dephd (empty) → 0.0
raw patch · 6 files changed
+710/−0 lines, 6 filesdep +basedep +biodep +bytestringsetup-changed
Dependencies added: base, bio, bytestring, directory, process, regex-compat
Files
- LICENSE +340/−0
- README +64/−0
- Setup.hs +5/−0
- TODO +11/−0
- dephd.cabal +25/−0
- src/Dephd.hs +265/−0
+ LICENSE view
@@ -0,0 +1,340 @@+ GNU GENERAL PUBLIC LICENSE+ Version 2, June 1991++ Copyright (C) 1989, 1991 Free Software Foundation, Inc.+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++ Preamble++ The licenses for most software are designed to take away your+freedom to share and change it. By contrast, the GNU General Public+License is intended to guarantee your freedom to share and change free+software--to make sure the software is free for all its users. This+General Public License applies to most of the Free Software+Foundation's software and to any other program whose authors commit to+using it. (Some other Free Software Foundation software is covered by+the GNU Library General Public License instead.) You can apply it to+your programs, too.++ When we speak of free software, we are referring to freedom, not+price. 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+ README view
@@ -0,0 +1,64 @@+ Synopsis+ --------++dephd - A simple tool for base calling and quality appraisal++Reads files in phd-format (phred output), either specified individually,+or in a directory (use the --dir option to read directories).++ Installation+ ------------++You need the GHC compiler, or if you know what you are doing, another+Haskell compiler or interpreter with Cabal. You also need to install+the 'bio' library (darcs get http://malde.org/~ketil/bio)++With those things in place, you should be able to do++ runhaskell Setup configure+ runhaskell Setup build+ sudo runhaskell Setup install++Optionally, add "--prefix $HOME" (without the quotes) after configure+to install to your home directory - in which case you don't need the 'sudo'.+++ Usage+ -----++ dephd --rank files..+ dephd --rank --dir dirs..++Outputs (to standard output) a summary of all phd files, including+sequence name, average quality, length of longest contiguous run with+qualities >= 15, 20 and 30, and longest run with sliding average+quality 20 or better.++ dephd --call files..+ dephd --call --dir dirs..++Produce files 'dephd.fasta' and 'dephd.qual' in the current directory,+containing sequence and quality data, respectively. Bases estimated+(currently very conservatively) to be of good quality are in upper+case, very low quality is output as lower case 'n's.++ dephd --plot files..+ dephd --plot --dir dirs..+ dephd --plot -X files..+ dephd --plot -X --dir dirs..++Produce a plot of sequence quality, along with a sliding average.+With -X display it directory, without -X, produce a jpg file with the+plot. A similar option --plotall generates and displays all plots+directly, instead of one at a time (only useful with -X as well).+++ Bugs+ ----++Not many, I hope. Specifying more than one action at a time will pull+all sequences into memory, but a single action should stream okay.+Approx 15K phd-files can be --call'ed OR --plot'ed OR --rank'ed with+less than 100Mb of RAM.++For further questions, email me at <ketil@malde.org>
+ Setup.hs view
@@ -0,0 +1,5 @@+#!/usr/bin/env runhaskell+ +import Distribution.Simple+main = defaultMain+
+ TODO view
@@ -0,0 +1,11 @@+TODO:++* plotall is unreliable - why? + prob 1: it terminates before spawning all gnuplots (few inputs)+ prob 2: it fails to terminate at all (on many inputs)++* check for gnuplot in $PATH, and give informative error message++* parse qual files as well as phd files++* do base calling with quality measures.
