slynx (empty) → 0.0.1
raw patch · 20 files changed
+2621/−0 lines, 20 filesdep +asyncdep +basedep +bytestring
Dependencies added: async, base, bytestring, containers, data-memocombinators, elynx-seq, elynx-tools, elynx-tree, hmatrix, integration, lens, math-functions, matrices, megaparsec, monad-logger, mwc-random, optparse-applicative, parallel, primitive, slynx, statistics, text, transformers, vector, vector-th-unbox, word8
Files
- ChangeLog.md +10/−0
- LICENSE +674/−0
- README.md +417/−0
- app/Main.hs +44/−0
- app/Options.hs +129/−0
- slynx.cabal +105/−0
- src/Concatenate/Concatenate.hs +43/−0
- src/Concatenate/Options.hs +47/−0
- src/Examine/Examine.hs +106/−0
- src/Examine/Options.hs +54/−0
- src/Filter/Filter.hs +76/−0
- src/Filter/Options.hs +88/−0
- src/Simulate/Options.hs +168/−0
- src/Simulate/PhyloModel.hs +188/−0
- src/Simulate/Simulate.hs +158/−0
- src/SubSample/Options.hs +69/−0
- src/SubSample/SubSample.hs +70/−0
- src/Tools.hs +53/−0
- src/Translate/Options.hs +71/−0
- src/Translate/Translate.hs +51/−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 +1,44 @@+{- |+Module : Main+Description : Work with molecular sequence data+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 Concatenate.Concatenate+import Examine.Examine+import Filter.Filter+import Simulate.Simulate+import SubSample.SubSample+import Translate.Translate++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+ Concatenate a -> runReaderT (eLynxWrapper lvl lf concatenateHeader $ concatenateCmd fn) a+ Examine a -> runReaderT (eLynxWrapper lvl lf examineHeader $ examineCmd fn) a+ FilterRows a -> runReaderT (eLynxWrapper lvl lf filterRowsHeader $ filterRowsCmd fn) a+ FilterColumns a -> runReaderT (eLynxWrapper lvl lf filterColumnsHeader $ filterColumnsCmd fn) a+ Simulate a -> runReaderT (eLynxWrapper lvl lf simulateHeader $ simulateCmd fn) a+ SubSample a -> runReaderT (eLynxWrapper lvl lf subSampleHeader $ subSampleCmd fn) a+ Translate a -> runReaderT (eLynxWrapper lvl lf translateHeader $ translateCmd fn) a
+ app/Options.hs view
@@ -0,0 +1,129 @@+{- |+Module : Options+Description : SLynx 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+ , concatenateHeader+ , examineHeader+ , filterRowsHeader+ , filterColumnsHeader+ , simulateHeader+ , subSampleHeader+ , translateHeader+ ) where++import Options.Applicative+import Options.Applicative.Help.Pretty++import Concatenate.Options+import Examine.Options+import Filter.Options+import Simulate.Options+import SubSample.Options+import Translate.Options++import ELynx.Data.Alphabet.Alphabet+import ELynx.Tools.Options++data CommandArguments =+ Concatenate ConcatenateArguments+ | Examine ExamineArguments+ | FilterRows FilterRowsArguments+ | FilterColumns FilterColumnsArguments+ | Simulate SimulateArguments+ | SubSample SubSampleArguments+ | Translate TranslateArguments++concatenateHeader, examineHeader, filterRowsHeader, filterColumnsHeader, simulateHeader, subSampleHeader, translateHeader :: String+concatenateHeader = "Concatenate sequences found in input files."+examineHeader = "Examine sequences."+filterRowsHeader = "Filter rows (or sequences) found in input files."+filterColumnsHeader = "Filter columns of multi-sequence alignments."+simulateHeader = "Simulate multi sequence alignments."+subSampleHeader = "Sub-sample columns from multi sequence alignments."+translateHeader = "Translate from DNA to Protein or DNAX to ProteinX."