStart) $ bin n = length bin- overlap (l, u) (IM.ClosedInterval l' u') + overlap (l, u) (IM.ClosedInterval l' u') | l' >= l = if u' <= u then u'-l'+1 else u-l'+1 | otherwise = if u' <= u then u'-l+1 else u-l+1 overlap _ _ = 0@@ -71,16 +69,16 @@ sink :: Sink BED IO (V.Vector Int) sink = do v <- lift $ VM.replicate (n+1) 0- CL.mapM_ $ \t -> do+ mapM_C $ \t -> do let set = M.lookup (_chrom t) featMap s = _chromStart t e = _chromEnd t b = (s, e) l = e - s + 1 intervals = case set of- Just iMap -> IM.intersecting iMap.toInterval $ b+ Just iMap -> IM.toList . IM.intersecting iMap . toInterval $ b _ -> []- forM_ intervals (\interval -> do + forM_ intervals (\interval -> do let i = snd interval nucl = overlap b . fst $ interval VM.write v i . (+nucl) =<< VM.read v i@@ -91,13 +89,13 @@ featMap = toMap.map (\x -> (_chrom x, (_chromStart x, _chromEnd x))) $ bin featWidth = V.fromList.map (\x -> _chromEnd x - _chromStart x) $ bin n = length bin- overlap (l, u) (IM.ClosedInterval l' u') + overlap (l, u) (IM.ClosedInterval l' u') | l' >= l = if u' <= u then u'-l'+1 else u-l'+1 | otherwise = if u' <= u then u'-l+1 else u-l+1 overlap _ _ = 0 normalize a b = fromIntegral a / fromIntegral b -overlapFragment, overlapNucl :: +overlapFragment, overlapNucl :: [(Int, Int)] -- ^ Ascending order list -> [(Int, Int)] -- ^ tags in any order -> V.Vector Int@@ -107,7 +105,7 @@ iMap = IM.fromAscList $ zip (map toInterval xs) [0..] go ts' v = do forM_ ts' (\x -> do- let indices = snd.unzip.IM.intersecting iMap.toInterval $ x+ let indices = IM.elems . IM.intersecting iMap . toInterval $ x forM_ indices (\i -> VM.write v i . (+1) =<< VM.read v i) ) return v@@ -118,15 +116,15 @@ iMap = IM.fromAscList $ zip (map toInterval xs) [0..] go ts' v = do forM_ ts' (\x -> do- let intervals = IM.intersecting iMap.toInterval $ x- forM_ intervals (\interval -> do + let intervals = IM.toList . IM.intersecting iMap . toInterval $ x+ forM_ intervals (\interval -> do let i = snd interval nucl = overlap x . fst $ interval VM.write v i . (+nucl) =<< VM.read v i ) ) return v- overlap (l, u) (IM.ClosedInterval l' u') + overlap (l, u) (IM.ClosedInterval l' u') | l' >= l = if u' <= u then u'-l'+1 else u-l'+1 | otherwise = if u' <= u then u'-l+1 else u-l+1 overlap _ _ = 0
+ tests/Tests/Bam.hs view
@@ -0,0 +1,21 @@+{-# LANGUAGE OverloadedStrings #-}++module Tests.Bam (tests) where++import Bio.Data.Bed+import Bio.Data.Bam+import Conduit+import Test.Tasty+import Test.Tasty.HUnit+import qualified Data.Vector as V++tests :: TestTree+tests = testGroup "Test: Bio.Data.Bam"+ [ testCase "bamToBed" bamToBedTest+ ]++bamToBedTest :: Assertion+bamToBedTest = do+ bed <- readBed' "tests/data/example.bed"+ bed' <- readBam "tests/data/example.bam" =$= bamToBed $$ sinkList+ bed @=? bed'
tests/test.hs view
@@ -1,4 +1,5 @@ import qualified Tests.Bed as Bed+import qualified Tests.Bam as Bam import qualified Tests.Motif as Motif import qualified Tests.ChIPSeq as ChIPSeq import qualified Tests.Seq as Seq@@ -7,6 +8,7 @@ main :: IO () main = defaultMain $ testGroup "Main" [ Bed.tests+ , Bam.tests , Seq.tests , ChIPSeq.tests , Motif.tests