flowsim (empty) → 0.2.6
raw patch · 12 files changed
+928/−0 lines, 12 filesdep +MonadRandomdep +arraydep +basesetup-changed
Dependencies added: MonadRandom, array, base, bio, bytestring, cmdargs, containers, directory, random
Files
- Setup.hs +3/−0
- flowsim.cabal +35/−0
- src/CloneSim.hs +82/−0
- src/Config.hs +147/−0
- src/EmpFile.hs +25/−0
- src/FlowSim.hs +186/−0
- src/Generations/Empirical.hs too large to diff
- src/Generations/GS20.hs +157/−0
- src/Generations/GenBase.hs +79/−0
- src/Generations/Titanium.hs +16/−0
- src/HPLCount.hs +44/−0
- src/Statistics.hs +154/−0
+ Setup.hs view
@@ -0,0 +1,3 @@+#!/usr/bin/env runhaskell+import Distribution.Simple+main = defaultMain
+ flowsim.cabal view
@@ -0,0 +1,35 @@+Name: flowsim+Version: 0.2.6+License: GPL++Author: Ketil Malde+Maintainer: Ketil Malde <ketil@malde.org>++Category: Bioinformatics+Synopsis: Simulate 454 pyrosequencing+Description: pyrosim - a simulator for 454 pyrosequencing data+ Simulate shotgun sequencing with Roche's 454 sequencing technology.+ .+ The Darcs repository is at <http://malde.org/~ketil/biohaskell/pyrosim>.++HomePage: http://bhlog.malde.org/+Build-Depends: bio >= 0.4.4, base >= 4 && <= 5, array >= 0.1, bytestring >= 0.9.1, random, MonadRandom, cmdargs, containers, directory+Build-Type: Simple+Tested-with: GHC==6.8.2++ -- Data-files: README+Executable: flowsim+Main-Is: FlowSim.hs+Other-Modules: Statistics, Config, EmpFile+ Generations.GenBase, Generations.GS20, + Generations.Titanium, Generations.Empirical+Hs-Source-Dirs: src++Executable: hplc+Main-Is: HPLCount.hs+Ghc-Options: -main-is HPLCount+Hs-Source-Dirs: src++Executable: clonesim+Main-Is: CloneSim.hs+Hs-Source-Dirs: src
+ src/CloneSim.hs view
@@ -0,0 +1,82 @@+{- | CloneSim - fragment a genome sequence to simulate cloning+ Factored out from flowsim in order to separate clone generation+ from flow simulation and base calling.+-}++{-# Language DeriveDataTypeable #-}++module Main where++import Bio.Sequence hiding ((!))+import Statistics++import System.IO (stdin,stdout,stderr,hPutStrLn)+import Control.Monad (forM)+import qualified Data.ByteString.Lazy as B+import Data.Int (Int64)+import System.Console.CmdArgs+import Data.Array++type Dist = String+data Conf = Conf + { lengths :: Dist+ , count :: Int+ , input :: [FilePath]+ } deriving (Data,Typeable,Show)++modes :: Mode Conf+modes = mode $ Conf { + lengths = "Uniform 400 800" &= text "model for clone lengths" & typ "DIST"+ , count = 10 &= text "number of reads to generate" & typ "INT"+ , input = def &= args & typFile+ } &= prog "clonesim"+ & text "simulate sequence cloning"+ & helpSuffix ["Available distributions (DIST):" + ," Uniform a b, Normal mu sigma, LogNormal mu sigma"]++version :: String+version = "clonesim v0.2.6, copyright 2010 Ketil Malde" ++data Dir = Fwd | Rev deriving (Eq,Enum,Bounded)++instance Random Dir where + random g = let (b,g') = random g in (if b then Fwd else Rev,g')+ randomR = error "randomR is undefined for Dir"++main :: IO ()+main = do+ conf <- cmdArgs version [modes]+ -- print conf+ let inf = case input conf of + [] -> hPutStrLn stderr "clonesim: reading from stdin" >> hReadFasta stdin+ [x] -> readFasta x+ _ -> error "Please specify only a single input file"+ ss <- map (defragSeq . castToNuc) `fmap` inf+ let sa = listArray (0,length ss-1) ss+ hWriteFasta stdout =<< evalRandIO (simulate conf sa)+ +type SeqArray = Array Int (Sequence Nuc)++-- | the real 'main'+simulate :: RandomGen g => Conf -> SeqArray -> Rand g [Sequence Nuc]+simulate conf sa = do+ let ldist = read $ lengths conf+ (_,asz) = bounds sa+ forM [1..count conf] $ const + (do i <- floor `fmap` sample (Uniform 0 $ 1+fromIntegral asz) -- inclusive?+ let s = sa!i+ p <- round `fmap` sample (Uniform 0 $ fromIntegral (seqlength s-1))+ l <- round `fmap` sample ldist+ dir <- getRandom+ return (mkClone dir p l s))+ +mkClone :: Dir -> Int64 -> Int64 -> Sequence Nuc -> Sequence Nuc+mkClone dir pos len (Seq h s mq) = + Seq (fromStr (toStr h++" "++show pos++case dir of Fwd -> "+"; Rev -> "-"))+ sd+ qual+ where sd = B.take len+ . (case dir of Fwd -> snd; Rev -> revcompl' . fst) + . B.splitAt pos $ s+ qual = B.take len `fmap` case dir of Fwd -> fst; Rev -> snd + `fmap` B.splitAt pos `fmap` mq