+ dephd.cabal view
@@ -0,0 +1,25 @@+Name: dephd+Version: 0.0+License: GPL+License-File: LICENSE++Author: Ketil Malde+Maintainer: Ketil Malde <ketil@malde.org>++Category: Bioinformatics+Synopsis: Analyze 'phred' output (.phd files)+Description: dephd - A simple tool for base calling and quality appraisal.+ .+ Reads files in phd-format (phred output), either specified individually,+ or in a directory (use the --dir option to read directories).+ The Darcs repository is at <http://malde.org/~ketil/dephd>.++Build-Depends: base>3, bio >= 0.3, regex-compat, bytestring==0.9.0.1, process, directory+Build-Type: Simple+Tested-with: GHC==6.8.3++Data-files: README, TODO+Executable: dephd+Main-Is: Dephd.hs+Hs-Source-Dirs: src+Ghc-Options: -Wall -O2 -funbox-strict-fields
+ src/Dephd.hs view
@@ -0,0 +1,265 @@+{- Dephd - decode phd (phred output) files.++ Generates seq/qual output, quality plots, or rankings.+-}++module Main where++import Control.Concurrent+import Control.Monad+import Data.Char+import Data.List (tails,groupBy,sortBy)+import Data.Maybe+import System.Console.GetOpt+import System.Directory+import System.Environment (getArgs)+import System.Exit+import System.IO+import System.IO.Unsafe+import System.Process+import Text.Printf+import Text.Regex+import qualified Data.ByteString.Lazy.Char8 as B++import Bio.Sequence++-- ------------------------------------------------------------+-- Option Handling+-- ------------------------------------------------------------++data MyOpts = O { actions :: [(FilePath,Sequence) -> IO ()] -- ^ Apply to each sequence+ , outputs :: [Handle] -- ^ Output handles that must be closed+ , filters :: (FilePath,Sequence) -> (FilePath,Sequence) -- ^ Filter sequences before processing+ , inputs :: [String] -> IO [(FilePath,Sequence)] -- ^ Turn args into sequences+ , verbose :: Bool -- ^ Verbose output (progress reporting) and sequence trimming+ }++defaultopts :: MyOpts+defaultopts = O { actions = [], outputs = [], filters = id+ , inputs = readFiles, verbose = False }++getOptions :: IO (MyOpts, [String], [String])+getOptions = do+ (os,ns,es) <- getArgs >>= (return . getOpt Permute options)+ os' <- foldl (>>=) (return defaultopts) os+ return (os',ns,es)++options :: [OptDescr (MyOpts -> IO MyOpts)]+options =+ [ Option ['v'] [] (NoArg (\opt -> return opt {verbose = True})) "Verbose output"+ , Option ['h'] ["help"] (NoArg (\_ -> do {putStrLn (usage []); exitWith ExitSuccess}))+ "Display usage information"+ -- Output options+ , Option ['R'] ["output-ranks"] (ReqArg setrank "file") "Set ranked output file"+ , Option ['F'] ["output-fasta"] (ReqArg setfasta "file") "Set fasta output file"+ , Option ['Q'] ["output-qual"] (ReqArg setqual "file") "Set quality output file"+ , Option ['P'] ["output-plot"] (NoArg (setplot False)) "Generate quality plots"+ , Option ['X'] ["output-xplot"] (NoArg (setplot True)) "Display quality plots"++ -- Filter options+ , Option ['t'] ["filter-trim"] (NoArg filterTrim) "Trim output sequences"+ , Option ['q'] ["filter-qual"] (NoArg filterQual) "Mask by quality"+ -- Input options+ , Option [] ["input-dirs"] (NoArg (\opt -> return opt { inputs = readDirs }))+ "Read directories containing PHD files"+ , Option [] ["input-list"] (NoArg inputList) "Read the files listed in an index file"+ , Option ['i'] ["input-fasta-qual"] (NoArg inputFQ) "Read a fasta- and optionally a qual file"+ ]+ where+ inputList opt = return $ opt { inputs = \args -> case args of+ [arg] -> do s <- readFile arg+ readFiles $ lines s+ _ -> error ("Please specify only one file for list input: "++show args)}+ inputFQ opt = return $ opt+ { inputs = \arg -> do ss <- case arg of [fa,q] -> readFastaQual fa q+ [fa] -> readFasta fa+ _ -> error ("Too many files specified for fasta/qual input: "++show arg)+ return $ map (\s -> (toStr $ seqlabel s, s)) ss }+ addFilter act opt = let f = filters opt in return $ opt { filters = f . act }+ filterTrim = addFilter trimSeq+ filterQual = addFilter (\(p,s) -> (p,qualAdjust s))+ addAction act arg opt = let as = actions opt+ hs = outputs opt+ in do h <- openFile arg WriteMode+ return opt { actions = act h:as+ , outputs = h:hs }++ setrank = addAction (\h -> hPutStrLn h . unwords {- columns -} . qualchk . snd)+ setfasta = addAction (\h -> hWriteFasta h . return . snd)+ setqual = addAction (\h -> hWriteQual h . return . snd)+ setplot b opt = do+ g <- hasgp+ if g then let as = actions opt in return $ opt { actions = plot b : as }+ else error ("You requested quality plots, but I can't find 'gnuplot' in your search path.\n")++trimSeq :: (FilePath,Sequence) -> (FilePath,Sequence)+trimSeq (i,s@(Seq h d mq)) = case trims s of+ [t1,t2] -> let clip = B.take (fromIntegral t2-fromIntegral t1) . B.drop (fromIntegral t1)+ in (i,Seq h (clip d) (case mq of Nothing -> Nothing+ Just q -> Just (clip q)))+ _ -> (i,s)++-- todo: clip only 'n's?++hasgp :: IO Bool+hasgp = return . isJust =<< findExecutable "gnuplot"++readDirs, readFiles :: [FilePath] -> IO [(FilePath,Sequence)]+readDirs dirs = mapM' myReadPhd =<< filterM isPhdFile =<< return . concat =<<+ mapM myGetDirectoryContents =<< filterM doesDirectoryExist dirs+readFiles = mapM' myReadPhd++mapM' :: (a -> IO b) -> [a] -> IO [b]+mapM' _ [] = hPutStrLn stderr "Warning: no files found" >> return []+mapM' action xs = mapM action xs++-- ------------------------------------------------------------+-- Processing+-- ------------------------------------------------------------++-- | Quality is divided into four categories, mainly based on length of+-- a sliding average of quality greater than 20.+data Quality = Junk | Poor | Good | Excl deriving (Show,Eq)++main :: IO ()+main = do+ (opts,fs,errs) <- getOptions+ when (not $ null errs) $ error $ usage errs+ let process xs = if not (verbose opts) then return xs+ else countIO ("processing "++show (length xs)++" sequences: ")+ ", done.\n" 100 xs+ mapM_ (sequence_ . zipWith ($) (actions opts) . repeat) =<< return . map (filters opts) =<< process =<< (inputs opts) fs+ mapM_ hClose (outputs opts)++phd_rx :: Regex+phd_rx = mkRegex ".phd(.[0-9]+)?$"++isPhdFile :: FilePath -> IO Bool+isPhdFile fn = do exists <- doesFileExist fn+ let matches = matchRegex phd_rx fn+ return (exists && isJust matches)++myGetDirectoryContents :: FilePath -> IO [FilePath]+myGetDirectoryContents d = return . map ((d++"/")++) =<< getDirectoryContents d++-- | Adjust sequence content according to quality.+-- Upper case is >20 and sliding avg >30+qualAdjust :: Sequence -> Sequence+qualAdjust (Seq _ _ Nothing) = error "no quality data - impossible!"+qualAdjust (Seq l d (Just q)) = Seq l (B.unfoldr conv avgs) (Just q)+ where avgs = (sliding_avg 1 q, sliding_avg 20 q, d)+ conv (a:as,s:ss,dd) = Just (if a>20 && s>25 then toUpper (B.head dd)+ else if a<4 || s<9 then 'n'+ else toLower (B.head dd),(as,ss,B.tail dd))+ conv ([],[],dd) | B.null dd = Nothing -- else broken invariant+ conv _ = error "internal error in 'qualAdjust/conv'"++myReadPhd :: FilePath -> IO (FilePath,Sequence)+myReadPhd f = unsafeInterleaveIO (do p <- readPhd f+ p `seq` return (f,p))++usage :: [String] -> String+usage errs = usageInfo msg options+ where msg = (if (not $ null errs) then concat errs++"\n"+ else "dephd: analyze phd files (phred output)\n")+ ++"Usage: dephd -[RFQPX] [phdfile..]\n"+ ++" dephd -[RFQPX] --input-dirs [phddir..]\n"++-- | Align columns: should be a standard function?