diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,6 +5,16 @@ ## Unreleased changes +## Version 0.6.0.0 + +- **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer` + too special and slow). +- **elynx-tree:** fix various tree instances; add zip trees with appropriate + instances. +- Remove `monad-logger` dependency and implement lighter alternative. +- Significant changes to the tool chain. + + ## Version 0.5.1.0 - **elynx-tree:** new functions `isValidPath`, `isLeaf`, `depth`; add conversion diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.5.1.0. +Version: 0.6.0.0. Reproducible evolution made easy.

@@ -39,7 +39,7 @@ # Installation -ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/). +ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [cabal-install](https://cabal.readthedocs.io/en/3.4/cabal-commands.html) or [Stack](https://docs.haskellstack.org/en/stable/README/). 1. Install Stack with your package manager, or directly from the web page. @@ -67,15 +67,15 @@ [PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly. -# SLynx +# Get help -Handle evolutionary sequences. +For example: - stack exec slynx -- --help | head -n -16 + slynx --help - ELynx Suite version 0.5.1.0. + ELynx Suite version 0.6.0.0. Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. + Compiled on September 3, 2021, at 20:56 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -84,7 +84,7 @@ Available options: -h,--help Show this help text -V,--version Show version - -v,--verbosity VALUE Be verbose; one of: Quiet Warning Info Debug + -v,--verbosity VALUE Be verbose; one of: Quiet Warn Info Debug (default: Info) -o,--output-file-basename NAME Specify base name of output file @@ -112,107 +112,33 @@ - Protein (amino acids) - ProteinX (amino acids; including gaps) - ProteinS (amino acids; including gaps, and translation stops) - - -## Concatenate - -Concatenate multi sequence alignments. - - stack exec slynx -- concatenate --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE - Concatenate sequences found in input files. - - Available options: - -h,--help Show this help text - -V,--version Show version - -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`. - - stack exec slynx -- examine --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] - Examine sequences. If data is a multi sequence alignment, additionally analyze columns. - - Available options: - -h,--help Show this help text - -V,--version Show version - -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`. - - stack exec slynx -- filter-rows --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] - [--shorter-than LENGTH] [--standard-characters] - Filter rows (or sequences) found in input files. - - Available options: - -h,--help Show this help text - -V,--version Show version - -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 - --standard-characters Only keep sequences containing at least one standard - (i.e., non-IUPAC) character - -h,--help Show this help text - -Filter columns of multi sequence alignments with `filter-columns`. - - stack exec slynx -- filter-columns --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. + - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes) + ELynx + ----- + A Haskell library and tool set for computational biology. The goal of ELynx is + reproducible research. Evolutionary sequences and phylogenetic trees can be + read, viewed, modified and simulated. The command line with all arguments is + logged consistently, and automatically. Data integrity is verified using SHA256 + sums so that validation of past analyses is possible without the need to + recompute the result. - Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE - [--standard-chars DOUBLE] - Filter columns of multi sequence alignments. + slynx Analyze, modify, and simulate evolutionary sequences. + tlynx Analyze, modify, and simulate phylogenetic trees. + elynx Validate and redo past analyses. - Available options: - -h,--help Show this help text - -V,--version Show version - -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 + Get help for sub commands: + slynx examine --help -## Simulate +## Sub command -Simulate sequences with `slynx simulate`. +The documentation of sub commands can be accessed separately: - stack exec slynx -- simulate --help + slynx simulate --help - ELynx Suite version 0.5.1.0. + ELynx Suite version 0.6.0.0. Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. + Compiled on September 3, 2021, at 20:56 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -281,315 +207,4 @@ LG exchangeabilities with site profiles (Phylobayes) given in FILES. -m "EDM(LG-Custom)" -p FILES For special mixture models, mixture weights are optional. - - -## Sub-sample - -Sub-sample columns from multi sequence alignments. - - stack exec slynx -- sub-sample --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE - (-n|--number-of-sites INT) - (-m|--number-of-alignments INT) [-S|--seed [INT]] - Sub-sample columns from multi sequence alignments. - - Available options: - -h,--help Show this help text - -V,--version Show version - -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 - - Create a given number of multi sequence alignments, each of which contains a given number of random sites drawn from the original multi sequence alignment. - - -## Translate - -Translate sequences. - - stack exec slynx -- translate --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) - (-u|--universal-code CODE) - Translate from DNA to Protein or DNAX to ProteinX. - - Available options: - -h,--help Show this help text - -V,--version Show version - -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. - - stack exec tlynx -- --help | head -n -16 - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] - [-f|--force] [--no-elynx-file] 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 - -f,--force Ignore previous analysis and overwrite existing - output files. - --no-elynx-file Do not write data required to reproduce an analysis. - - Available commands: - compare Compare two phylogenetic trees (compute distances and branch-wise differences). - connect Connect two phylogenetic trees in all ways (possibly honoring constraints). - distance Compute distances between many phylogenetic trees. - examine Compute summary statistics of phylogenetic trees. - shuffle Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves). - simulate Simulate phylogenetic trees using a birth and death or coalescent process. - - - Available tree file formats: - - Newick Standard: Branch support values are stored in square brackets after branch lengths. - - Newick IqTree: Branch support values are stored as node names after the closing bracket of forests. - - Newick RevBayes: Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment. - - -## Compare - -Compute distances between phylogenetic trees. - - stack exec tlynx -- compare --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] - [-f|--newick-format FORMAT] NAMES - Compare two phylogenetic trees (compute distances and branch-wise differences). - - Available options: - -h,--help Show this help text - -V,--version Show version - -n,--normalize Normalize trees before comparison - -b,--bipartitions Print and plot common and missing bipartitions - -t,--intersect Compare intersections; i.e., before comparison, drop - leaves that are not present in the other tree - -f,--newick-format FORMAT - Newick tree format: Standard, IqTree, or RevBayes; - default: Standard; for detailed help, see 'tlynx - --help' - NAMES Tree files - -h,--help Show this help text - - -## Connect - -Connect two phylogenetic tree in all ways (possibly honoring constraints). - - stack exec tlynx -- connect --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx connect [-f|--newick-format FORMAT] [-c|--contraints CONSTRAINTS] - TREE-FILE-A TREE-FILE-B - Connect two phylogenetic trees in all ways (possibly honoring constraints). - - Available options: - -h,--help Show this help text - -V,--version Show version - -f,--newick-format FORMAT - Newick tree format: Standard, IqTree, or RevBayes; - default: Standard; for detailed help, see 'tlynx - --help' - -c,--contraints CONSTRAINTS - File containing one or more Newick trees to be used - as constraints - TREE-FILE-A File containing the first Newick tree - TREE-FILE-B File containing the second Newick tree - -h,--help Show this help text - - -## Distancce - -Compute distances between many phylogenetic trees. - - stack exec tlynx -- distance --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx distance (-d|--distance MEASURE) [-n|--normalize] [-t|--intersect] - [-s|--summary-statistics] - [-m|--master-tree-file MASTER-TREE-File] - [-f|--newick-format FORMAT] [INPUT-FILES] - Compute distances between many phylogenetic trees. - - Available options: - -h,--help Show this help text - -V,--version Show version - -d,--distance MEASURE Type of distance to calculate (available distance - measures are listed below) - -n,--normalize Normalize trees before distance calculation; only - affect distances depending on branch lengths - -t,--intersect Compare intersections; i.e., before comparison, drop - leaves that are not present in the other tree - -s,--summary-statistics Report summary statistics only - -m,--master-tree-file MASTER-TREE-File - Compare all trees to the tree in the master tree - file. - -f,--newick-format FORMAT - Newick tree format: Standard, IqTree, or RevBayes; - default: Standard; for detailed help, see 'tlynx - --help' - 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 - - Distance measures: - symmetric Symmetric distance (Robinson-Foulds distance). - incompatible-split[VAL] Incompatible split distance. Collapse branches with (normalized) - support less than 0.0<=VAL<=1.0 before distance calculation; - if, let's say, VAL>0.7, only well supported differences contribute - to the total distance. - branch-score Branch score distance. - - -## Examine - -Compute summary statistics of phylogenetic trees. - - stack exec tlynx -- examine --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] - Compute summary statistics of phylogenetic trees. - - Available options: - -h,--help Show this help text - -V,--version Show version - INPUT-FILE Read trees from INPUT-FILE - -f,--newick-format FORMAT - Newick tree format: Standard, IqTree, or RevBayes; - default: Standard; for detailed help, see 'tlynx - --help' - -h,--help Show this help text - - -## Shuffle - -Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and -leaves). - - stack exec tlynx -- shuffle --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx shuffle [-f|--newick-format FORMAT] [-n|--replicates N] TREE-FILE - [-S|--seed [INT]] - Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves). - - Available options: - -h,--help Show this help text - -V,--version Show version - -f,--newick-format FORMAT - Newick tree format: Standard, IqTree, or RevBayes; - default: Standard; for detailed help, see 'tlynx - --help' - -n,--replicates N Number of trees to generate - TREE-FILE File containing a Newick tree - -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 - - -## Simulate - -Simulate phylogenetic trees using birth and death processes. - - stack exec tlynx -- simulate --help - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS - [-u|--sub-sample DOUBLE] [-s|--summary-statistics] - [-S|--seed [INT]] - Simulate phylogenetic trees using a birth and death or coalescent process. - - Available options: - -h,--help Show this help text - -V,--version Show version - -t,--nTrees INT Number of trees - -n,--nLeaves INT Number of leaves per tree - -u,--sub-sample DOUBLE Perform sub-sampling; see below. - -s,--summary-statistics For each branch, print length and number of children - -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 - - Available processes: - birthdeath Birth and death process - coalescent Coalescent process - - See, for example, 'tlynx simulate birthdeath --help'. - Sub-sample with probability p: - 1. Simulate one big tree with n'=round(n/p), n'>=n, leaves; - 2. Randomly sample sub-trees with n leaves. - (With p=1.0, the same tree is reported over and over again.) - - -# ELynx - -Validate and (optionally) redo past ELynx analyses. - - stack exec elynx -- --help | head -n -16 - - ELynx Suite version 0.5.1.0. - Developed by Dominik Schrempf. - Compiled on June 12, 2021, at 14:54 pm, UTC. - - Usage: elynx COMMAND - Validate and redo past ELynx analyses - - Available options: - -h,--help Show this help text - -V,--version Show version - - Available commands: - validate Validate an ELynx analysis - redo Redo an ELynx analysis diff --git a/src/TLynx/Compare/Compare.hs b/src/TLynx/Compare/Compare.hs --- a/src/TLynx/Compare/Compare.hs +++ b/src/TLynx/Compare/Compare.hs @@ -19,21 +19,14 @@ import Control.Monad import Control.Monad.IO.Class -import Control.Monad.Logger import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL import Data.List (intercalate) import qualified Data.Map as M import qualified Data.Set as S import qualified Data.Text as T -import qualified Data.Text.Encoding as E import qualified Data.Text.IO as T import ELynx.Tools - ( Arguments (..), - ELynx, - GlobalArguments (..), - outHandle, - ) import ELynx.Tree import Graphics.Gnuplot.Simple import System.IO @@ -47,8 +40,8 @@ CompareArguments (Tree Phylo Name, Tree Phylo Name) treesOneFile tf = do - nwF <- argsNewickFormat . local <$> ask - $(logInfo) $ T.pack $ "Parse file '" ++ tf ++ "'." + nwF <- argsNewickFormat . localArguments <$> ask + logInfoS $ "Parse file '" ++ tf ++ "'." ts <- liftIO $ parseTrees nwF tf let n = length ts case compare n 2 of @@ -64,25 +57,25 @@ CompareArguments (Tree Phylo Name, Tree Phylo Name) treesTwoFiles tf1 tf2 = do - nwF <- argsNewickFormat . local <$> ask - $(logInfo) $ T.pack $ "Parse first tree file '" ++ tf1 ++ "'." + nwF <- argsNewickFormat . localArguments <$> ask + logInfoS $ "Parse first tree file '" ++ tf1 ++ "'." t1 <- liftIO $ parseTree nwF tf1 - $(logInfo) $ T.pack $ "Parse second tree file '" ++ tf2 ++ "'." + logInfoS $ "Parse second tree file '" ++ tf2 ++ "'." t2 <- liftIO $ parseTree nwF tf2 return (t1, t2) -- | More detailed comparison of two trees. compareCmd :: ELynx CompareArguments () compareCmd = do - l <- local <$> ask + l <- localArguments <$> ask -- Determine output handle (stdout or file). outH <- outHandle "results" ".out" -- Read input. - let inFiles = argsInFiles l - nFiles = length inFiles - (tr1, tr2) <- case nFiles of - 1 -> treesOneFile (head inFiles) - 2 -> treesTwoFiles (head inFiles) (head . tail $ inFiles) + let inFs = argsInFiles l + nFs = length inFs + (tr1, tr2) <- case nFs of + 1 -> treesOneFile (head inFs) + 2 -> treesTwoFiles (head inFs) (head . tail $ inFs) _ -> error "Need two input files with one tree each or one input file with two trees." @@ -122,7 +115,7 @@ formatD "Symmetric" (T.pack $ show $ symmetric t1 t2) - case (phyloToLengthTree t1, phyloToLengthTree t2) of + case (toLengthTree t1, toLengthTree t2) of (Right t1', Right t2') -> do liftIO $ T.hPutStrLn outH $ @@ -130,15 +123,15 @@ "Branch score" (T.pack $ show $ branchScore t1' t2') _ -> do - $(logInfo) "Some branches do not have length values." - $(logInfo) "Distances involving length cannot be calculated." + logInfoS "Some branches do not have length values." + logInfoS "Distances involving length cannot be calculated." case (toExplicitTree t1, toExplicitTree t2) of (Right t1', Right t2') -> do let t1n = normalizeBranchSupport t1' t2n = normalizeBranchSupport t2' - $(logDebug) "Trees with normalized branch support values:" - $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t1n - $(logDebug) $ E.decodeUtf8 $ BL.toStrict $ toNewick $ toPhyloTree t2n + logDebugS "Trees with normalized branch support values:" + logDebugB $ toNewick $ toPhyloTree t1n + logDebugB $ toNewick $ toPhyloTree t2n liftIO $ T.hPutStrLn outH $ formatD @@ -172,8 +165,8 @@ -- (T.pack $ show $ incompatibleSplits (collapse 1.01 t1n) (collapse 1.01 t2n)) -- liftIO $ BL.hPutStrLn outH $ toNewick (collapse 1.01 t1n) _ -> do - $(logInfo) "Some branches do not have support values." - $(logInfo) "Distances involving branch support cannot be calculated." + logInfoS "Some branches do not have support values." + logInfoS "Distances involving branch support cannot be calculated." analyzeBipartitions :: Handle -> @@ -181,7 +174,7 @@ Tree Phylo Name -> ELynx CompareArguments () analyzeBipartitions outH t1 t2 = - case (phyloToLengthTree t1, phyloToLengthTree t2) of + case (toLengthTree t1, toLengthTree t2) of (Right t1l, Right t2l) -> do let bp1 = either error id $ bipartitions t1l bp2 = either error id $ bipartitions t2l @@ -214,8 +207,8 @@ liftIO $ hPutStrLn outH "There are no common bipartitions." liftIO $ hPutStrLn outH "No plots have been generated." else do - let bpToBrLen1 = M.map (fromLength . getLen) $ either error id $ bipartitionToBranch t1l - bpToBrLen2 = M.map (fromLength . getLen) $ either error id $ bipartitionToBranch t2l + let bpToBrLen1 = M.map (fromLength . getLength) $ either error id $ bipartitionToBranch t1l + bpToBrLen2 = M.map (fromLength . getLength) $ either error id $ bipartitionToBranch t2l liftIO $ hPutStrLn outH @@ -230,19 +223,19 @@ ) -- XXX: This circumvents the extension checking, and hash creation for -- elynx files. - bn <- outFileBaseName . global <$> ask + bn <- outFileBaseName . globalArguments <$> ask case bn of Nothing -> - $(logInfo) "No output file name provided. Do not generate plots." + logInfoS "No output file name provided. Do not generate plots." Just fn -> do let compareCommonBps = [ (bpToBrLen1 M.! b, bpToBrLen2 M.! b) | b <- S.toList bpCommon ] liftIO $ epspdfPlot fn (plotBps compareCommonBps) - $(logInfo) + logInfoS "Comparison of branch lengths plot generated (EPS and PDF)" - _ -> $(logWarn) "Not all branches have a length! Can not analyze bipartitions." + _ -> logWarnS "Not all branches have a length! Can not analyze bipartitions." header :: String header = intercalate " " $ cols ++ ["Bipartition"] diff --git a/src/TLynx/Connect/Connect.hs b/src/TLynx/Connect/Connect.hs --- a/src/TLynx/Connect/Connect.hs +++ b/src/TLynx/Connect/Connect.hs @@ -18,17 +18,11 @@ where import Control.Monad.IO.Class -import Control.Monad.Logger import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL +import Data.Default.Class import qualified Data.Set as S import ELynx.Tools - ( Arguments (..), - ELynx, - fromBs, - outHandle, - tShow, - ) import ELynx.Tree import System.IO import TLynx.Connect.Options @@ -43,7 +37,13 @@ -- introduced. -- -- Return 'Left' if one tree has a non-bifurcating root node. -connect :: (Semigroup e, Splittable e) => e -> a -> Tree e a -> Tree e a -> Either String (Forest e a) +connect :: + (Semigroup e, Splittable e, Default a) => + e -> + a -> + Tree e a -> + Tree e a -> + Either String (Forest e a) connect br lb l r = do ls <- roots l rs <- roots r @@ -55,7 +55,7 @@ -- nodes, respectively, there are (n-2)*(m-2) ways to connect them. connectCmd :: ELynx ConnectArguments () connectCmd = do - lArgs <- local <$> ask + lArgs <- localArguments <$> ask outH <- outHandle "results" ".out" -- Do we have constraints or not? let cs = constraints lArgs @@ -104,34 +104,34 @@ ConnectArguments (Tree Length Name, Tree Length Name) parseTreeTuple l r = do - nwF <- nwFormat . local <$> ask + nwF <- nwFormat . localArguments <$> ask tl <- liftIO $ parseTree nwF l tr <- liftIO $ parseTree nwF r - $(logInfo) "Tree 1:" - $(logInfo) $ fromBs $ toNewick tl - $(logInfo) "Tree 2:" - $(logInfo) $ fromBs $ toNewick tr - return (either error id $ phyloToLengthTree tl, either error id $ phyloToLengthTree tr) + logInfoS "Tree 1:" + logInfoB $ toNewick tl + logInfoS "Tree 2:" + logInfoB $ toNewick tr + return (either error id $ toLengthTree tl, either error id $ toLengthTree tr) connectOnly :: Handle -> FilePath -> FilePath -> ELynx ConnectArguments () connectOnly h l r = do (tl, tr) <- parseTreeTuple l r let ts = connectTrees tl tr - $(logInfo) $ "Connected trees: " <> tShow (length ts) - liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts + logInfoS $ "Connected trees: " <> show (length ts) + liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts connectAndFilter :: Handle -> FilePath -> FilePath -> FilePath -> ELynx ConnectArguments () connectAndFilter h c l r = do - nwF <- nwFormat . local <$> ask + nwF <- nwFormat . localArguments <$> ask cts <- liftIO $ parseTrees nwF c - $(logInfo) "Constraints:" - $(logInfo) $ fromBs $ BL.intercalate "\n" $ map toNewick cts + logInfoS "Constraints:" + logInfoB $ BL.intercalate "\n" $ map toNewick cts (tl, tr) <- parseTreeTuple