+ src/Config.hs view
@@ -0,0 +1,147 @@+{-| Module Config - replaces Options, use CmdArgs instead -}+{-# LANGUAGE DeriveDataTypeable #-}++module Config (Config(..), mkconf+ ,inform, whenLoud, whenNotQuiet) where++import Data.Char (toLower)+import Data.List (isPrefixOf, intersperse)+import System.Console.CmdArgs+import System.Directory (doesFileExist)+import Control.Monad (when)+import System.IO (hPutStrLn, stderr, stdin)+import EmpFile++import Bio.Sequence++import Generations.GenBase+import Generations.GS20+import Generations.Titanium+import Generations.Empirical++version :: String+version = "flowsim v0.2.6, copyright 2010 Ketil Malde"++-- data GenName = Titanium | FLX | GS20 deriving (Typeable, Data, Show, Eq)+type GenName = String+type Dist = String++data Config = Conf { generation :: GenName+ , degradation:: Dist+ , model :: FilePath+ , qualmethod :: GenName+ , discardfilters :: [String]+ , trimfilters :: [String]+ , flowkey :: String+ , hplinput :: FilePath+ , flowlength :: Int+ , flowcycle :: String+ , inputs :: [FilePath]+ , output :: FilePath+ } deriving (Typeable, Data, Show, Read)++modes :: Mode Config+modes = mode $ Conf + { generation = "Titanium" &= text "454 generation to simulate" & typ "GEN" & flag "G"+ , degradation = def &= text "model for degradation of the flow model" & typ "DIST"+ , model = def &= text "empirical distribution for flow generation" & typFile+ , qualmethod = def &= text "method for calculating quality" & typ "STRING"+ , discardfilters = def &= text "discarding filters to apply" & typ "DFILT"+ , trimfilters = def &= text "trimming filters to apply" & typ "TFILT"+ , flowkey = def &= text "sequence key to start each read (TCAG)"+ , hplinput = def &= text "input genome for HPL count estimate" & typFile+ , flowlength = def &= text "number of flow cycles to run"+ , flowcycle = def &= text "sequence nucleotides in each flow cycle (TACG)"+ , inputs = def &= args & typFile+ , output = def &= text "output file"+ } &= prog "flowsim"+ & text "simulate 454 pyrosequencing."+ & helpSuffix hs+ where + hs = ["Generations (GEN): "++concat (intersperse ", " $ map fst generations)+ , "Distributions (DIST): Uniform a b, Normal mu sigma, LogNormal mu sigma"+ , "Discarding filters (DFILT): ...."+ , "Trimming filters (TFILT): ...."]+ +mkconf :: IO (Generation,IO [Sequence Nuc],HPLprob,FilePath)+mkconf = do+ cf <- cmdArgs version [modes]+ let inp = map castToNuc `fmap` if null (inputs cf) then hReadFasta stdin else concat `fmap` mapM readFasta (inputs cf)+ gen <- mkgen cf+ whenLoud $ inform ("Generation: "++generation cf ++ "\n" ++ show gen)+ when (null $ output cf) $ error "Please specify an output file with -o"+ hplc <- case hplinput cf of + [] -> return default_hplc+ file -> (mkHPLprobs . freqtable . concatMap (hpls (f_cycle gen) . seqdata)) `fmap` readFasta file+ return (gen, inp, hplc, output cf)+ +default_hplc :: HPLprob+default_hplc _ l = 3/4**fromIntegral l++generations :: [(GenName,Generation)]+generations = [("GS20", gs20), ("Titanium",titanium),("EmpTitanium",tiEmp)]++lookupGen :: String -> Generation +lookupGen g = case map snd . filter (isPrefixOf (map toLower g) . map toLower . fst) $ generations of+ [x] -> x+ _ -> error ("Generation '"++g++"' is non-existing or ambigous\nAvailable generations are: "++show (map fst generations))++-- if non-null, pick field f from generation str, else pick it from the default+setFromGen :: Generation -> (Generation -> field) -> String -> field+setFromGen dflt f str = if null str then f dflt else f (lookupGen str)++-- similar, but use Read to parse the string+setFromStr :: (Read a) => Generation -> (Generation -> a) -> String -> a+setFromStr dflt f str = if null str then f dflt else read str+ +mkgen :: Config -> IO Generation +mkgen (Conf g deg fm qm df tf fk hpl fl fc _inputs _output) = do+ let gen = lookupGen g+ setG = setFromGen gen+ setD = setFromStr gen + setF fs | null fs = disc_filters gen+ | otherwise = concatMap (maybe [] id) $ map (flip lookup filterlist) fs+ setT fs | null fs = trim_filters gen+ | otherwise = concatMap (maybe [] id) $ map (flip lookup trimlist) fs+ my_qcall = if null qm then qcall gen + else case qm of + "gs20tab" -> qual_gs20_tab+ "dexact" -> qual_exact_decreasing+ "fexact" -> qual_exact_fixed + _ -> error ("No such quality call method:"++show qm+ ++"\nAvailable methods: gs20tab, dexact, fexact.")+ my_model <- if null fm then return (models gen)+ else do+ f <- doesFileExist fm+ ms <- if f then readPdf fm else return (parse_models fm)+ return $ combine_models (models gen) ms+ return $ gen + { qcall = my_qcall+ , degrade = setD degrade deg+ , models = my_model+ , disc_filters = setF df + , trim_filters = setT tf+ , f_key = setG f_key fk+ , f_len = if fl > 0 then fl else f_len gen+ , f_cycle = setG f_cycle fc+ }++parse_models :: String -> [Distribution]+parse_models str = read ("["++str++"]")++-- filterlist :: [DiscardFilter]+filterlist = [] -- todo: export from SFF_filters++-- trimlist :: [Trimfilter]+trimlist = [] ++-- Logging+inform :: String -> IO ()+inform = hPutStrLn stderr++whenLoud, whenNotQuiet :: IO () -> IO ()+whenLoud action = flip when action =<< isLoud+-- note that isQuiet = return False in CmdArgs!+whenNotQuiet action = do n <- isNormal+ l <- isLoud+ when (n || l) action
+ src/EmpFile.hs view
@@ -0,0 +1,25 @@+module EmpFile where++import Statistics+import Control.Monad (when)++readPdf :: FilePath -> IO [Distribution]+readPdf f = do + cs <- lines `fmap` readFile f+ return (parsePdf ("file '"++f++"'") cs) + +parsePdf :: String -> [String] -> [Distribution]+parsePdf f cs = + let (_:fs:vss) = transpose (map words cs)+ in if (or $ zipWith (/=) [0..] (map read fs))+ then error ("Flow index from "++f++" isn't [0..]!")+ else map (fromPdf 0 0.01 . map (P . read)) vss++transpose xs = let r0 = map head xs + rest = map tail xs+ in if any null rest then [r0] else r0 : transpose rest++-- currently this only works for a single model+combine_models :: [Int -> Distribution] -> [Distribution] -> [Int -> Distribution]+combine_models [f] ds = [\i -> if i < length ds then ds!!i else f i]+combine_models _ _ = error "Can't combine multiple models"
+ src/FlowSim.hs view
@@ -0,0 +1,186 @@+{- | FlowSim - simulate 454 flowgrams from a reference genome ++ Flow values are modelled from a log-normal noise, and a sequence of+ normal distributions, one for each homopolymer length. These distributions+ can be estimated from real data.++ Todo:+ * Paired ends models B-linker-A+ * Support multiple sequences:+ - scan seqs + lenghts+ - gen n numbers (0..total length), transform to deltas (cf. rselect)+ - sort and generate++-}+{-# options -XParallelListComp #-}++module Main where++import Bio.Sequence+import Bio.Sequence.SFF++import qualified Data.ByteString.Lazy.Char8 as B+import qualified Data.ByteString.Lazy as BL+import qualified Data.ByteString.Char8 as BS+import qualified Data.ByteString as BS2++import Data.Char (toUpper)+import Data.Int++import Statistics+import Generations.GenBase+import Config++import Control.Monad (when)++-- ------------------------------------------------------------+-- picking random postions/directions for reads++data Dir = Fwd | Rev deriving (Eq,Enum,Bounded)++instance Random Dir where + random g = let (b,g') = random g in (if b then Fwd else Rev,g')+ randomR = error "randomR is undefined for Dir"++main :: IO ()+main = do+ (gen,is,hplc,o) <- mkconf+ + ss <- is+ case ss of [] -> error ("Input appears to be empty?")