++concatenateCommand :: Mod CommandFields CommandArguments+concatenateCommand = command "concatenate" $+ info (Concatenate <$> concatenateArguments)+ $ header concatenateHeader++examineCommand :: Mod CommandFields CommandArguments+examineCommand = command "examine" $+ info (Examine <$> examineArguments)+ ( fullDesc+ <> header examineHeader+ <> progDesc "If data is a multi sequence alignment, additionally analyze columns." )++filterRowsCommand :: Mod CommandFields CommandArguments+filterRowsCommand = command "filter-rows" $+ info (FilterRows <$> filterRowsArguments)+ $ header filterRowsHeader++filterColumnsCommand :: Mod CommandFields CommandArguments+filterColumnsCommand = command "filter-columns" $+ info (FilterColumns <$> filterColumnsArguments)+ $ header filterColumnsHeader++simulateCommand :: Mod CommandFields CommandArguments+simulateCommand = command "simulate" $+ info (Simulate <$> simulateArguments)+ (fullDesc+ <> header simulateHeader+ <> footerDoc (Just $ pretty simulateFooter) )++subSampleCommand :: Mod CommandFields CommandArguments+subSampleCommand = command "sub-sample" $+ info (SubSample <$> subSampleArguments)+ ( fullDesc+ <> header subSampleHeader+ <> progDesc "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." )++translateCommand :: Mod CommandFields CommandArguments+translateCommand = command "translate" $+ info (Translate <$> translateArguments)+ $ header translateHeader++commandArguments :: Parser CommandArguments+commandArguments = hsubparser $+ concatenateCommand+ <> examineCommand+ <> filterRowsCommand+ <> filterColumnsCommand+ <> simulateCommand+ <> subSampleCommand+ <> translateCommand++data Arguments = Arguments+ { globalArgs :: GlobalArguments+ , cmdArgs :: CommandArguments }++parseArguments :: IO Arguments+parseArguments = parseArgumentsWith desc ftr $+ Arguments+ <$> globalArguments+ <*> commandArguments++desc :: [String]+desc = [ "Analyze, and simulate multi sequence alignments." ]++ftr :: [String]+ftr = [ "File formats:" ] ++ fs +++ [ "", "Alphabet types:" ] ++ as+ where+ toListItem = (" - " ++)+ fs = map toListItem ["FASTA"]+ as = map (toListItem . alphabetNameVerbose) [(minBound :: Alphabet) ..]
+ slynx.cabal view
@@ -0,0 +1,105 @@+cabal-version: 1.12+name: slynx+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 molecular sequences+description:+ Examine, modify, and simulate molecular sequences 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:+ Concatenate.Concatenate+ Concatenate.Options+ Examine.Examine+ Examine.Options+ Filter.Filter+ Filter.Options+ Simulate.Options+ Simulate.PhyloModel+ Simulate.Simulate+ SubSample.Options+ SubSample.SubSample+ Tools+ Translate.Options+ Translate.Translate+ hs-source-dirs: src+ other-modules:+ Paths_slynx+ default-language: Haskell2010+ ghc-options: -Wall+ build-depends:+ async >=2.2.2 && <2.3,+ base >=4.12.0.0 && <4.13,+ bytestring >=0.10.8.2 && <0.11,+ containers >=0.6.0.1 && <0.7,+ data-memocombinators >=0.5.1 && <0.6,+ elynx-seq >=0.0.1 && <0.1,+ elynx-tools >=0.0.1 && <0.1,+ elynx-tree >=0.0.1 && <0.1,+ hmatrix >=0.20.0.0 && <0.21,+ integration >=0.2.1 && <0.3,+ lens >=4.17.1 && <4.18,+ math-functions >=0.3.1.0 && <0.4,+ matrices >=0.5.0 && <0.6,+ 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,+ 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,+ vector-th-unbox >=0.2.1.6 && <0.3,+ word8 >=0.1.3 && <0.2++executable slynx+ main-is: Main.hs+ hs-source-dirs: app+ other-modules:+ Options+ Paths_slynx+ default-language: Haskell2010+ ghc-options: -Wall -eventlog -threaded -rtsopts -with-rtsopts=-N+ build-depends:+ async >=2.2.2 && <2.3,+ base >=4.12.0.0 && <4.13,+ bytestring >=0.10.8.2 && <0.11,+ containers >=0.6.0.1 && <0.7,+ data-memocombinators >=0.5.1 && <0.6,+ elynx-seq >=0.0.1 && <0.1,+ elynx-tools >=0.0.1 && <0.1,+ hmatrix >=0.20.0.0 && <0.21,+ integration >=0.2.1 && <0.3,+ lens >=4.17.1 && <4.18,+ math-functions >=0.3.1.0 && <0.4,+ matrices >=0.5.0 && <0.6,+ 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,+ slynx -any,+ 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,+ vector-th-unbox >=0.2.1.6 && <0.3,+ word8 >=0.1.3 && <0.2
