diff --git a/ChangeLog.md b/ChangeLog.md new file mode 100644 --- /dev/null +++ b/ChangeLog.md @@ -0,0 +1,10 @@ + +# Table of Contents + +1. [Changelog for ELynx](#org9916021) + + + + +# Changelog for ELynx + diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +the GNU General Public License is intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. 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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 Lesser General +Public License instead of this License. But first, please read +. diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,417 @@ + + +# The ELynx Suite + +Version: 0.0.1. +Reproducible evolution made easy. + +The ELynx Suite is a Haskell library and a tool set for computational biology. +The goal of the ELynx Suite is reproducible research. Evolutionary sequences and +phylogenetic trees can be read, viewed, modified and simulated. Exact +specification of all options is necessary, and nothing is assumed about the data +(e.g., the type of code). The command line with all arguments is consistently, +and automatically logged. The work overhead in the beginning usually pays off in +the end. + +The Elynx Suite consists of three library packages and two executables providing +a range of sub commands. + +The library packages are: + +- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments; +- **elynx-tree:** Handle phylogenetic trees; +- **elynx-tools:** Tools for the provided executables; + +The executables are: + +- **SLynx:** Analyze, modify, and simulate evolutionary sequences (FASTA format); +- **TLynx:** Analyze, modify, and simulate phylogenetic trees (Newick format). + +**ELynx is still under development. We happily receive comments, ideas, feature +requests, or pull requests!** + + +# Installation + +ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/). + +1. Install Stack with your package manager, or directly from the web + page. + + curl -sSL https://get.haskellstack.org/ | sh + +2. Clone the ELynx repository. + + git clone clone https://github.com/dschrempf/elynx + +3. Navigate to the newly created `elynx` folder and build the binaries. + This will take a while. + + stack build + +4. Run a binary from within the project directory. For example, + + stack exec tlynx -- --help + +5. If needed, install the binaries. + + stack install + + The binaries are installed into `~/.local/bin/` which has to be added [PATH](https://en.wikipedia.org/wiki/PATH_(variable)). + Then, they can be used directly. + + +# SLynx + +Handle evolutionary sequences. + + slynx --help + + ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September + 9, 2019, at 10:48 am, UTC. + + Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] COMMAND + Analyze, and simulate multi sequence alignments. + + Available options: + -h,--help Show this help text + -V,--version Show version + -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info + Debug (default: Info) + -o,--output-file-basename NAME + Specify base name of output file + + Available commands: + concatenate + examine If data is a multi sequence alignment, additionally + analyze columns. + filter-rows + filter-columns + simulate + sub-sample Create a given number of multi sequence alignments, + each of which containing a given number of random + sites drawn from the original multi sequence + alignment. + translate + + File formats: + - FASTA + + Alphabet types: + - DNA (nucleotides) + - DNAX (nucleotides; including gaps) + - DNAI (nucleotides; including gaps, and IUPAC codes) + - Protein (amino acids) + - ProteinX (amino acids; including gaps) + - ProteinS (amino acids; including gaps, and translation stops) + - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes) + + The ELynx Suite. + A Haskell library and a tool set for computational biology. The goal of the + ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic + trees can be read, viewed, modified and simulated. Exact specification of all + options is necessary, and nothing is assumed about the data (e.g., the type of + code). The command line with all arguments is consistently, and automatically + logged. The work overhead in the beginning usually pays off in the end. + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + + +## Concatenate + +Concatenate multi sequence alignments. + + slynx concatenate --help + + Concatenate sequences found in input files. + + Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + -h,--help Show this help text + + +## Examine + +Examine sequence with `slynx examine`. + + slynx examine --help + + Examine sequences. + + Usage: slynx examine (-a|--alphabet NAME) [INPUT-FILE] [--per-site] + If data is a multi sequence alignment, additionally analyze columns. + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + --per-site Report per site summary statistics + -h,--help Show this help text + + +## Filter + +Filter sequences with `filer-rows`. + + slynx filter-rows --help + + Filter rows (or sequences) found in input files. + + Usage: slynx filter-rows (-a|--alphabet NAME) [INPUT-FILE] + [--longer-than LENGTH] [--shorter-than LENGTH] + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + --longer-than LENGTH Only keep sequences longer than LENGTH + --shorter-than LENGTH Only keep sequences shorter than LENGTH + -h,--help Show this help text + +Filter columns of multi sequence alignments with `filter-columns`. + + slynx filter-columns --help + + Filter columns of multi-sequence alignments. + + Usage: slynx filter-columns (-a|--alphabet NAME) [INPUT-FILE] + [--standard-chars DOUBLE] + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + --standard-chars DOUBLE Keep columns with a proportion standard (non-IUPAC) + characters larger than DOUBLE in [0,1] + -h,--help Show this help text + + +## Simulate + +Simulate sequences with `slynx simulate`. + + slynx simulate --help + + Simulate multi sequence alignments. + + Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] + [-m|--mixture-model MODEL] [-e|--edm-file NAME] + [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"] + [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"] + (-l|--length NUMBER) [-S|--seed [INT]] + + Available options: + -t,--tree-file Name Read trees from file NAME + -s,--substitution-model MODEL + Set the phylogenetic substitution model; available + models are shown below (mutually exclusive with -m + option) + -m,--mixture-model MODEL Set the phylogenetic mixture model; available models + are shown below (mutually exclusive with -s option) + -e,--edm-file NAME Empirical distribution model file NAME in Phylobayes + format + -w,--mixture-model-weights "[DOUBLE,DOUBLE,...]" + Weights of mixture model components + -g,--gamma-rate-heterogeneity "(NCAT,SHAPE)" + Number of gamma rate categories and shape parameter + -l,--length NUMBER Set alignment length to NUMBER + -S,--seed [INT] Seed for random number generator; list of 32 bit + integers with up to 256 elements (default: random) + -h,--help Show this help text + + Substitution models: + -s "MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}" + Supported DNA models: JC, HKY. + For example, + -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE} + Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom. + MODEL-Custom means that only the exchangeabilities of MODEL are used, + and a custom stationary distribution is provided. + For example, + -s LG-Custom{...} + + Mixture models: + -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2)" + For example, + -m "MIXTURE(JC,HKY[6.0]{0.3,0.2,0.2,0.3})" + Mixture weights have to be provided with the -w option. + + Special mixture models: + -m CXX + where XX is 10, 20, 30, 40, 50, or 60; CXX models, Quang et al., 2008. + -m "EDM(EXCHANGEABILITIES)" + Arbitrary empirical distribution mixture (EDM) models. + Stationary distributions have to be provided with the -e option. + For example, + LG exchangeabilities with stationary distributions given in FILE. + -m "EDM(LG-Custom)" -e FILE + For special mixture models, mixture weights are optional. + + +## Sub-sample + +Sub-sample columns from multi sequence alignments. + + slynx sub-sample --help + + Usage: slynx sub-sample (-a|--alphabet NAME) [INPUT-FILE] + (-n|--number-of-sites INT) + (-m|--number-of-alignments INT) [-S|--seed [INT]] + Create a given number of multi sequence alignments, each of which containing a + given number of random sites drawn from the original multi sequence alignment. + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + -n,--number-of-sites INT Number of sites randomly drawn with replacement + -m,--number-of-alignments INT + Number of multi sequence alignments to be created + -S,--seed [INT] Seed for random number generator; list of 32 bit + integers with up to 256 elements (default: random) + -h,--help Show this help text + + +## Translate + +Translate sequences. + + slynx translate --help + + Translate from DNA to Protein or DNAX to ProteinX. + + Usage: slynx translate (-a|--alphabet NAME) [INPUT-FILE] + (-r|--reading-frame INT) (-u|--universal-code CODE) + + Available options: + -a,--alphabet NAME Specify alphabet type NAME + INPUT-FILE Read sequences from INPUT-FILE + -r,--reading-frame INT Reading frame [0|1|2]. + -u,--universal-code CODE universal code; one of: Standard, + VertebrateMitochondrial. + -h,--help Show this help text + + +# TLynx + +Handle phylogenetic trees in Newick format. + + tlynx --help + + ELynx Suite version 0.5.1. Developed by Dominik Schrempf. Compiled on September + 9, 2019, at 10:48 am, UTC. + + Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] COMMAND + Compare, examine, and simulate phylogenetic trees. + + Available options: + -h,--help Show this help text + -V,--version Show version + -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info + Debug (default: Info) + -o,--output-file-basename NAME + Specify base name of output file + + Available commands: + compare + examine + simulate Simulate reconstructed trees using the point process. + See Gernhard, T. (2008). The conditioned + reconstructed process. Journal of Theoretical + Biology, 253(4), 769–778. + http://doi.org/10.1016/j.jtbi.2008.04.005 + + File formats: + - Newick + + The ELynx Suite. + A Haskell library and a tool set for computational biology. The goal of the + ELynx Suite is reproducible research. Evolutionary sequences and phylogenetic + trees can be read, viewed, modified and simulated. Exact specification of all + options is necessary, and nothing is assumed about the data (e.g., the type of + code). The command line with all arguments is consistently, and automatically + logged. The work overhead in the beginning usually pays off in the end. + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + + +## Compare + +Compute distances between phylogenetic trees. + + tlynx compare --help + + Compute distances between phylogenetic trees. + + Usage: tlynx compare (-d|--distance MEASURE) [-s|--summary-statistics] + [INPUT-FILES] + + Available options: + -d,--distance MEASURE Type of distance to calculate (available distance + measures are listed below) + -s,--summary-statistics Report summary statistics only + INPUT-FILES Read tree(s) from INPUT-FILES; if more files are + given, one tree is expected per file + -h,--help Show this help text + + Available distance measures: + Symmetric distance: -d symmetric + Incompatible split distance: -d incompatible-split[VAL] + Collapse branches with support less than VAL before distance calculation; + in this way, only well supported difference contribute to the distance measure. + + +## Examine + +Compute summary statistics of phylogenetic trees. + + tlynx examine --help + + Compute summary statistics of phylogenetic trees. + + Usage: tlynx examine [INPUT-FILE] + + Available options: + INPUT-FILE Read trees from INPUT-FILE + -h,--help Show this help text + + +## Simulate + +Simulate phylogenetic trees using birth and death processes. + + tlynx simulate --help + + Simulate phylogenetic trees using birth and death processes. + + Usage: tlynx simulate [-t|--nTrees INT] [-n|--nLeaves INT] [-H|--height DOUBLE] + [-M|--condition-on-mrca] [-l|--lambda DOUBLE] + [-m|--mu DOUBLE] [-r|--rho DOUBLE] [-u|--sub-sample] + [-s|--summary-statistics] [-S|--seed [INT]] + Simulate reconstructed trees using the point process. See Gernhard, T. (2008). + The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), + 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005 + + Available options: + -t,--nTrees INT Number of trees (default: 10) + -n,--nLeaves INT Number of leaves per tree (default: 5) + -H,--height DOUBLE Fix tree height (no default) + -M,--condition-on-mrca Do not condition on height of origin but on height of + MRCA + -l,--lambda DOUBLE Birth rate lambda (default: 1.0) + -m,--mu DOUBLE Death rate mu (default: 0.9) + -r,--rho DOUBLE Sampling probability rho (default: 1.0) + -u,--sub-sample Perform sub-sampling; see below. + -s,--summary-statistics Only output number of children for each branch + -S,--seed [INT] Seed for random number generator; list of 32 bit + integers with up to 256 elements (default: random) + -h,--help Show this help text + + Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate. + Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character. + Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again. + + +# ELynx + +Documentation of the library can be found on Hackage. + diff --git a/app/Main.hs b/app/Main.hs new file mode 100644 --- /dev/null +++ b/app/Main.hs @@ -0,0 +1,39 @@ +{-# LANGUAGE TemplateHaskell #-} + +{- | +Module : Main +Description : Work with phylogenetic trees +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Thu Sep 5 21:53:07 2019. + +-} + +module Main where + +import Control.Monad.Trans.Reader + +import Options + +import Compare.Compare +import Examine.Examine +import Simulate.Simulate + +import ELynx.Tools.Logger +import ELynx.Tools.Options + +main :: IO () +main = do + Arguments g c <- parseArguments + let fn = outFileBaseName g + lvl = verbosity g + lf = (++ ".log") <$> fn + case c of + Compare a -> runReaderT (eLynxWrapper lvl lf compareHeader $ compareTrees fn) a + Examine a -> runReaderT (eLynxWrapper lvl lf examineHeader $ examine fn) a + Simulate a -> runReaderT (eLynxWrapper lvl lf simulateHeader $ simulate fn) a diff --git a/app/Options.hs b/app/Options.hs new file mode 100644 --- /dev/null +++ b/app/Options.hs @@ -0,0 +1,86 @@ +{- | +Module : Options +Description : TLynx general options +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Sat Sep 7 18:55:03 2019. + +-} + +module Options + ( Arguments (..) + , CommandArguments (..) + , parseArguments + , compareHeader + , examineHeader + , simulateHeader + ) where + +import Options.Applicative +import Options.Applicative.Help.Pretty + +import Compare.Options +import Examine.Options +import