+ _ -> return ()+ sff <- evalRandIO $ sim454 gen hplc ss+ n <- writeSFF' o sff+ whenLoud $ inform ("Wrote "++show n++" reads to '"++o++"'.")++-- testing+test_s :: Sequence Nuc+test_s = Seq (fromStr "foo") (fromStr "aacacattcgtggtnagctacggaacacattcgtggtnagctacggaacacattcgtggtnagctacggaacacattcgtggtnagctacgg") Nothing++-- | Heavy lifting. Building an SFF file from the specified information+sim454 :: RandomGen g => Generation -> HPLprob -> [Sequence Nuc] -> Rand g SFF+sim454 gen hplc ss = do+ let ch = makeCommonHeader gen+ tf r = foldr ($) r $ trim_filters gen + df r = and $ zipWith ($) (disc_filters gen) (repeat r)+ rbs <- map tf `fmap` filter df `fmap` mapM (\s -> makeReadBlock gen hplc s ch) ss+ return (SFF ch rbs)++-- Generate a sequence of models+-- The generation specifies a series of initial models, this function+-- uses these with the degradation to generate a progression of models to use +makeModels :: RandomGen g => Generation -> Rand g [Model] +makeModels gen = case models gen of+ [m] -> iterativeWorsen (f_len gen) (degrade gen) m+ im@(_:_) -> do+ let ns = f_len gen `div` length im+ return $ concat $ map (replicate ns) im++iterativeWorsen :: RandomGen g => Int -> Distribution -> Model -> Rand g [Model]+iterativeWorsen 0 _ _ = return []+iterativeWorsen count deg m = do + ps <- perturbs 1 count+ return $ zipWith (fmap . worsen) ps $ replicate count m+ where perturbs _ 0 = return []+ perturbs cur n = do + w <- sample deg+ let new = cur+w+ rest <- perturbs new (n-1)+ return (new : rest)++-- --------------------------------------------------+-- Generate the flow values++-- generate the "absolute" flow values from the cycle and the origin sequence data+makeFlows :: [Char] -> SeqData -> [(Char,Int)]+makeFlows c s | B.null s = []+ | otherwise = let (c1,s1) = makeCycle [] (take 4 c) s + s2 = case B.uncons s1 of Just (x,_) -> if not (toUpper x `elem` "ACGT") then B.tail s1 else s1; _ -> s1+ in c1 ++ makeFlows c s2++makeCycle :: [(Char,Int)] -> [Char] -> SeqData -> ([(Char,Int)],SeqData)+makeCycle acc [] s = (reverse acc, s)+makeCycle acc (c:cs) s = let (this,rest) = B.span ((==toUpper c).toUpper) s+ in makeCycle ((c,fromIntegral $ B.length this):acc) cs rest++-- | Takes a sequence of flows with exact homopolymer lengths, +-- permutes and calls them. Next step is prepareData+permuteAndCall :: RandomGen g => Generation -> HPLprob -> [(Char,Int)] -> + Rand g [(Flow,[Char],[Qual])]+permuteAndCall gen hplc fs = do+ -- when (trace (show fs) False) (return ())+ let n = fromIntegral $ f_len gen+ flow_cont = drop (length fs `mod` length (f_cycle gen)) $ cycle (f_cycle gen)+ xs = fs ++ zip flow_cont (replicate (n-length fs) 0)+ ms <- makeModels gen+ -- if and $ zipWith (==) (map fst xs) (cycle $ f_cycle gen) then return () + -- else error (map fst xs ++ "\n don't cycle: "++f_cycle gen)+ sequence $ take n $ zipWith (my_call (qcall gen) hplc) ms xs++-- Titanium base/quality calling+my_call :: RandomGen g => QualMethod -> HPLprob -> Model -> (Char,Int) -> + Rand g (Flow,[Char],[Qual])+my_call qm ft md (c,hpl) = do+ f <- sample (md hpl)+ let fi = max 0 . round . (100*) $ f+ n = fromIntegral ((fi+50) `div` 100)+ cs = replicate n c+ qs = qm ft md (c,fi)+ when (length qs /= n) $ error ("Qual mismatch: "++show (f,fi,n,cs,qs))+ return (fi, cs, qs)++-- | Somewhat advanced unzip, calculating the index in the process.