+ src/Concatenate/Concatenate.hs view
@@ -0,0 +1,43 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Analyze.Analyze+Description : Parse sequence file formats and analyze them+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Oct 5 08:41:05 2018.++-}++module Concatenate.Concatenate+ ( concatenateCmd+ )+where++import Control.Monad.Logger+import Control.Monad.Trans.Class+import Control.Monad.Trans.Reader++import Concatenate.Options+import Tools++import ELynx.Data.Sequence.Sequence+import ELynx.Export.Sequence.Fasta+import ELynx.Tools.InputOutput++-- | Concatenate sequences.+concatenateCmd :: Maybe FilePath -> Concatenate ()+concatenateCmd outFileBaseName = do+ $(logInfo) "Command: Concatenate sequences."+ ConcatenateArguments al fps <- lift ask+ sss <- mapM (readSeqs al . Just) fps+ let result = sequencesToFasta $ concatenateSeqs sss+ let outFilePath = (++ ".fasta") <$> outFileBaseName+ io "concatenated multi sequence alignment " result outFilePath+
+ src/Concatenate/Options.hs view
@@ -0,0 +1,47 @@+{- |+Module : Concatenate.Options+Description : ELynxSeq argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++-}++module Concatenate.Options+ ( ConcatenateArguments (..)+ , Concatenate+ , concatenateArguments+ ) where++import Control.Applicative+import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Options.Applicative++import Tools++import ELynx.Data.Alphabet.Alphabet++-- | Arguments needed to concatenate multi sequence alignments.+data ConcatenateArguments = ConcatenateArguments+ { ccAlphabet :: Alphabet+ , ccInFiles :: [FilePath] }++-- | Logger and Reader type.+type Concatenate = LoggingT (ReaderT ConcatenateArguments IO)++-- | Command line parser.+concatenateArguments :: Parser ConcatenateArguments+concatenateArguments = ConcatenateArguments+ <$> alphabetOpt+ <*> some inFileArg++inFileArg :: Parser FilePath+inFileArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read sequences from INPUT-FILE"
+ src/Examine/Examine.hs view
@@ -0,0 +1,106 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |++Module : Analyze.Analyze+Description : Parse sequence file formats and analyze them+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Oct 5 08:41:05 2018.++-}++module Examine.Examine+ ( examineCmd+ )+ where++import Control.Monad.Logger+import Control.Monad.Trans.Class+import Control.Monad.Trans.Reader+import qualified Data.ByteString.Lazy.Char8 as L+import Text.Printf++import Examine.Options+import Tools++import ELynx.Data.Sequence.MultiSequenceAlignment+import ELynx.Data.Sequence.Sequence+import ELynx.Tools.InputOutput++examineMSA :: Bool -> MultiSequenceAlignment -> L.ByteString+examineMSA perSiteFlag msa =+ L.unlines [ L.pack $ "Total number of columns in alignment: "+ ++ show (msaLength msa)+ , L.pack $ "Number of columns without gaps: "+ ++ show (msaLength msaNoGaps)+ , L.pack $ "Number of columns with standard characters only: "+ ++ show (msaLength msaOnlyStd)+ , L.empty+ , L.pack $ "Total number of characters: " ++ show nTot+ , L.pack $ "Standard (i.e., not extended IUPAC) characters: "+ ++ show (nTot - nIUPAC - nGaps - nUnknowns)+ , L.pack $ "Extended IUPAC characters: " ++ show nIUPAC+ , L.pack $ "Gaps: " ++ show nGaps+ , L.pack $ "Unknowns: " ++ show nUnknowns+ , L.pack $ "Percentage