Simulate.Options + +import ELynx.Tools.Options + +data CommandArguments = + Compare CompareArguments + | Examine ExamineArguments + | Simulate SimulateArguments + +compareHeader, examineHeader, simulateHeader :: String +compareHeader = "Compute distances between phylogenetic trees." +examineHeader = "Compute summary statistics of phylogenetic trees." +simulateHeader = "Simulate phylogenetic trees using birth and death processes." + +compareCommand :: Mod CommandFields CommandArguments +compareCommand = command "compare" $ + info (Compare <$> compareArguments) + ( fullDesc + <> header compareHeader + <> footerDoc (Just $ pretty compareFooter) ) + +examineCommand :: Mod CommandFields CommandArguments +examineCommand = command "examine" $ + info (Examine <$> examineArguments) + $ header examineHeader + +simulateCommand :: Mod CommandFields CommandArguments +simulateCommand = command "simulate" $ + info (Simulate <$> simulateArguments) + ( fullDesc + <> header simulateHeader + <> progDesc simulateDesc + <> footerDoc (Just $ pretty simulateFooter) ) + +commandArguments :: Parser CommandArguments +commandArguments = hsubparser $ + compareCommand + <> examineCommand + <> simulateCommand + +data Arguments = Arguments + { globalArgs :: GlobalArguments + , cmdArgs :: CommandArguments } + +parseArguments :: IO Arguments +parseArguments = parseArgumentsWith desc ftr $ + Arguments + <$> globalArguments + <*> commandArguments + +desc :: [String] +desc = [ "Compare, examine, and simulate phylogenetic trees." ] + +ftr :: [String] +ftr = "File formats:" : fs + where + toListItem = (" - " ++) + fs = map toListItem ["Newick"] diff --git a/src/Compare/Compare.hs b/src/Compare/Compare.hs new file mode 100644 --- /dev/null +++ b/src/Compare/Compare.hs @@ -0,0 +1,144 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE TemplateHaskell #-} + +{- | +Description : Compute distances between trees +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Wed May 29 18:09:39 2019. + +- Symmetric (Robinson-Foulds) distance. +- Incompatible splits distance. + +-} + +module Compare.Compare + ( compareTrees + ) +where + +import Control.Monad +import Control.Monad.IO.Class +import Control.Monad.Logger +import Control.Monad.Trans.Class +import Control.Monad.Trans.Reader +import qualified Data.ByteString.Lazy.Char8 as L +import qualified Data.Text as T +import qualified Data.Text.IO as T +import qualified Data.Text.Lazy as LT +import qualified Data.Text.Lazy.Encoding as LT +import Data.Tree +import qualified Data.Vector.Unboxed as V +import Statistics.Sample +import System.IO +import Text.Printf + +import Compare.Options + +import ELynx.Data.Tree.BranchSupportTree as B +import ELynx.Data.Tree.Distance +import ELynx.Data.Tree.MeasurableTree as M +import ELynx.Data.Tree.NamedTree +import ELynx.Data.Tree.PhyloTree +import ELynx.Export.Tree.Newick +import ELynx.Import.Tree.Newick +import ELynx.Tools.ByteString (alignLeft, alignRight) +import ELynx.Tools.InputOutput +import ELynx.Tools.Logger + +pf :: String +pf = "%.3f" + +header :: Int -> Distance -> L.ByteString +header n d = alignLeft (n+2) "Tree 1" + <> alignLeft (n+2) "Tree 2" + <> alignRight 20 (L.pack $ show d) + +showTriplet :: (PrintfArg a) => Int -> [String] -> (Int, Int, a) -> L.ByteString +showTriplet n args (i, j, d) = i' <> j' <> d' + where i' = alignLeft (n+2) $ L.pack (args !! i) + j' = alignLeft (n+2) $ L.pack (args !! j) + d' = alignRight 20 $ L.pack (printf pf d) + +-- | Compute distance functions between phylogenetic trees. +compareTrees :: Maybe FilePath -> Compare () +compareTrees outFileBN = do + a <- lift ask + -- Determine output handle (stdout or file). + let outFile = (++ ".out") <$> outFileBN + outH <- liftIO $ maybe (pure stdout) (`openFile` WriteMode) outFile + let tfps = argsInFiles a + (trees, names) <- + if length tfps <= 1 + then + do ts <- if null tfps + then do $(logInfo) "Read trees from standard input." + liftIO $ parseIOWith manyNewick + else do let f = head tfps + $(logInfo) $ T.pack $ "Read trees from file: " <> f <> "." + liftIO $ parseFileWith manyNewick f + let n = length ts + when (n <= 1) (error "Not enough trees found in file.") + $(logInfo) "Compute pairwise distances between trees in the same file." + $(logInfo) $ T.pack $ "Trees are numbered from 0 to " ++ show (n-1) ++ "." + return (ts, take n (map show [0 :: Int ..])) + else + do $(logInfo) "Read trees from files." + ts <- liftIO $ mapM (parseFileWith newick) tfps + when (length ts <= 1) (error "Not enough trees found in files.") + $(logInfo) "Compute pairwise distances between trees from different files." + $(logInfo) "Trees are named according to their file names." + return (ts, tfps) + $(logDebug) "The trees are:" + $(logDebug) $ LT.toStrict $ LT.decodeUtf8 $ L.unlines $ map toNewick trees + case outFile of + Nothing -> logNewSection "Write results to standard output." + Just f -> logNewSection $ T.pack $ "Write results to file " <> f <> "." + let