diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -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. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + + To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + + For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + + We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + + Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + + Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + + The precise terms and conditions for copying, distribution and +modification follow. + + GNU GENERAL PUBLIC LICENSE + TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + 0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not +covered by this License; they are outside its scope. The act of +running the Program is not restricted, and the output from the Program +is covered only if its contents constitute a work based on the +Program (independent of having been made by running the Program). +Whether that is true depends on what the Program does. + + 1. You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + + 2. You may modify your copy or copies of the Program or any portion +of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 +above, provided that you also meet all of these conditions: + + a) You must cause the modified files to carry prominent notices + stating that you changed the files and the date of any change. + + b) You must cause any work that you distribute or publish, that in + whole or in part contains or is derived from the Program or any + part thereof, to be licensed as a whole at no charge to all third + parties under the terms of this License. + + c) If the modified program normally reads commands interactively + when run, you must cause it, when started running for such + interactive use in the most ordinary way, to print or display an + announcement including an appropriate copyright notice and a + notice that there is no warranty (or else, saying that you provide + a warranty) and that users may redistribute the program under + these conditions, and telling the user how to view a copy of this + License. (Exception: if the Program itself is interactive but + does not normally print such an announcement, your work based on + the Program is not required to print an announcement.) + +These requirements apply to the modified work as a whole. If +identifiable sections of that work are not derived from the Program, +and can be reasonably considered independent and separate works in +themselves, then this License, and its terms, do not apply to those +sections when you distribute them as separate works. But when you +distribute the same sections as part of a whole which is a work based +on the Program, the distribution of the whole must be on the terms of +this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest +your rights to work written entirely by you; rather, the intent is to +exercise the right to control the distribution of derivative or +collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program +with the Program (or with a work based on the Program) on a volume of +a storage or distribution medium does not bring the other work under +the scope of this License. + + 3. You may copy and distribute the Program (or a work based on it, +under Section 2) in object code or executable form under the terms of +Sections 1 and 2 above provided that you also do one of the following: + + a) Accompany it with the complete corresponding machine-readable + source code, which must be distributed under the terms of Sections + 1 and 2 above on a medium customarily used for software interchange; or, + + b) Accompany it with a written offer, valid for at least three + years, to give any third party, for a charge no more than your + cost of physically performing source distribution, a complete + machine-readable copy of the corresponding source code, to be + distributed under the terms of Sections 1 and 2 above on a medium + customarily used for software interchange; or, + + c) Accompany it with the information you received as to the offer + to distribute corresponding source code. (This alternative is + allowed only for noncommercial distribution and only if you + received the program in object code or executable form with such + an offer, in accord with Subsection b above.) + +The source code for a work means the preferred form of the work for +making modifications to it. For an executable work, complete source +code means all the source code for all modules it contains, plus any +associated interface definition files, plus the scripts used to +control compilation and installation of the executable. However, as a +special exception, the source code distributed need not include +anything that is normally distributed (in either source or binary +form) with the major components (compiler, kernel, and so on) of the +operating system on which the executable runs, unless that component +itself accompanies the executable. + +If distribution of executable or object code is made by offering +access to copy from a designated place, then offering equivalent +access to copy the source code from the same place counts as +distribution of the source code, even though third parties are not +compelled to copy the source along with the object code. + + 4. You may not copy, modify, sublicense, or distribute the Program +except as expressly provided under this License. Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + + 5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + 6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + + 7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by +all those who receive copies directly or indirectly through you, then +the only way you could satisfy both it and this License would be to +refrain entirely from distribution of the Program. + +If any portion of this section is held invalid or unenforceable under +any particular circumstance, the balance of the section is intended to +apply and the section as a whole is intended to apply in other +circumstances. + +It is not the purpose of this section to induce you to infringe any +patents or other property right claims or to contest validity of any +such claims; this section has the sole purpose of protecting the +integrity of the free software distribution system, which is +implemented by public license practices. Many people have made +generous contributions to the wide range of software distributed +through that system in reliance on consistent application of that +system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot +impose that choice. + +This section is intended to make thoroughly clear what is believed to +be a consequence of the rest of this License. + + 8. If the distribution and/or use of the Program is restricted in +certain countries either by patents or by copyrighted interfaces, the +original copyright holder who places the Program under this License +may add an explicit geographical distribution limitation excluding +those countries, so that distribution is permitted only in or among +countries not thus excluded. In such case, this License incorporates +the limitation as if written in the body of this License. + + 9. The Free Software Foundation may publish revised and/or new versions +of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +later version", you have the option of following the terms and conditions +either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + + 10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes +make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and +of promoting the sharing and reuse of software generally. + + NO WARRANTY + + 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + + 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software + Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: + + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. + +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: + + Yoyodyne, Inc., hereby disclaims all copyright interest in the program + `Gnomovision' (which makes passes at compilers) written by James Hacker. + + , 1 April 1989 + Ty Coon, President of Vice + +This General Public License does not permit incorporating your program into +proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Library General +Public License instead of this License. diff --git a/README b/README new file mode 100644 --- /dev/null +++ b/README @@ -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 diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,5 @@ +#!/usr/bin/env runhaskell + +import Distribution.Simple +main = defaultMain + diff --git a/TODO b/TODO new file mode 100644 --- /dev/null +++ b/TODO @@ -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. diff --git a/dephd.cabal b/dephd.cabal new file mode 100644 --- /dev/null +++ b/dephd.cabal @@ -0,0 +1,25 @@ +Name: dephd +Version: 0.0 +License: GPL +License-File: LICENSE + +Author: Ketil Malde +Maintainer: Ketil Malde + +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 . + +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 diff --git a/src/Dephd.hs b/src/Dephd.hs new file mode 100644 --- /dev/null +++ b/src/Dephd.hs @@ -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)