+columns :: [[String]] -> [String]+columns ls = map (pad (head lens:map negate (tail lens))) ls+ where lens = collens ls++pad :: [Int] -> [String] -> String+pad x = unwords . zipWith padto x+ where padto l s = if l<0 then replicate (negate l-length s) ' '++s+ else s ++ replicate (l-length s) ' '++collens :: [[String]] -> [Int]+collens ls = let ls' = filter (not . null) ls+ in if null ls' then []+ else (maximum . map (length . head) $ ls'):collens (map tail ls')++-- ugly hack+myhead :: [Int] -> Int+myhead x = if null x then 0 else head x++-- | Report (various?) quality estimates+qualchk :: Sequence -> [String]+qualchk s = [toStr $ seqlabel s+ ,printf "%.1f" avgqual]+ ++ map show [s15, s30, a20] ++[show qtot]+ where+ s15 = stretch 15 qs+ s30 = stretch 30 qs+ a20 = stretch 20 . sliding_avg 20 . seqqual $ s+ qtot | a20 < 75 && s15 < 50 = Junk+ | a20 < 150 = Poor+ | a20 < 250 || s30 < 150 = Good+ | otherwise = Excl++ qs = map (fromIntegral . ord) . toStr . seqqual $ s+ avgqual = sum qs / fromIntegral (seqlength s) :: Double+ stretch i = myhead . stretches i+ stretches i = sortOn negate . map (subtract 1 . length)+ . groupBy (const (>i))+ sortOn f = sortBy (\x y -> compare (f x) (f y))++-- | Plot the quality of a sequence in the background+bgplot :: Bool -> (FilePath,Sequence) -> IO ThreadId+bgplot x = forkIO . plot x++-- | Feed the quality data to gnuplot (check if installed?)+plot :: Bool -> (FilePath,Sequence) -> IO ()+plot z (f,s) = case seqlength s of+ 0 -> hPutStrLn stderr ("cannot plot empty sequence: "++f) >> return ()+ _ -> do (i,o,e,p) <- runInteractiveCommand "gnuplot -persist"+ hPutStr i header+ hPutStr i $ unlines $ map (show . ord) $ toStr $ seqqual s+ hPutStr i "e\n"+ hPutStr i $ unlines $ map show $ sliding_avg 20 $ seqqual s+ hPutStr i "e\n"+ hClose i+ x <- waitForProcess p+ hGetContents o >>= hPutStr stderr+ hGetContents e >>= hPutStr stderr+ case x of ExitSuccess -> return ()+ ExitFailure j -> hPutStr stderr (errmsg++show j)+ >> return ()+ where name = toStr (seqlabel s)+ f' = subRegex phd_rx f ".jpg"+ arrow (i,c) = "set arrow "++show i++" from "++show c++",0 to "++show c ++",20 nohead\n"+ mtrim = concatMap arrow $ zip [(1::Int)..] (trims s)+ header = (if z then "" else "set term jpeg\nset out \""++f'++"\"\n")+ ++"set xlabel \"position\"\nset ylabel \"quality\"\n"+ ++ mtrim+ ++ "set title \""++name++"\"\nset yrange [0:75]\nplot \"-\" t \"qual\" with points,\"-\" t \"avg\" with lines, 20 with lines t \"thresh\"\n"+ errmsg = "'gnuplot' failed for "++f++" with exit code "++trims :: Sequence -> [Int]+trims s = case dropWhile ((/=) (B.pack "TRIM:")) (B.words $ seqheader s) of+ (_:x:y:_) -> [read $ B.unpack x, read $ B.unpack y]+ _ -> []++-- | Calculate a sliding average. Slightly biased for even i.+sliding_avg :: Int -> QualData -> [Double]+sliding_avg i q = map avg $ take (fromIntegral $ B.length q) (iblocks i qs)+ where avg xs = fromIntegral (sum xs) / fromIntegral (length xs)+ qs = map ord . toStr $ q++-- | select centered words+iblocks :: Int -> [a] -> [[a]]+iblocks i ss = [take n ss | n <- [(i+1) `div` 2..(i-1)]] ++ map (take i) (tails ss)++-- copied from RBR+countIO :: String -> String -> Int -> [a] -> IO [a]+countIO msg post step xs = sequence $ map unsafeInterleaveIO ((blank >> outmsg (0::Int) >> c):cs)+ where (c:cs) = ct 0 xs+ output = hPutStr stderr+ blank = output ('\r':take 70 (repeat ' '))+ outmsg x = output ('\r':msg++show x) >> hFlush stderr+ ct s ys = let (a,b) = splitAt (step-1) ys+ next = s+step+ in case b of [b1] -> map return a ++ [outmsg (s+step) >> hPutStr stderr post >> return b1]+ [] -> map return (init a) ++ [outmsg (s+length a) >> hPutStr stderr post >> return (last a)]+ _ -> map return a ++ [outmsg s >> return (head b)] ++ ct next (tail b)