n = maximum $ 6 : map length names + distance = argsDistance a + case distance of + Symmetric -> $(logInfo) "Use symmetric (Robinson-Foulds) distance." + IncompatibleSplit val -> do + $(logInfo) "Use incompatible split distance." + $(logInfo) $ T.pack $ "Collapse nodes with support less than " ++ show val ++ "." + BranchScore False -> $(logInfo) "Use branch score distance without normalization." + BranchScore True -> $(logInfo) "Use branch score distance with normalization." + let distanceMeasure :: Tree PhyloByteStringLabel -> Tree PhyloByteStringLabel -> Double + distanceMeasure = case distance of + Symmetric -> \t1 t2 -> fromIntegral $ symmetricDistanceWith getName t1 t2 + IncompatibleSplit _ -> \t1 t2 -> fromIntegral $ incompatibleSplitsDistanceWith getName t1 t2 + BranchScore _ -> branchScoreDistance + normalizeF = case distance of + BranchScore True -> M.normalize + _ -> id + collapseF = case distance of + -- For the incompatible split distance we have to collapse branches with + -- support lower than the given value. Before doing so, we normalize the + -- branch support values. + IncompatibleSplit val -> collapse val . B.normalize + _ -> id + trees' = map (collapseF . normalizeF) trees + $(logDebug) "The prepared trees are:" + $(logDebug) $ LT.toStrict $ LT.decodeUtf8 $ L.unlines $ map toNewick trees' + let dsTriplets = computePairwiseDistances distanceMeasure trees' + ds = map (\(_, _, x) -> x) dsTriplets + dsVec = V.fromList ds + -- XXX: It may be good to use the common 'io' function also here. + liftIO $ hPutStrLn outH $ "Summary statistics of " ++ show distance ++ " Distance:" + liftIO $ T.hPutStrLn outH $ T.justifyLeft 10 ' ' "Mean: " <> T.pack (printf pf (mean dsVec)) + liftIO $ T.hPutStrLn outH $ T.justifyLeft 10 ' ' "Variance: " <> T.pack (printf pf (variance dsVec)) + -- L.putStrLn $ L.unlines $ map toNewick ts + -- L.putStrLn $ L.unlines $ map toNewick tsN + -- L.putStrLn $ L.unlines $ map toNewick tsC + lift $ unless (argsSummaryStatistics a) ( + do + lift $ hPutStrLn outH "" + lift $ L.hPutStrLn outH $ header n distance + lift $ L.hPutStr outH $ L.unlines (map (showTriplet n names) dsTriplets) + ) + liftIO $ hClose outH diff --git a/src/Compare/Options.hs b/src/Compare/Options.hs new file mode 100644 --- /dev/null +++ b/src/Compare/Options.hs @@ -0,0 +1,126 @@ +{- | +Module : Compare.Options +Description : Options of tree-dist +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Thu Aug 29 13:02:22 2019. + +-} + +module Compare.Options + ( CompareArguments (..) + , Compare + , Distance (..) + , compareArguments + , compareFooter + ) where + +import Control.Monad.Logger +import Control.Monad.Trans.Reader +import Data.List +import Data.Void +import Options.Applicative +import Text.Megaparsec (Parsec, try) +import Text.Megaparsec.Char (char, string) +import Text.Megaparsec.Char.Lexer (float) +import Text.Printf + +import ELynx.Tools.Options + +-- | Supported distance measures. +data Distance = + Symmetric -- ^ Symmetric distance. + | IncompatibleSplit Double -- ^ Incompatible split distance; collapse nodes + -- with branch support below given value. + | BranchScore Bool -- ^ Branch score distance. If given, normalize + -- the trees before comparison. + +instance Show Distance where + show Symmetric = "Symmetric" + show (IncompatibleSplit c) = "Incompatible Split (" ++ printf "%.1f" c ++ ")" + show (BranchScore False) = "Branch Score" + show (BranchScore True ) = "Branch Score (normalized)" + +-- | Arguments needed to compute distance measures. +data CompareArguments = CompareArguments + { argsDistance :: Distance + , argsSummaryStatistics :: Bool + , argsInFiles :: [FilePath] + } + +-- | Lgger and reader data type. +type Compare = LoggingT (ReaderT CompareArguments IO) + +-- | COmmand line parser. +compareArguments :: Parser CompareArguments +compareArguments = CompareArguments <$> + distanceOpt + <*> summaryStatisticsSwitch + <*> many inFilesArg + +inFilesArg :: Parser FilePath +inFilesArg = strArgument $ + metavar "INPUT-FILES" <> + help "Read tree(s) from INPUT-FILES; if more files are given, one tree is expected per file" + +symmetric :: Parsec Void String Distance +symmetric = do + _ <- string "symmetric" + pure Symmetric + +incompatibleSplit :: Parsec Void String Distance +incompatibleSplit = do + _ <- string "incompatible-split" + _ <- char '[' + f <- float + _ <- char ']' + if (0 < f) && (f < 1) + then pure $ IncompatibleSplit f + else error "Branch support has to be between 0 and 1." + +branchScore :: Parsec Void String Distance +branchScore = do + _ <- string "branch-score" + pure (BranchScore False) + +branchScoreNormalized :: Parsec Void String Distance +branchScoreNormalized = do + _ <- string "branch-score-normalized" + pure (BranchScore True) + +distanceParser :: Parsec Void String Distance +distanceParser = try symmetric + <|> try incompatibleSplit + -- Try first the normalized one, since the normal branch score + -- parser