+-- Also replace three consequtive empty lists with Ns+convertCalls :: [(Flow,[Char],[Qual])] -> ([Flow],[Char],[Qual],[Int])+convertCalls = go 0 . addDots+ where go _ [] = ([],[],[],[])+ go p ((f,cs,qs):fs) + | null cs = let (f',c',q',i') = go (p+1) fs+ in (f:f',c',q',i')+ | otherwise = let (f',c',q',i') = go 0 fs+ in (f:f',cs++c',qs++q',(p+1):replicate (length cs-1) 0 ++ i')+ + addDots ((f1,cs1,qs1):(f2,cs2,qs2):(f3,cs3,qs3):(f4,cs4,qs4):rest)+ | null cs1 && null cs2 && null cs3 && not (null cs4) = (f1,cs1,qs1):(f2,cs2,qs2):(f3,"N",[0]):addDots ((f4,cs4,qs4):rest)+ | otherwise = (f1,cs1,qs1) : addDots ((f2,cs2,qs2):(f3,cs3,qs3):(f4,cs4,qs4):rest)+ addDots fewerThanThree = fewerThanThree++-- | Generate a ReadBlock+-- direction and position chosen at random, and encoded in the read name+makeReadBlock :: RandomGen g => Generation -> HPLprob -> Sequence Nuc -> CommonHeader -> Rand g ReadBlock+makeReadBlock g hplc sq ch = do+ let sdata = seqdata sq+ rn = BS.concat $ BL.toChunks $ seqlabel sq+ fs = makeFlows (BS.unpack $ flow ch) $ BL.concat [BL.fromChunks [key ch], {- B.take (floor cl) $ -} sdata]+ (pfs,cs,qs,is) <- convertCalls `fmap` permuteAndCall g hplc fs+ return $ verifyRB (flow_length ch) $ ReadBlock {+ read_header = ReadHeader {+ name_length = fromIntegral $ BS.length rn -- :: Int16+ , num_bases = fromIntegral $ length cs -- :: Int32+ , clip_qual_left = 5 -- :: Int16+ , clip_qual_right = fromIntegral $ length cs -- :: Int16+ , clip_adapter_left = 0 -- :: Int16+ , clip_adapter_right = 0 -- :: Int16+ , read_name = rn -- :: ByteString+ }+ -- The data block+ , flow_data = packFlows pfs -- :: [Flow]+ , flow_index = BS2.pack $ map fromIntegral is -- :: ByteString+ , bases = fromStr cs -- :: SeqData+ , quality = BL.pack qs -- :: QualData+ }++-- | Consistency check on generated ReadBlocks.+verifyRB :: Int16 -> ReadBlock -> ReadBlock+verifyRB fl rb + | name_length rh == 0 = err "name_length is zero"+ | num_bases rh == 0 = err "num_bases is zero"+-- | clip_qual_left rh > clip_qual_right rh = err "clipping gives negative sequence"+ | BS2.length (read_name rh) /= (fromIntegral $ name_length rh) = err "read_name has incorrect length"+ | BS.length (flow_data rb) `div` 2 /= fromIntegral fl = err ("Number of flows ("++show (BS.length (flow_data rb) `div` 2)++")do not match flow_length of "++show fl++" in CommonHeader")+ | BS.length (flow_data rb) `div` 2 < (fromIntegral $ sum $ BS2.unpack $ flow_index rb) = err "flow_index longer than flows"+ | B.length (bases rb) /= (fromIntegral $ BS.length $ flow_index rb) = err ("bases ("++show (B.length (bases rb))++") and flow_index ("++show (BS.length $ flow_index rb)++") have different lengths")+ | B.length (quality rb) /= (fromIntegral $ BS.length $ flow_index rb) = err ("quality ("++show (B.length (quality rb))++") and flow_index ("++show (BS.length $ flow_index rb)++") have different lengths")+ | otherwise = rb+ where rh = read_header rb + err str = error (str ++ "\n" ++ show rb)
+ src/Generations/Empirical.hs view
file too large to diff
+ src/Generations/GS20.hs view
@@ -0,0 +1,157 @@+module Generations.GS20 where++import Generations.GenBase++import Data.Array+import qualified Data.ByteString.Char8 as BC+import qualified Data.ByteString as B+import Control.Monad (when)++type QualTable = Array Flow B.ByteString++-- | Wrapper around 'array' that interpolates missing values+-- Todo: make this more sophisticated!+mkQualTable :: (Flow,Flow) -> [(Flow,B.ByteString)] -> QualTable+mkQualTable is = array is . map extend . interpolate++interpolate :: [(Flow,B.ByteString)] -> [(Flow,B.ByteString)]+interpolate ((x1,y1):(x2,y2):rest)+ = [(x,y1) | x <- [x1..x2-1]]++interpolate ((x2,y2):rest)+interpolate xs = xs++extend :: (Flow,B.ByteString)-> (Flow,B.ByteString)+extend (x,y) = let delta = ((x+50) `div` 100) - fromIntegral (B.length y)+ in (x,B.concat [y,B.replicate (fromIntegral delta) 1])++gs20 :: Generation+gs20 = Gen {+ name = "GS20"+ , models = [\h -> let h' = fromIntegral h + in if h == 0 then LogNormal (negate 2.5) 0.2 else Normal h' (0.04+0.06*h')]+ , qcall = qual_gs20_tab+ , degrade = Normal 0.005 0.002+ , disc_filters = [filter_key,filter_empty]+ , trim_filters = []+ + , f_key = "TCAG"+ , f_len = 168 -- :: Int16+ , f_cycle = "TACG"+ }+++qual_gs20_tab :: QualMethod+qual_gs20_tab _ _ (_,fi) = B.unpack (gs20qt!fi)++gs20qt :: QualTable+gs20qt = mkQualTable (0,3100) $ map (\(x,y) -> (x,BC.pack y)) [+ (0,""),(1,""),(2,""),(3,""),(4,""),(5,""),(6,""),(7,""),(8,""),(9,""),(10,"")+ ,(11,""),(12,""),(13,""),(14,""),(15,""),(16,""),(17,""),(18,""),(19,""),(20,"")+ ,(21,""),(22,""),(23,""),(24,""),(25,""),(26,""),(27,""),(28,""),(29,""),(30,"")+ ,(31,""),(32,""),(33,""),(34,""),(35,""),(36,""),(37,""),(38,""),(39,"")+ ,(40,""),(41,""),(42,""),(43,""),(44,""),(45,""),(46,""),(47,""),(48,""),(49,"")+ ,(50,"\b"),(51,"\b"),(52,"\b"),(53,"\t"),(54,"\t"),(55,"\n"),(56,"\n"),(57,"\n"),(58,"\n"),(59,"\v")+ ,(60,"\v"),(61,"\f"),(62,"\r"),(63,"\r"),(64,"\r"),(65,"\r"),(66,"\SO"),(67,"\SI"),(68,"\SI"),(69,"\DLE")+ 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+ src/Generations/GenBase.hs view
@@ -0,0 +1,79 @@+module Generations.GenBase ( Model, QualMethod+ , Generation(..), makeCommonHeader+ , qual_exact_fixed, qual_exact_decreasing+ , module Bio.Sequence.SFF+ , module Bio.Sequence.SFF_filters+ , module Statistics + , module HPLCount+ ) where++import qualified Data.ByteString.Char8 as BC+import Bio.Sequence.SFF+import Bio.Sequence.SFF_filters++import Debug.Trace (trace)++import Statistics+import HPLCount hiding (main)++type Model = Int -> Distribution -- ^ each hpl length has its own distribution of flow values++type QualMethod = HPLprob -> Model -> (Char,Flow) -> [Qual]++data Generation = Gen {+ name :: String+ , qcall :: QualMethod -- ^ use the current model and hpl lenght to generate qual data+ , models :: [Model] -- ^ a progression of initial models for the sequence of flows+ , degrade :: Distribution -- the amount to increase a stdev multiplier each position+ , disc_filters :: [DiscardFilter]+ , trim_filters :: [TrimFilter]+ -- stuff to build the commonheader from+ , f_key :: String+ , f_len :: Int+ , f_cycle :: String+ -- readblock :: [ReadBlock] ?+ }++instance Show Generation where+ show g = "Config:\n" ++ unlines (map (" "++)+ ["key: "++f_key g+ ,"flowlength: "++show (f_len g), "flow cycle: "++show (f_cycle g)+ ])+-- ,"flow distributions:"])+-- ++ unlines [" "++show i++": "++show (model g i) | i <- [0..6]]++-- | Calculate exact qualities from model using Bayes' theorem+-- This should emulate Marguiles et al.'s method. +qual_exact_decreasing :: HPLprob -> Model -> (Char,Flow) -> [Qual]+qual_exact_decreasing ft m (c,flow) = + let f = fromIntegral flow / 100+ prob hpl | hpl > 20 = error "can't handle hpls > 20" + | otherwise = ft c hpl * pdf (m hpl) f / sum [pdf (m x) f * ft c x | x <- [0..20]]+ probs = drop 1 $ scanl (+) 0 $ map prob [0..20]+ quals = map (round . max 0 . min 60 . ((-10)*) . logBase 10) $ probs+ in -- trace ("#"++show (c,flow) ++"\n"++show probs ++"\n"++show quals) $+ take (fromIntegral $ (flow+50) `div` 100) $ quals+ +-- | Using Bayes, but only calculating the probablity of the call lenght+-- being correct. Should be similar to Titanium (but is it?)+qual_exact_fixed :: HPLprob -> Model -> (Char,Flow) -> [Qual]+qual_exact_fixed ft m (c,flow) = + let f = fromIntegral flow / 100+ hpl = fromIntegral $ (flow+50) `div` 100+ prob = ft c hpl * pdf (m hpl) f / sum [pdf (m x) f * ft c x | x <- [0..20]]+ in replicate hpl (round $ max 0 . min 60 $ (-10) * logBase 10 (1-prob))++-- --------------------------------------------------+-- Putting it together+makeCommonHeader :: Generation -> CommonHeader+makeCommonHeader g = CommonHeader+ { index_offset = 0+ , index_length = 0+ , key_length = fromIntegral $ length $ f_key g+ , flowgram_fmt = 1+ , key = BC.pack $ f_key g++ , num_reads = 0 -- fromIntegral $ n_reads g+ , flow_length = fromIntegral $ f_len g+ , flow = BC.pack $ concat $ replicate (f_len g `div` (length $ f_cycle g)) $ f_cycle g+ }