of standard characters: "+ ++ printf "%.3f" (1.0 - percentageIUPAC - percentageGaps - percentageUnknowns)+ , L.pack $ "Percentage of extended IUPAC characters: "+ ++ printf "%.3f" percentageIUPAC+ , L.pack $ "Percentage of gaps: "+ ++ printf "%.3f" percentageGaps+ , L.pack $ "Percentage of unknowns: "+ ++ printf "%.3f" percentageUnknowns+ , L.empty+ , L.pack "Mean effective number of states (measured using entropy):"+ , L.pack "Across whole alignment: "+ <> L.pack (printf "%.3f" kEffMean)+ , L.pack "Across columns without gaps: "+ <> L.pack (printf "%.3f" kEffMeanNoGaps)+ , L.pack "Across columns without extended IUPAC characters: "+ <> L.pack (printf "%.3f" kEffMeanOnlyStd)+ ]+ <> perSiteBS+ where+ nTot = msaLength msa * msaNSequences msa+ nIUPAC = countIUPACChars msa+ nGaps = countGaps msa+ nUnknowns = countUnknowns msa+ percentageIUPAC = fromIntegral nIUPAC / fromIntegral nTot :: Double+ percentageGaps = fromIntegral nGaps / fromIntegral nTot :: Double+ percentageUnknowns = fromIntegral nUnknowns / fromIntegral nTot :: Double+ msaNoGaps = filterColumnsNoGaps msa+ msaOnlyStd = filterColumnsOnlyStd msaNoGaps+ kEffs = kEffEntropy . toFrequencyData $ msa+ kEffsNoGaps = kEffEntropy . toFrequencyData $ msaNoGaps+ kEffsOnlyStd = kEffEntropy . toFrequencyData $ msaOnlyStd+ kEffMean = sum kEffs / fromIntegral (length kEffs)+ kEffMeanNoGaps = sum kEffsNoGaps / fromIntegral (length kEffsNoGaps)+ kEffMeanOnlyStd = sum kEffsOnlyStd / fromIntegral (length kEffsOnlyStd)+ perSiteBS = if perSiteFlag+ then L.unlines [ L.pack "Effective number of used states per site:"+ , L.pack . show $ kEffs+ ]+ else L.empty++examine :: Bool -> [Sequence] -> L.ByteString+examine perSiteFlag ss = summarizeSequenceList ss <>+ case fromSequenceList ss of+ Left _ -> L.empty+ Right msa -> L.pack "\n" <> examineMSA perSiteFlag msa++-- | Examine sequences.+examineCmd :: Maybe FilePath -> Examine ()+examineCmd outFileBaseName = do+ $(logInfo) "Command: Examine sequences."+ ExamineArguments al inFile perSiteFlag <- lift ask+ ss <- readSeqs al inFile+ let result = examine perSiteFlag ss+ let outFilePath = (++ ".out") <$> outFileBaseName+ io "result of examination" result outFilePath
+ src/Examine/Options.hs view
@@ -0,0 +1,54 @@+{- |+Module : Examine.Options+Description : ELynxSeq argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++-}++module Examine.Options+ ( ExamineArguments (..)+ , Examine+ , examineArguments+ ) where++import Control.Applicative+import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Options.Applicative++import Tools++import ELynx.Data.Alphabet.Alphabet++-- | Arguments needed to examine sequences.+data ExamineArguments = ExamineArguments+ { exAlphabet :: Alphabet+ , exInFile :: Maybe FilePath+ , exPerSite :: Bool }++-- | Logger and Reader type.+type Examine = LoggingT (ReaderT ExamineArguments IO)++-- | Command line parser.+examineArguments :: Parser ExamineArguments+examineArguments = ExamineArguments+ <$> alphabetOpt+ <*> optional filePathArg+ <*> examinePerSiteOpt++examinePerSiteOpt :: Parser Bool+examinePerSiteOpt = switch $+ long "per-site" <>+ help "Report per site summary statistics"++filePathArg :: Parser FilePath+filePathArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read sequences from INPUT-FILE"
+ src/Filter/Filter.hs view