also succeeds in this case. + <|> try branchScoreNormalized + <|> try branchScore + +distanceOpt :: Parser Distance +distanceOpt = option (megaReadM distanceParser) $ + long "distance" <> + short 'd' <> + metavar "MEASURE" <> + help "Type of distance to calculate (available distance measures are listed below)" + +summaryStatisticsSwitch :: Parser Bool +summaryStatisticsSwitch = switch $ + long "summary-statistics" <> + short 's' <> + help "Report summary statistics only" + +-- | Information about provided distance types. +compareFooter :: String +compareFooter = intercalate "\n" + [ "Available distance measures:" + , " Symmetric distance: -d symmetric" + , " Incompatible split distance: -d incompatible-split[VAL]" + , " Collapse branches with support less than VAL before distance calculation;" + , " in this way, only well supported difference contribute to the distance measure." + , " Branch score distance : -d branch-score" + , " -d branch-score-normalized (normalize trees before comparison)" ] diff --git a/src/Examine/Examine.hs b/src/Examine/Examine.hs new file mode 100644 --- /dev/null +++ b/src/Examine/Examine.hs @@ -0,0 +1,53 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE TemplateHaskell #-} + +{- | +Description : Analyze trees +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Fri May 24 13:47:56 2019. + +-} + +module Examine.Examine + ( examine + ) +where + +import Control.Monad.IO.Class +import Control.Monad.Logger +import Control.Monad.Trans.Class +import Control.Monad.Trans.Reader +import qualified Data.ByteString.Lazy.Char8 as L +import qualified Data.Text as T +import Data.Tree + +import Examine.Options + +import ELynx.Data.Tree.MeasurableTree +import ELynx.Data.Tree.PhyloTree +import ELynx.Import.Tree.Newick +import ELynx.Tools.InputOutput +import ELynx.Tools.Logger + +readTrees :: Maybe FilePath -> Examine [Tree PhyloByteStringLabel] +readTrees mfp = do + case mfp of + Nothing -> $(logInfo) "Read tree(s) from standard input." + Just fp -> $(logInfo) $ T.pack $ "Read tree(s) from file " <> fp <> "." + liftIO $ parseFileOrIOWith manyNewick mfp + +-- | Examine phylogenetic trees. +examine :: Maybe FilePath -> Examine () +examine outFn = do + ExamineArguments inFn <- lift ask + trs <- readTrees inFn + let lsStrs = map summarize trs + let outFilePath = (++ ".out") <$> outFn + logNewSection "Results." + io "results of tree analysis" (L.intercalate (L.pack "\n") lsStrs) outFilePath diff --git a/src/Examine/Options.hs b/src/Examine/Options.hs new file mode 100644 --- /dev/null +++ b/src/Examine/Options.hs @@ -0,0 +1,39 @@ +{- | +Module : Examine.Options +Description : Tree analysis options +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Thu Aug 29 08:16:45 2019. + +-} + +module Examine.Options + ( ExamineArguments (..) + , Examine + , examineArguments + ) where + +import Control.Monad.Logger +import Control.Monad.Trans.Reader +import Options.Applicative + +-- | Arguments needed to examine phylogenetic trees. +newtype ExamineArguments = ExamineArguments + { inFile :: Maybe FilePath } + +-- | Logger and reader data type. +type Examine = LoggingT (ReaderT ExamineArguments IO) + +-- | Command line parser. +examineArguments :: Parser ExamineArguments +examineArguments = ExamineArguments <$> optional inFileArg + +inFileArg :: Parser FilePath +inFileArg = strArgument $ + metavar "INPUT-FILE" <> + help "Read trees from INPUT-FILE" diff --git a/src/Simulate/Options.hs b/src/Simulate/Options.hs new file mode 100644 --- /dev/null +++ b/src/Simulate/Options.hs @@ -0,0 +1,164 @@ +{- | +Module : Simulate.Options +Description : Argument parser for seq-ana +Copyright : (c) Dominik Schrempf 2019 +License : GPL-3 + +Maintainer : dominik.schrempf@gmail.com +Stability : unstable +Portability : portable + +Creation date: Fri May 3 11:51:07 2019. + +-} + +module Simulate.Options + ( SimulateArguments (..) + , Simulate + , simulateArguments + , reportSimulateArguments + , simulateDesc + , simulateFooter + ) where + +import Control.Monad.Logger +import Control.Monad.Trans.Reader +import Data.List +import Data.Word +import Options.Applicative + +import ELynx.Tools.Options + +-- | Arguments need to simulate phylogenetic trees. +data SimulateArguments = SimulateArguments + { argsNTrees :: Int -- ^ Simulated trees. + , argsNLeaves :: Int -- ^ Number of leaves. + , argsHeight :: Maybe Double -- ^ Tree height (time to origin or MRCA). + , argsConditionMRCA :: Bool -- ^ False: condition on origin; True: + -- condition on MRCA. + , argsLambda :: Double -- ^ Birth rate. + , argsMu :: Double -- ^ Death rate. + , argsRho :: Double -- ^ Smapling rate. + , argsSubSample :: Bool -- ^ Perform actual sub-sampling. + , argsSumStat :: Bool -- ^ Only print summary statistics? + , argsSeed :: Maybe [Word32] -- ^ Seed of NRG, random if 'Nothing'. + } + +-- | Logger and reader data type. +type Simulate = LoggingT (ReaderT SimulateArguments IO) + +-- | Print useful information about