l r let ts = connectTrees tl tr cs = map S.fromList $ concatMap multifurcatingGroups cts :: [Constraint Name] -- Only collect trees that are compatible with the constraints. ts' = filter (compatibleWith getName cs) ts - $(logInfo) $ "Connected trees: " <> tShow (length ts) - $(logInfo) $ "Compatible trees: " <> tShow (length ts') - liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts' + logInfoS $ "Connected trees: " <> show (length ts) + logInfoS $ "Compatible trees: " <> show (length ts') + liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts' diff --git a/src/TLynx/Distance/Distance.hs b/src/TLynx/Distance/Distance.hs --- a/src/TLynx/Distance/Distance.hs +++ b/src/TLynx/Distance/Distance.hs @@ -24,10 +24,6 @@ when, ) import Control.Monad.IO.Class -import Control.Monad.Logger - ( logDebug, - logInfo, - ) import Control.Monad.Trans.Class import Control.Monad.Trans.Reader hiding (local) import Data.Bifunctor @@ -36,8 +32,6 @@ import Data.Maybe 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 qualified Data.Vector.Unboxed as V import ELynx.Tools import ELynx.Tree @@ -87,7 +81,7 @@ -- | Compute distance functions between phylogenetic trees. distance :: ELynx DistanceArguments () distance = do - l <- local <$> ask + l <- localArguments <$> ask let nwFormat = argsNewickFormat l -- Determine output handle (stdout or file). outH <- outHandle "results" ".out" @@ -96,44 +90,43 @@ mtree <- case mname of Nothing -> return Nothing Just f -> do - $(logInfo) $ T.pack $ "Read master tree from file: " <> f <> "." + logInfoS $ "Read master tree from file: " <> f <> "." t <- liftIO $ parseTree nwFormat f - $(logInfo) "Compute distances between all trees and master tree." + logInfoS "Compute distances between all trees and master tree." return $ Just t let tfps = argsInFiles l (trees, names) <- case tfps of [] -> error "No tree input files given." [tf] -> do - $(logInfo) "Read trees from single file." + logInfoS "Read trees from single file." ts <- liftIO $ parseTrees nwFormat tf - $(logInfo) $ tShow (length ts) <> " trees found in file." - $(logInfo) "Trees are indexed with integers." + logInfoS $ show (length ts) <> " trees found in file." + logInfoS "Trees are indexed with integers." return (ts, map show [0 .. length ts - 1]) _ -> do - $(logInfo) "Read trees from files." + logInfoS "Read trees from files." ts <- liftIO $ mapM (parseTree nwFormat) tfps - $(logInfo) "Trees are named according to their file names." + logInfoS "Trees are named according to their file names." return (ts, tfps) when (null trees) (error "Not enough trees found in files.") when (isNothing mtree && length trees == 1) (error "Not enough trees found in files.") - -- when (isNothing mtree) $ $(logInfo) + -- when (isNothing mtree) $ logInfoS -- "Compute pairwise distances between trees from different files." - $(logDebug) "The trees are:" - $(logDebug) $ LT.toStrict $ LT.decodeUtf8 $ BL.unlines $ map toNewick trees + logDebugS "The trees are:" + logDebugB $ BL.unlines $ map toNewick trees -- Set the distance measure. let dist = argsDistance l case argsDistance l of - Symmetric -> $(logInfo) "Use symmetric (Robinson-Foulds) distance." + Symmetric -> logInfoS "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 -> $(logInfo) "Use branch score distance." + logInfoS "Use incompatible split distance." + logInfoS $ + "Collapse nodes with support less than " + ++ show val + ++ "." + BranchScore -> logInfoS "Use branch score distance." let distanceMeasure' :: Tree Phylo Name -> Tree Phylo Name -> @@ -143,15 +136,17 @@ IncompatibleSplit val -> second fromIntegral $ incompatibleSplits - (collapse val $ normalizeBranchSupport $ either error id $ phyloToSupportTree t1) - (collapse val $ normalizeBranchSupport $ either error id $ phyloToSupportTree t2) + (collapse val $ normalizeBranchSupport $ either error id $ toSupportTree t1) + (collapse val $ normalizeBranchSupport $ either error id $ toSupportTree t2) BranchScore -> - branchScore (normalizeF $ either error id $ phyloToLengthTree t1) (normalizeF $ either error id $ phyloToLengthTree t2) + branchScore + (normalizeF $ either error id $ toLengthTree t1) + (normalizeF $ either error id $ toLengthTree t2) where normalizeF = if argsNormalize l then normalizeBranchLengths else id -- Possibly intersect trees before distance calculation. when (argsIntersect l) $ - $(logInfo) "Intersect trees before calculation of distances." + logInfoS "Intersect trees before calculation of distances." let distanceMeasure = if argsIntersect l then @@ -162,12 +157,13 @@ else distanceMeasure' -- Possibly normalize trees. when (argsNormalize l) $ - $(logInfo) "Normalize trees before calculation of distances." + logInfoS "Normalize trees before calculation of distances." let dsTriplets = case mtree of Nothing -> pairwise distanceMeasure trees Just masterTree -> [(0, i, distanceMeasure masterTree t') | (i, t') <- zip [1 ..] trees] ds = map (\(_, _, x) -> x) dsTriplets dsVec = V.fromList ds + -- TODO: This should never happen (hPutStrLn??). liftIO $ hPutStrLn outH $ "Summary statistics of " @@ -192,24 +188,23 @@ -- BS.putStrLn $ BS.unlines $ map toNewick tsN -- BS.putStrLn $ BS.unlines $ map toNewick tsC - lift $ - unless - (argsSummaryStatistics l) - ( do - let n = maximum $ 6 : map length names - m = length $ show dist - lift $ hPutStrLn outH "" - lift $ BL.hPutStrLn outH $ header n m dist - case mname of - Nothing -> - lift $ - BL.hPutStr outH $ - BL.unlines - (map (showTriplet n m names) dsTriplets) - Just mn -> - lift $ - BL.hPutStr outH $ - BL.unlines - (map (showTriplet n m (mn : names)) dsTriplets) - ) + unless + (argsSummaryStatistics l) + ( do + let n = maximum $ 6 : map length names + m = length $ show dist + lift $ hPutStrLn outH "" + lift $ BL.hPutStrLn outH $ header n m dist + case mname of + Nothing -> + lift $ + BL.hPutStr outH $ + BL.unlines + (map (showTriplet n m names) dsTriplets) + Just mn -> + lift $ + BL.hPutStr outH $ + BL.unlines + (map (showTriplet n m (mn : names)) dsTriplets) + ) liftIO $ hClose outH diff --git a/src/TLynx/Examine/Examine.hs b/src/TLynx/Examine/Examine.hs --- a/src/TLynx/Examine/Examine.hs +++ b/src/TLynx/Examine/Examine.hs @@ -18,12 +18,10 @@ import Control.Monad (unless) import Control.Monad.IO.Class -import Control.Monad.Logger import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL import Data.Containers.ListUtils (nubOrd) import Data.List ((\\)) -import qualified Data.Text as T import ELynx.Tools import ELynx.Tree import System.IO @@ -60,14 +58,14 @@ readTrees :: FilePath -> ELynx ExamineArguments (Forest Phylo Name) readTrees fp = do - $(logInfo) $ T.pack $ "Read tree(s) from file " <> fp <> "." - nf <- argsNewickFormat . local <$> ask + logInfoS $ "Read tree(s) from file " <> fp <> "." + nf <- argsNewickFormat . localArguments <$> ask liftIO $ parseTrees nf fp examineTree :: HasName a => Handle -> Tree Phylo a -> IO () examineTree h t = do hPutStrLn h $ "Number of leaves: " ++ show (length lvs) - let l = phyloToLengthTree t + let l = toLengthTree t case l of Left _ -> hPutStrLn h "Branch lengths not available." Right t' -> BL.hPutStrLn h $ summarizeLengths t' @@ -82,7 +80,7 @@ -- | Examine phylogenetic trees. examine :: ELynx ExamineArguments () examine = do - l <- local <$> ask + l <- localArguments <$> ask let inFn = argsInFile l trs <- readTrees inFn outH <- outHandle "results" ".out" diff --git a/src/TLynx/Shuffle/Options.hs b/src/TLynx/Shuffle/Options.hs --- a/src/TLynx/Shuffle/Options.hs +++ b/src/TLynx/Shuffle/Options.hs @@ -26,7 +26,7 @@ { nwFormat :: NewickFormat, nReplicates :: Int, inFile :: FilePath, - argsSeed :: Seed + argsSeed :: SeedOpt } deriving (Eq, Show, Generic) @@ -34,7 +34,7 @@ inFiles = pure . inFile outSuffixes _ = [".tree"] getSeed = Just . argsSeed - setSeed a s = a {argsSeed = Fixed s} + setSeed a s = a {argsSeed = s} parser = shuffleArguments cmdName = "shuffle" cmdDsc = diff --git a/src/TLynx/Shuffle/Shuffle.hs b/src/TLynx/Shuffle/Shuffle.hs --- a/src/TLynx/Shuffle/Shuffle.hs +++ b/src/TLynx/Shuffle/Shuffle.hs @@ -23,7 +23,6 @@ import qualified Control.Comonad as C import Control.Monad (when) import Control.Monad.IO.Class (liftIO) -import Control.Monad.Logger (logDebug, logInfo) import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Lazy.Char8 as BL import ELynx.Tools @@ -34,8 +33,8 @@ ) import System.IO (hClose) import System.Random.MWC (GenIO, initialize) -import TLynx.Shuffle.Options import TLynx.Parsers +import TLynx.Shuffle.Options -- | Shuffle a tree. Get all coalescent times, shuffle them. Get all leaves, -- shuffle them. Connect the shuffled leaves with the shuffled coalescent times. @@ -43,32 +42,34 @@ -- times and leaves. shuffleCmd :: ELynx ShuffleArguments () shuffleCmd = do - l <- local <$> ask + l <- localArguments <$> ask h <- outHandle "results" ".tree" let nwF = nwFormat l tPhylo <- liftIO $ parseTree nwF (inFile l) - $(logInfo) "Input tree:" - $(logInfo) $ fromBs $ toNewick tPhylo - let t = either error id $ phyloToLengthTree tPhylo + logInfoS "Input tree:" + logInfoB $ toNewick tPhylo + let t = either error id $ toLengthTree tPhylo -- Check if tree is ultrametric enough. let dh = sum $ map (height t -) (distancesOriginLeaves t) - $(logDebug) $ "Distance in branch length to being ultrametric: " <> tShow dh + logDebugS $ "Distance in branch length to being ultrametric: " <> show dh when (dh > 2e-4) (error "Tree is not ultrametric.") when (dh > toLengthUnsafe eps && dh < 2e-4) $ - $(logInfo) + logInfoS "Tree is nearly ultrametric, ignore branch length differences smaller than 2e-4." - when (dh < toLengthUnsafe eps) $ $(logInfo) "Tree is ultrametric." + when (dh < toLengthUnsafe eps) $ logInfoS "Tree is ultrametric." let cs = filter (> 0) $ labels $ C.extend rootHeight t ls = map getName $ leaves t - $(logDebug) $ "Number of coalescent times: " <> tShow (length cs) - $(logDebug) $ "Number of leaves: " <> tShow (length ls) - $(logDebug) "The coalescent times are: " - $(logDebug) $ tShow cs - gen <- case argsSeed l of - Random -> error "Seed not available; please contact maintainer." - Fixed s -> liftIO $ initialize s + logDebugS $ "Number of coalescent times: " <> show (length cs) + logDebugS $ "Number of leaves: " <> show (length ls) + logDebugS "The coalescent times are: " + logDebugS $ show cs + gen <- liftIO $ + initialize $ case argsSeed l of + RandomUnset -> error "Seed not available; please contact maintainer." + RandomSet s -> s + Fixed s -> s ts <- liftIO $ shuffleT (nReplicates l) (height t) cs ls gen - liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . measurableToPhyloTree) ts + liftIO $ BL.hPutStr h $ BL.unlines $ map (toNewick . lengthToPhyloTree) ts liftIO $ hClose h shuffleT :: diff --git a/src/TLynx/Simulate/Options.hs b/src/TLynx/Simulate/Options.hs --- a/src/TLynx/Simulate/Options.hs +++ b/src/TLynx/Simulate/Options.hs @@ -24,7 +24,7 @@ import Data.List import Data.Maybe -import ELynx.Tools hiding (Random) +import ELynx.Tools import ELynx.Tree.Simulate.PointProcess (TimeSpec (..)) import Options.Applicative @@ -85,7 +85,7 @@ -- | Only print summary statistics? argsSumStat :: Bool, -- | Seed of NRG, random if 'Nothing'. - argsSeed :: Seed + argsSeed :: SeedOpt } deriving (Eq, Show, Generic) @@ -93,7 +93,7 @@ inFiles _ = [] outSuffixes _ = [".tree"] getSeed = Just . argsSeed - setSeed a s = a {argsSeed = Fixed s} + setSeed a s = a {argsSeed = s} parser = simulateArguments cmdName = "simulate" cmdDsc = ["Simulate phylogenetic trees using a birth and death or coalescent process."] @@ -243,5 +243,5 @@ simulateFooter :: [String] simulateFooter = [ "See, for example, 'tlynx simulate birthdeath --help'.", - "Sub-sample with probability p:\n 1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;\n 2. Randomly sample sub-trees with n leaves.\n (With p=1.0, the same tree is reported over and over again.)" + "Sub-sample with probability p:\n 1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;\n 2. Randomly sample sub trees with n leaves.\n (With p=1.0, the same tree is reported over and over again.)" ] diff --git a/src/TLynx/Simulate/Simulate.hs b/src/TLynx/Simulate/Simulate.hs --- a/src/TLynx/Simulate/Simulate.hs +++ b/src/TLynx/Simulate/Simulate.hs @@ -26,12 +26,11 @@ where import Control.Concurrent (getNumCapabilities) -import Control.Concurrent.Async.Lifted.Safe +import Control.Concurrent.Async ( mapConcurrently, ) import Control.Monad import Control.Monad.IO.Class -import Control.Monad.Logger import Control.Monad.Trans.Reader hiding (local) import Control.Parallel.Strategies import qualified Data.ByteString.Builder as BB @@ -40,9 +39,6 @@ import Data.Maybe import qualified Data.Sequence as Seq import qualified Data.Set as Set -import qualified Data.Text as T -import qualified Data.Text.Lazy as LT -import qualified Data.Text.Lazy.Encoding as LT import ELynx.Tools import ELynx.Tree import qualified ELynx.Tree.Simulate.Coalescent as CS @@ -53,12 +49,12 @@ -- | Simulate phylogenetic trees using birth and death process. simulate :: ELynx SimulateArguments () simulate = do - l@(SimulateArguments nTrees nLeaves pr subS sumS (Fixed s)) <- local <$> ask + l@(SimulateArguments nTrees nLeaves pr subS sumS (Fixed s)) <- localArguments <$> ask c <- liftIO getNumCapabilities - logNewSection "Arguments" - $(logInfo) $ T.pack $ reportSimulateArguments l - logNewSection "Simulation" - $(logInfo) $ T.pack $ "Number of used cores: " <> show c + logInfoNewSection "Arguments" + logInfoS $ reportSimulateArguments l + logInfoNewSection "Simulation" + logInfoS $ "Number of used cores: " <> show c gs <- liftIO $ initialize s >>= \gen -> splitGen c gen let chunks = getChunks c nTrees trs <- case pr of @@ -82,7 +78,7 @@ let ls = if sumS then parMap rpar (formatNChildSumStat . toNChildSumStat) trs - else parMap rpar toNewick $ map measurableToPhyloTree trs + else parMap rpar toNewick $ map lengthToPhyloTree trs let res = BL.unlines ls out "simulated trees" res ".tree" @@ -130,21 +126,19 @@ let nLeavesBigTree = (round $ fromIntegral nLeaves / p) :: Int l' = l * r m' = m - l * (1.0 - r) - logNewSection $ - T.pack $ - "Simulate one big tree with " - <> show nLeavesBigTree - <> " leaves." + logInfoNewSection $ + "Simulate one big tree with " + <> show nLeavesBigTree + <> " leaves." tr <- liftIO $ PP.simulateReconstructedTree nLeavesBigTree timeSpec l' m' (head gs) -- Log the base tree. - $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ measurableToPhyloTree tr - logNewSection $ - T.pack $ - "Sub sample " - <> show (sum chunks) - <> " trees with " - <> show nLeaves - <> " leaves." + logInfoB $ toNewick $ lengthToPhyloTree tr + logInfoNewSection $ + "Sub sample " + <> show (sum chunks) + <> " trees with " + <> show nLeaves + <> " leaves." let lvs = Seq.fromList $ leaves tr trss <- liftIO $ @@ -162,21 +156,19 @@ ELynx SimulateArguments (Forest Length Int) coalSimulateAndSubSampleNTreesConcurrently nL p chunks gs = do let nLeavesBigTree = (round $ fromIntegral nL / p) :: Int - logNewSection $ - T.pack $ - "Simulate one big tree with " - <> show nLeavesBigTree - <> " leaves." + logInfoNewSection $ + "Simulate one big tree with " + <> show nLeavesBigTree + <> " leaves." tr <- liftIO $ CS.simulate nLeavesBigTree (head gs) -- Log the base tree. - $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ toNewick $ measurableToPhyloTree tr - logNewSection $ - T.pack $ - "Sub sample " - <> show (sum chunks) - <> " trees with " - <> show nL - <> " leaves." + logInfoB $ toNewick $ lengthToPhyloTree tr + logInfoNewSection $ + "Sub sample " + <> show (sum chunks) + <> " trees with " + <> show nL + <> " leaves." let lvs = Seq.fromList $ leaves tr trss <- liftIO $ @@ -232,8 +224,8 @@ -- Compute NChilSumStat for a phylogenetic tree. toNChildSumStat :: HasLength e => Tree e a -> NChildSumStat -toNChildSumStat (Node br _ []) = [(getLen br, 1)] -toNChildSumStat (Node br _ ts) = (getLen br, sumCh) : concat nChSS +toNChildSumStat (Node br _ []) = [(getLength br, 1)] +toNChildSumStat (Node br _ ts) = (getLength br, sumCh) : concat nChSS where nChSS = map toNChildSumStat ts sumCh = sum $ map (snd . head) nChSS diff --git a/src/TLynx/TLynx.hs b/src/TLynx/TLynx.hs --- a/src/TLynx/TLynx.hs +++ b/src/TLynx/TLynx.hs @@ -24,23 +24,17 @@ import TLynx.Shuffle.Shuffle import TLynx.Simulate.Simulate --- TODO: Use a class here (e.g., elynx-wrappable) which defines the extractor function. - -- | Run TLynx with given arguments. tlynx :: Arguments CommandArguments -> IO () tlynx c = case local c of - Compare _ -> - eLynxWrapper c (\(Arguments g (Compare l)) -> Arguments g l) compareCmd - Connect _ -> - eLynxWrapper c (\(Arguments g (Connect l)) -> Arguments g l) connectCmd - Distance _ -> - eLynxWrapper c (\(Arguments g (Distance l)) -> Arguments g l) distance - Examine _ -> - eLynxWrapper c (\(Arguments g (Examine l)) -> Arguments g l) examine - Shuffle _ -> - eLynxWrapper c (\(Arguments g (Shuffle l)) -> Arguments g l) shuffleCmd - Simulate _ -> - eLynxWrapper c (\(Arguments g (Simulate l)) -> Arguments g l) simulate + Compare l -> eLynxWrapper g l Compare compareCmd + Connect l -> eLynxWrapper g l Connect connectCmd + Distance l -> eLynxWrapper g l Distance distance + Examine l -> eLynxWrapper g l Examine examine + Shuffle l -> eLynxWrapper g l Shuffle shuffleCmd + Simulate l -> eLynxWrapper g l Simulate simulate + where + g = global c -- | Run TLynx, parse arguments from command line. rTLynx :: IO () diff --git a/tlynx.cabal b/tlynx.cabal --- a/tlynx.cabal +++ b/tlynx.cabal @@ -1,78 +1,79 @@ -cabal-version: 2.2 -name: tlynx -version: 0.5.1.1 -license: GPL-3.0-or-later -license-file: LICENSE -copyright: Dominik Schrempf (2021) -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 . +cabal-version: 2.2 +name: tlynx +version: 0.6.0.0 +synopsis: Handle phylogenetic trees +description: Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at . +category: Bioinformatics +homepage: https://github.com/dschrempf/elynx#readme +bug-reports: https://github.com/dschrempf/elynx/issues +author: Dominik Schrempf +maintainer: dominik.schrempf@gmail.com +copyright: Dominik Schrempf (2021) +license: GPL-3.0-or-later +license-file: LICENSE +build-type: Simple -category: Bioinformatics -build-type: Simple extra-source-files: README.md ChangeLog.md source-repository head - type: git - location: https://github.com/dschrempf/elynx + type: git + location: https://github.com/dschrempf/elynx library - exposed-modules: - TLynx.Compare.Compare - TLynx.Compare.Options - TLynx.Connect.Connect - TLynx.Connect.Options - TLynx.Distance.Distance - TLynx.Distance.Options - TLynx.Examine.Examine - TLynx.Examine.Options - TLynx.Options - TLynx.Parsers - TLynx.Shuffle.Options - TLynx.Shuffle.Shuffle - TLynx.Simulate.Options - TLynx.Simulate.Simulate - TLynx.TLynx - - hs-source-dirs: src - other-modules: Paths_tlynx - autogen-modules: Paths_tlynx - default-language: Haskell2010 - ghc-options: -Wall -Wunused-packages - build-depends: - aeson >=1.5.6.0, - attoparsec >=0.13.2.5, - base >=4.7 && <5, - bytestring >=0.10.12.0, - comonad >=5.0.8, - containers >=0.6.2.1, - elynx-tools >=0.5.1.1, - elynx-tree >=0.5.1.1, - gnuplot >=0.5.6.1, - lifted-async >=0.10.2, - monad-logger >=0.3.36, - mwc-random >=0.15.0.1, - optparse-applicative >=0.16.1.0, - parallel >=3.2.2.0, - statistics >=0.15.2.0, - text >=1.2.4.1, - transformers >=0.5.6.2, - vector >=0.12.3.0 + exposed-modules: + TLynx.Compare.Compare + TLynx.Compare.Options + TLynx.Connect.Connect + TLynx.Connect.Options + TLynx.Distance.Distance + TLynx.Distance.Options + TLynx.Examine.Examine + TLynx.Examine.Options + TLynx.Options + TLynx.Parsers + TLynx.Shuffle.Options + TLynx.Shuffle.Shuffle + TLynx.Simulate.Options + TLynx.Simulate.Simulate + TLynx.TLynx + other-modules: + Paths_tlynx + autogen-modules: + Paths_tlynx + hs-source-dirs: src + ghc-options: -Wall -Wunused-packages + build-depends: + aeson + , async + , attoparsec + , base >=4.7 && <5 + , bytestring + , comonad + , containers + , data-default-class + , elynx-tools + , elynx-tree + , gnuplot + , mwc-random + , optparse-applicative + , parallel + , statistics + , text + , transformers + , vector + default-language: Haskell2010 executable tlynx - main-is: Main.hs - hs-source-dirs: app - other-modules: Paths_tlynx - default-language: Haskell2010 - ghc-options: - -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N - - build-depends: - base >=4.7 && <5, - tlynx -any + main-is: Main.hs + other-modules: + Paths_tlynx + autogen-modules: + Paths_tlynx + hs-source-dirs: app + ghc-options: -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N + build-depends: + base >=4.7 && <5 + , tlynx + default-language: Haskell2010