+ src/Generations/Titanium.hs view
@@ -0,0 +1,16 @@+module Generations.Titanium where+import Generations.GenBase++titanium :: Generation+titanium = Gen+ { name = "Titanium"+ , qcall = qual_exact_fixed+ , models = [\h -> let h' = fromIntegral h + in if h == 0 then LogNormal (negate 2.5) 0.2 else Normal h' (0.04+0.05*h')]+ , degrade = Normal 0.001 0.001+ , disc_filters = [filter_key,filter_empty]+ , trim_filters = []+ , f_key = "TCAG"+ , f_len = 800 -- :: Int16+ , f_cycle = "TACG"+ }
+ src/HPLCount.hs view
@@ -0,0 +1,44 @@+-- count homopolymer distributions in a fasta file+module HPLCount where++import Bio.Sequence+import qualified Data.ByteString.Lazy.Char8 as B+import qualified Data.Map as M+import Text.Printf+import Data.Char (toUpper)+import Data.List (intersperse)+import Data.Maybe (fromJust)+import System.Environment++type HPLprob = Char -> Int -> Double++-- lookup and return probability of this hpl length for this letter+mkHPLprobs :: M.Map (Char,Int) Int -> HPLprob+mkHPLprobs ft = let totals = [(c, fromIntegral $ sum [M.findWithDefault 0 (c,x) ft | x <- [0..50]]) | c <- "ACGT" ]+ in \ch n -> fromIntegral (M.findWithDefault 0 (ch,n) ft) / fromJust (lookup ch totals)++main = do+ [f] <- getArgs+ display "tacg" . freqtable . concatMap (hpls "tacg" . seqdata) =<< readFasta f++display :: [Char] -> M.Map (Char,Int) Int -> IO ()+display fs m = let imax = maximum $ map snd $ M.keys m+ header = concat ("len\t " : intersperse "\t " (map (return . toUpper) fs))+ in putStrLn $ unlines (header : [ printf "%3d" i ++ concat [ printf "\t%5d" (M.findWithDefault 0 (c,i) m) | c <- map toUpper fs ] | i <- [0..imax]])++freqtable :: [(Char,Int)] -> M.Map (Char,Int) Int+freqtable = go M.empty + where+ go m [] = m+ go m (i:is) = let v = M.findWithDefault 0 i m + v' = v+1+ m' = M.insert i v' m+ in v' `seq` m' `seq` go m' is+ +hpls :: [Char] -> SeqData -> [(Char,Int)]+hpls xs = go (cycle xs')+ where xs' = map toUpper xs+ go (f:fs) sd | B.null sd = []+ | not (elem (toUpper $ B.head sd) xs') = go (f:fs) (B.tail sd)+ | otherwise = let (this,rest) = B.span ((==f).toUpper) sd+ in (f,fromIntegral (B.length this)) : go fs rest
+ src/Statistics.hs view
@@ -0,0 +1,154 @@+{-# LANGUAGE ForeignFunctionInterface #-}++-- | Yet another simple module for implementing statistics stuff.+module Statistics (sample, samples, normal, normals+ , stdnormal, stdnormals, Distribution(..), Prob(..)+ , pdf, pvalue, fromPdf, invcum, worsen+ , module Control.Monad.Random+ ) where++import Control.Monad.Random+import Data.Array.Unboxed++foreign import ccall "erf" erf :: Double -> Double++newtype Prob = P Double deriving Show++instance Random Prob where+ random g = let (a,g') = randomR (0,1) g in (P a,g')+ randomR = error "Specifying a range for a probability makes no sense."++-- Todo: implement+data Distribution = Normal Double Double -- ^ mu and sigma+ | LogNormal Double Double -- ^ mu and sigma+ | Uniform Double Double -- ^ from/to inclusive+ | Empirical Double Double (UArray Int Double) + -- ^ Stores a cumulative distribution, centered on first + -- param (ref. 'worsen'), and second param is step size+ deriving (Show,Read)+ -- add more: StudentsT, SkewNormal, SkewT++-- dummy to make deriving Read work+instance Read (UArray i d) where++-- | Build an empirical probablility distribution by mapping the given probabilities+-- to uniformly spaced points starting at 'start' with 'step' points per unit.