the provided arguments. +reportSimulateArguments :: SimulateArguments -> String +reportSimulateArguments a = + intercalate "\n" [ "Number of simulated trees: " ++ show (argsNTrees a) + , "Number of leaves per tree: " ++ show (argsNLeaves a) + , "Height of trees: " ++ hStr + , "Birth rate: " ++ show (argsLambda a) + , "Death rate: " ++ show (argsMu a) + , "Sampling probability: " ++ show (argsRho a) + , "Perform sub-sampling: " ++ show (argsSubSample a) + , "Summary statistics only: " ++ show (argsSumStat a) + , "Seed: " ++ sStr ] + where hStr = case argsHeight a of Nothing -> "Random height of origin" + Just h -> show h ++ ", conditioned on " + ++ if argsConditionMRCA a then "MRCA" else "origin" + sStr = case argsSeed a of Nothing -> "Random" + Just i -> show i + +-- | Command line parser. +simulateArguments :: Parser SimulateArguments +simulateArguments = SimulateArguments + <$> nTreeOpt + <*> nLeavesOpt + <*> treeHeightOpt + <*> conditionMRCAOpt + <*> lambdaOpt + <*> muOpt + <*> rhoOpt + <*> subSampleOpt + <*> sumStatOpt + <*> seedOpt + +nTreeOpt :: Parser Int +nTreeOpt = option auto $ + long "nTrees" + <> short 't' + <> metavar "INT" + <> value 10 + <> showDefault + <> help "Number of trees" + +nLeavesOpt :: Parser Int +nLeavesOpt = option auto $ + long "nLeaves" + <> short 'n' + <> metavar "INT" + <> value 5 + <> showDefault + <> help "Number of leaves per tree" + +treeHeightOpt :: Parser (Maybe Double) +treeHeightOpt = optional $ option auto $ + long "height" + <> short 'H' + <> metavar "DOUBLE" + <> help "Fix tree height (no default)" + +conditionMRCAOpt :: Parser Bool +conditionMRCAOpt = switch $ + long "condition-on-mrca" + <> short 'M' + <> showDefault + <> help "Do not condition on height of origin but on height of MRCA" + +lambdaOpt :: Parser Double +lambdaOpt = option auto $ + long "lambda" + <> short 'l' + <> metavar "DOUBLE" + <> value 1.0 + <> showDefault + <> help "Birth rate lambda" + +muOpt :: Parser Double +muOpt = option auto $ + long "mu" + <> short 'm' + <> metavar "DOUBLE" + <> value 0.9 + <> showDefault + <> help "Death rate mu" + +rhoOpt :: Parser Double +rhoOpt = option auto $ + long "rho" + <> short 'r' + <> metavar "DOUBLE" + <> value 1.0 + <> help "Sampling probability rho (default: 1.0)" + +subSampleOpt :: Parser Bool +subSampleOpt = switch $ + long "sub-sample" + <> short 'u' + <> showDefault + <> help "Perform sub-sampling; see below." + +sumStatOpt :: Parser Bool +sumStatOpt = switch $ + long "summary-statistics" + <> short 's' + <> showDefault + <> help "Only output number of children for each branch" + +-- | Simulation is a little more involved, so we provide a description. +simulateDesc :: String +simulateDesc = "Simulate reconstructed trees using the point process. See Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005" + +-- | And a footer. +simulateFooter :: String +simulateFooter = intercalate "\n" + [ "Height of Trees: if no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate." + , "Summary statistics only: only print (NumberOfExtantChildren BranchLength) pairs for each branch of each tree. The trees are separated by a newline character." + , "Sub-sampling: simulate one big tree with n'=round(n/rho), n'>=n, leaves, and randomly sample sub-trees with n leaves. Hence, with rho=1.0, the same tree is reported over and over again." + ] diff --git a/src/Simulate/Simulate.hs b/src/Simulate/Simulate.hs new file mode 100644 --- /dev/null +++ b/src/Simulate/Simulate.hs @@ -0,0 +1,113 @@ +{-# LANGUAGE OverloadedStrings #-} +{-# LANGUAGE TemplateHaskell #-} +{-# LANGUAGE TupleSections #-} + +{- | + Description : Simulate reconstructed trees + Copyright : (c) Dominik Schrempf 2018 + License : GPL-3 + + Maintainer : dominik.schrempf@gmail.com + Stability : unstable + Portability : portable + +Creation date: Tue Feb 27 17:27:16 2018. + +See Gernhard, T. (2008). The conditioned reconstructed process. Journal of +Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005. + +Mon Feb 4 14:26:11 CET 2019: Adding sampling probability rho. See Article +(Stadler2009) Stadler, T. On incomplete sampling under birth–death models and +connections to the sampling-based coalescent Journal of Theoretical Biology, +Elsevier BV, 2009, 261, 58-66 + +-} + +module Simulate.Simulate + ( simulate + ) +where + +import Control.Concurrent (getNumCapabilities) +import Control.Concurrent.Async.Lifted.Safe (mapConcurrently) +import Control.Monad +import Control.Monad.IO.Class +import Control.Monad.Logger +import Control.Monad.Trans.Class +import Control.Monad.Trans.Reader +import Control.Parallel.Strategies +import qualified Data.ByteString.Lazy.Char8 as L +import Data.Maybe +import qualified Data.Sequence as Seq +import qualified Data.Text as T +import qualified Data.Text.Lazy as LT +import qualified Data.Text.Lazy.Encoding as LT +import Data.Tree + +import Simulate.Options + +import ELynx.Data.Tree.MeasurableTree +import ELynx.Data.Tree.PhyloTree (PhyloIntLabel) +import ELynx.Data.Tree.SumStat (formatNChildSumStat, + toNChildSumStat) +import ELynx.Data.Tree.Tree +import ELynx.Export.Tree.Newick (toNewick) +import ELynx.Simulate.PointProcess (simulateNReconstructedTrees, + simulateReconstructedTree) +import ELynx.Tools.Concurrent +import ELynx.Tools.InputOutput +import ELynx.Tools.Logger + +-- | Simulate phylogenetic trees. +simulate :: Maybe FilePath -> Simulate () +simulate outFile = do + a <- lift ask + when (isNothing (argsHeight a) && argsConditionMRCA a) $ + error "Cannot condition on MRCA (-M) when height is not given (-H)." + let s = argsSumStat a + nCap <- liftIO getNumCapabilities + logNewSection "Arguments" + $(logInfo) $ T.pack $ reportSimulateArguments a + logNewSection "Simulation" + $(logInfo) $ T.pack $ "Number of used cores: " <> show nCap + trs <- if argsSubSample a + then simulateAndSubSampleNTreesConcurrently nCap + else simulateNTreesConcurrently nCap + let ls = if s + then parMap rpar (formatNChildSumStat . toNChildSumStat) trs + else parMap rpar toNewick trs + let outFile' = (++ ".tree") <$> outFile + let res = L.unlines ls + io "simulated trees" res outFile' + +simulateNTreesConcurrently :: Int -> Simulate [Tree PhyloIntLabel] +simulateNTreesConcurrently c = do + (SimulateArguments nT nL h cM l m r _ _ s) <- lift ask + let l' = l * r + m' = m - l * (1.0 - r) + gs <- liftIO $ getNGen c s + let chunks = getChunks c nT + timeSpec = fmap (, cM) h + trss <- liftIO $ mapConcurrently + (\(n, g) -> simulateNReconstructedTrees n nL timeSpec l' m' g) + (zip chunks gs) + return $ concat trss + +simulateAndSubSampleNTreesConcurrently :: Int -> Simulate [Tree PhyloIntLabel] +simulateAndSubSampleNTreesConcurrently c = do + (SimulateArguments nT nL h cM l m r _ _ s) <- lift ask + let nLeavesBigTree = (round $ fromIntegral nL / r) :: Int + gs <- liftIO $ getNGen c s + let chunks = getChunks c nT + timeSpec = fmap (, cM) h + tr <- liftIO $ simulateReconstructedTree nLeavesBigTree timeSpec l m (head gs) + logNewSection $ T.pack $ "Simulate one big tree with " <> show nLeavesBigTree <> " leaves." + -- Log the base tree. + $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick tr + logNewSection $ T.pack $ "Sub sample " <> show nT <> " trees with " <> show nL <> " leaves." + let lvs = Seq.fromList $ leaves tr + trss <- liftIO $ mapConcurrently + (\(nSamples, g) -> nSubSamples nSamples lvs nL tr g) + (zip chunks gs) + let trs = catMaybes $ concat trss + return $ map prune trs diff --git a/tlynx.cabal b/tlynx.cabal new file mode 100644 --- /dev/null +++ b/tlynx.cabal @@ -0,0 +1,87 @@ +cabal-version: 1.12 +name: tlynx +version: 0.0.1 +license: GPL-3 +license-file: LICENSE +copyright: Dominik Schrempf (2019) +maintainer: dominik.schrempf@gmail.com +author: Dominik Schrempf +homepage: https://github.com/dschrempf/elynx#readme +bug-reports: https://github.com/dschrempf/elynx/issues +synopsis: Handle phylogenetic trees +description: + Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at . +category: Bioinformatics +build-type: Simple +extra-source-files: + README.md + ChangeLog.md + +source-repository head + type: git + location: https://github.com/dschrempf/elynx + +library + exposed-modules: + Compare.Compare + Compare.Options + Examine.Examine + Examine.Options + Simulate.Options + Simulate.Simulate + hs-source-dirs: src + other-modules: + Paths_tlynx + default-language: Haskell2010 + ghc-options: -Wall + build-depends: + QuickCheck >=2.13.2 && <2.14, + base >=4.12.0.0 && <4.13, + bytestring >=0.10.8.2 && <0.11, + containers >=0.6.0.1 && <0.7, + elynx-seq >=0.0.1 && <0.1, + elynx-tools >=0.0.1 && <0.1, + elynx-tree >=0.0.1 && <0.1, + lifted-async >=0.10.0.4 && <0.11, + math-functions >=0.3.1.0 && <0.4, + megaparsec >=7.0.5 && <7.1, + monad-logger >=0.3.30 && <0.4, + mwc-random >=0.14.0.0 && <0.15, + optparse-applicative >=0.14.3.0 && <0.15, + parallel >=3.2.2.0 && <3.3, + primitive >=0.6.4.0 && <0.7, + quickcheck-instances >=0.3.22 && <0.4, + statistics >=0.15.0.0 && <0.16, + text >=1.2.3.1 && <1.3, + transformers >=0.5.6.2 && <0.6, + vector >=0.12.0.3 && <0.13 + +executable tlynx + main-is: Main.hs + hs-source-dirs: app + other-modules: + Options + Paths_tlynx + default-language: Haskell2010 + ghc-options: -Wall -eventlog -threaded -rtsopts -with-rtsopts=-N + build-depends: + QuickCheck >=2.13.2 && <2.14, + base >=4.12.0.0 && <4.13, + bytestring >=0.10.8.2 && <0.11, + containers >=0.6.0.1 && <0.7, + elynx-tools >=0.0.1 && <0.1, + elynx-tree >=0.0.1 && <0.1, + lifted-async >=0.10.0.4 && <0.11, + math-functions >=0.3.1.0 && <0.4, + megaparsec >=7.0.5 && <7.1, + monad-logger >=0.3.30 && <0.4, + mwc-random >=0.14.0.0 && <0.15, + optparse-applicative >=0.14.3.0 && <0.15, + parallel >=3.2.2.0 && <3.3, + primitive >=0.6.4.0 && <0.7, + quickcheck-instances >=0.3.22 && <0.4, + statistics >=0.15.0.0 && <0.16, + text >=1.2.3.1 && <1.3, + tlynx -any, + transformers >=0.5.6.2 && <0.6, + vector >=0.12.0.3 && <0.13