tlynx (empty) → 0.0.1
raw patch · 12 files changed
+1952/−0 lines, 12 filesdep +QuickCheckdep +basedep +bytestring
Dependencies added: QuickCheck, base, bytestring, containers, elynx-seq, elynx-tools, elynx-tree, lifted-async, math-functions, megaparsec, monad-logger, mwc-random, optparse-applicative, parallel, primitive, quickcheck-instances, statistics, text, tlynx, transformers, vector
Files
- ChangeLog.md +10/−0
- LICENSE +674/−0
- README.md +417/−0
- app/Main.hs +39/−0
- app/Options.hs +86/−0
- src/Compare/Compare.hs +144/−0
- src/Compare/Options.hs +126/−0
- src/Examine/Examine.hs +53/−0
- src/Examine/Options.hs +39/−0
- src/Simulate/Options.hs +164/−0
- src/Simulate/Simulate.hs +113/−0
- tlynx.cabal +87/−0
+ ChangeLog.md view
@@ -0,0 +1,10 @@++# Table of Contents++1. [Changelog for ELynx](#org9916021)+++<a id="org9916021"></a>++# Changelog for ELynx+
+ LICENSE view
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+ README.md view
@@ -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.+
+ app/Main.hs view
@@ -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
+ app/Options.hs view
@@ -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"]
+ src/Compare/Compare.hs view
@@ -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
+ src/Compare/Options.hs view
@@ -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)" ]
+ src/Examine/Examine.hs view
@@ -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") <$> outFn+ logNewSection "Results."+ io "results of tree analysis" (L.intercalate (L.pack "\n") lsStrs) outFilePath
+ src/Examine/Options.hs view
@@ -0,0 +1,39 @@+{- |+Module : Examine.Options+Description : Tree analysis options+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Thu Aug 29 08:16:45 2019.++-}++module Examine.Options+ ( ExamineArguments (..)+ , Examine+ , examineArguments+ ) where++import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Options.Applicative++-- | Arguments needed to examine phylogenetic trees.+newtype ExamineArguments = ExamineArguments+ { inFile :: Maybe FilePath }++-- | Logger and reader data type.+type Examine = LoggingT (ReaderT ExamineArguments IO)++-- | Command line parser.+examineArguments :: Parser ExamineArguments+examineArguments = ExamineArguments <$> optional inFileArg++inFileArg :: Parser FilePath+inFileArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read trees from INPUT-FILE"
+ src/Simulate/Options.hs view
@@ -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."+ ]
+ src/Simulate/Simulate.hs view
@@ -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
+ tlynx.cabal view
@@ -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 <https://github.com/dschrempf/elynx>.+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