@@ -0,0 +1,76 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Analyze.Analyze+Description : Parse sequence file formats and analyze them+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Oct 5 08:41:05 2018.++-}++module Filter.Filter+ ( filterRowsCmd+ , filterColumnsCmd+ )+ where++import Control.Monad.Logger+import Control.Monad.Trans.Class+import Control.Monad.Trans.Reader+import qualified Data.ByteString.Lazy.Char8 as L+import Data.Maybe (fromMaybe)+import qualified Data.Text as T++import Filter.Options+import Tools++import ELynx.Data.Sequence.MultiSequenceAlignment+import ELynx.Data.Sequence.Sequence+import ELynx.Export.Sequence.Fasta+import ELynx.Tools.InputOutput+import ELynx.Tools.Misc++filterRows :: Maybe Int -> Maybe Int -> [Sequence] -> L.ByteString+filterRows ml ms ss = sequencesToFasta $ compose filters ss+ where filters = map (fromMaybe id) [filterLongerThan <$> ml, filterShorterThan <$> ms]++-- | Filter sequences.+filterRowsCmd :: Maybe FilePath -> FilterRows ()+filterRowsCmd outFileBaseName = do+ $(logInfo) "Command: Filter sequences of a list of sequences."+ FilterRowsArguments al inFile long short <- lift ask+ maybe (return ())+ (\val -> $(logInfo) $ T.pack $ " Keep sequences longer than " <> show val <> ".") long+ maybe (return ())+ (\val -> $(logInfo) $ T.pack $ " Keep sequences shorter than " <> show val <> ".") short+ ss <- readSeqs al inFile+ let result = filterRows long short ss+ let outFilePath = (++ ".fasta") <$> outFileBaseName+ io "filtered sequences" result outFilePath++filterColumns :: Maybe Double -> [Sequence] -> L.ByteString+filterColumns ms ss = sequencesToFasta . toSequenceList $ compose filters msa+ where msa = either error id (fromSequenceList ss)+ filters = map (fromMaybe id) [ filterColumnsStd <$> ms ]++-- | Filter columns.+filterColumnsCmd :: Maybe FilePath -> FilterColumns ()+filterColumnsCmd outFileBaseName = do+ $(logInfo) "Command: Filter columns of a multi sequence alignment."+ FilterColumnsArguments al inFile standard <- lift ask+ case standard of+ Nothing -> return ()+ Just p -> $(logInfo) $ T.pack $+ " Keep columns with a proportion of standard (non-IUPAC) characters larger than "+ ++ show p ++ "."+ ss <- readSeqs al inFile+ let result = filterColumns standard ss+ let outFilePath = (++ ".fasta") <$> outFileBaseName+ io "filtered sequences" result outFilePath
+ src/Filter/Options.hs view
@@ -0,0 +1,88 @@+{- |+Module : Filter.Options+Description : ELynxSeq argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++-}++module Filter.Options+ ( FilterRowsArguments (..)+ , FilterColumnsArguments (..)+ , FilterRows+ , FilterColumns+ , filterRowsArguments+ , filterColumnsArguments+ ) where++import Control.Applicative+import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Options.Applicative++import Tools++import ELynx.Data.Alphabet.Alphabet++-- | Arguments needed for filtering sequences.+data FilterRowsArguments = FilterRowsArguments+ { frAlphabet :: Alphabet+ , frInFile :: Maybe FilePath+ , frLonger :: Maybe Int+ , frShorter :: Maybe Int }++-- | Arguments needed for filtering columns of a multi sequence alignment.+data FilterColumnsArguments = FilterColumnsArguments+ { fcAlphabet :: Alphabet+ , fcInFile :: Maybe FilePath+ , fcStandard :: Maybe Double }++-- | Logger and Reader for sequence filtering.+type FilterRows = LoggingT (ReaderT FilterRowsArguments IO)++-- | Logger and Reader for column filtering.+type FilterColumns = LoggingT (ReaderT FilterColumnsArguments IO)++-- | Command line parser.+filterRowsArguments :: Parser FilterRowsArguments+filterRowsArguments = FilterRowsArguments+ <$> alphabetOpt+ <*> optional inFileArg+ <*> filterLongerThanOpt+ <*> filterShorterThanOpt++filterLongerThanOpt :: Parser (Maybe Int)+filterLongerThanOpt = optional $ option auto $+ long "longer-than" <>+ metavar "LENGTH" <>+ help "Only keep sequences longer than LENGTH"++filterShorterThanOpt :: Parser (Maybe Int)+filterShorterThanOpt = optional $ option auto $+ long "shorter-than" <>+ metavar "LENGTH" <>+ help "Only keep sequences shorter than LENGTH"++-- | Command line parser.