+-- Automatically center on pvalue = 50. +fromPdf :: Double -> Double -> [Prob] -> Distribution+fromPdf start h ps = let ps' = acc 0 $ map ((/scale) . unprob) $ ps+ mu = start+(fromIntegral . length . takeWhile (<0.5)) ps'*h-h/2+ a = floor ((start-mu)/h)+ b = a+length ps'+ scale = sum [ x | P x <- ps]+ unprob (P x) = x+ acc _ [] = [1]+ acc c (x:xs) = let v = c+x+ in if v >= 1 then [1] else v : acc v xs+ in Empirical mu h $ listArray (a,b) (0:ps')++invcum :: Distribution -> Prob -> Double+invcum (Normal mu sigma) (P z) = invcumnorm mu sigma z+invcum (LogNormal mu sigma) (P z) = exp $ invcum (Normal mu sigma) (P z)+invcum (Uniform a b) (P z) = a+(b-a)*z+invcum (Empirical mu h cd) (P z) = let (a,b) = bounds cd in mu+bisect ((cd!).round) (fromIntegral a) (fromIntegral b) z * h+++-- | Calculate probability of sampling less than x+-- (i.e. the cumulative distribution's value in x)+pvalue :: Distribution -> Double -> Prob+pvalue (Normal mu sigma) x = P (cumnorm mu sigma x)+pvalue (Uniform a b) x | x <= a = P 0 + | x >= b = P 1+ | otherwise = P ((x-a)/(b-a))+pvalue (LogNormal mu sigma) x | x<1e-10 = P 0 -- not sufficient!+ | otherwise = P (cumlognorm mu sigma x)+pvalue (Empirical mu h cd) x = let (a,b) = bounds cd+ x' = (x-mu)/h+ in if x' < fromIntegral a then P 0+ else if x' >= fromIntegral b then P 1+ else let x1 = floor x'+ x2 = x1+1+ y1 = cd!x1+ y2 = cd!x2+ in P (y1 + (y2-y1)*(x'-fromIntegral x1))++-- general functions for sampling++sample :: RandomGen g => Distribution -> Rand g Double+sample d = invcum d `fmap` getRandom++-- sample (Uniform a b) = getRandomR (a,b)+-- todo: replace with general function:+samples :: RandomGen g => Distribution -> Rand g [Double]+samples (Normal mu sigma) = normals mu sigma+samples (LogNormal mu sigma) = map exp `fmap` samples (Normal mu sigma)+samples (Uniform a b) = getRandomRs (a,b)+samples (Empirical _mu _h _cds) = error "todo: implement 'samples' for Empirical distributions"++-- | The probability density function+pdf :: Distribution -> Double -> Double -- Prob?+pdf (Normal mu sigma) x = exp(negate(square (x-mu)/(2*square sigma)))/(sigma*sqrt(2*pi))+pdf (LogNormal mu sigma) x+ | x>0 = exp(negate(square (log x-mu)/(2*square sigma)))/(x*sigma*sqrt(2*pi))+ | otherwise = 0+pdf (Uniform a b) x+ | x<b && x>= a = 1/(b-a) -- interval is open on the right, to work correctly with empirical below+ | otherwise = 0+pdf (Empirical mu h cd) x = let (a,b) = bounds cd+ x' = (x-mu)/h+ in if x' < fromIntegral a then 0+ else if x' >= fromIntegral b then 0+ else let x1 = floor x'+ x2 = x1+1+ y1 = cd!x1+ y2 = cd!x2+ in (y2-y1)/h+-- ------------------------------+-- Specifics+-- ------------------------------+square :: Double -> Double+square x = x * x++stdnormal :: RandomGen g => Rand g Double+stdnormal = normal 0 1++stdnormals :: RandomGen g => Rand g [Double]+stdnormals = normals 0 1++normal :: RandomGen g => Double -> Double -> Rand g Double+normal mu sigma = do x <- getRandomR (0,1)+ return (invcumnorm mu sigma x)++normals :: RandomGen g => Double -> Double -> Rand g [Double]+normals mu sigma = do x <- normal mu sigma+ xs <- normals mu sigma+ return (x : xs)++-- support+invcumnorm :: Double -> Double -> Double -> Double+invcumnorm mu sigma z = mu + bisect (cumnorm 0 sigma) (-limit*sigma) (limit*sigma) z++bisect :: (Double -> Double) -> Double -> Double -> Double -> Double+bisect f a b z = let c = (a+b)/2+ cn = f c+ in if abs (z - cn) < 10*epsilon || abs (a-b) < epsilon then c+ else if cn > z then bisect f a c z+ else bisect f c b z++cumnorm :: Double -> Double -> Double -> Double+cumnorm mu sigma x = 0.5*(1+erf((x-mu)/(sigma*sqrt 2)))++cumlognorm :: Double -> Double -> Double -> Double+cumlognorm mu sigma x = 0.5+0.5*erf ((log x-mu)/(sigma*sqrt 2))++epsilon, limit :: Double+epsilon = 0.0000000001+limit = 4.4++-- | Make a distribution wider by expanding (or contracting, if less than 1) +-- its stdev by some factor+worsen :: Double -> Distribution -> Distribution+worsen d (Normal mu sigma) = Normal mu (sigma*d)+worsen d (LogNormal mu sigma) = LogNormal mu (sigma*d)+worsen d (Uniform a b) = Uniform (a*(1-d)) (b*d) -- assumption alert?+worsen d (Empirical mu h ds) = Empirical mu (h*d) ds