+filterColumnsArguments :: Parser FilterColumnsArguments+filterColumnsArguments = FilterColumnsArguments+ <$> alphabetOpt+ <*> optional inFileArg+ <*> filterStandardOpt++filterStandardOpt :: Parser (Maybe Double)+filterStandardOpt = optional $ option auto $+ long "standard-chars" <>+ metavar "DOUBLE" <>+ help "Keep columns with a proportion standard (non-IUPAC) characters larger than DOUBLE in [0,1]"++inFileArg :: Parser FilePath+inFileArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read sequences from INPUT-FILE"
+ src/Simulate/Options.hs view
@@ -0,0 +1,168 @@+{- |+Module : Simulate.Options+Description : ELynxSim argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++Available options:+ -h,--help Show this help text+ -v,--version Show version+ -t,--tree-file NAME Specify tree file NAME+ -s,--substitution-model MODEL+ Set the phylogenetic substitution model; available+ models are shown below+ -m,--mixture-model MODEL Set the phylogenetic mixture model; available models+ are shown below+ -l,--length NUMBER Set alignment length to NUMBER+ -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+ -e,--seed [INT] Set seed for the random number generator; list of 32+ bit integers with up to 256 elements (default: [0])+ -q,--quiet Be quiet+ -o,--output-file NAME Specify output file NAME+++-}+++module Simulate.Options+ ( GammaRateHeterogeneityParams+ , SimulateArguments (..)+ , Simulate+ , simulateArguments+ , simulateFooter+ ) where++import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Data.List+import Data.Word+import Options.Applicative++import ELynx.Tools.Options++-- | Number of gamma rate categories and alpha parameter.+type GammaRateHeterogeneityParams = (Int, Double)++-- | Arguments needed to simulate sequences.+data SimulateArguments = SimulateArguments+ { argsTreeFile :: FilePath+ , argsSubstitutionModelString :: Maybe String+ , argsMixtureModelString :: Maybe String+ , argsEDMFile :: Maybe FilePath+ , argsMixtureWeights :: Maybe [Double]+ , argsGammaParams :: Maybe GammaRateHeterogeneityParams+ , argsLength :: Int+ , argsMaybeSeed :: Maybe [Word32]+ }++-- | A simulation can log stuff and read the necessary arguments.+type Simulate = LoggingT (ReaderT SimulateArguments IO)++-- | Sub command parser.+simulateArguments :: Parser SimulateArguments+simulateArguments = SimulateArguments+ <$> treeFileOpt+ <*> phyloSubstitutionModelOpt+ <*> phyloMixtureModelOpt+ <*> maybeEDMFileOpt+ <*> maybeMixtureWeights+ <*> maybeGammaParams+ <*> lengthOpt+ <*> seedOpt++treeFileOpt :: Parser FilePath+treeFileOpt = strOption $+ long "tree-file"+ <> short 't'+ <> metavar "Name"+ <> help "Read trees from file NAME"++phyloSubstitutionModelOpt :: Parser (Maybe String)+phyloSubstitutionModelOpt = optional $ strOption $+ long "substitution-model"+ <> short 's'+ <> metavar "MODEL"+ <> help "Set the phylogenetic substitution model; available models are shown below (mutually exclusive with -m option)"++phyloMixtureModelOpt :: Parser (Maybe String)+phyloMixtureModelOpt = optional $ strOption+ ( long "mixture-model"+ <> short 'm'+ <> metavar "MODEL"+ <> help "Set the phylogenetic mixture model; available models are shown below (mutually exclusive with -s option)" )++maybeEDMFileOpt :: Parser (Maybe FilePath)+maybeEDMFileOpt = optional $ strOption+ ( long "edm-file"+ <> short 'e'+ <> metavar "NAME"+ <> help "Empirical distribution model file NAME in Phylobayes format" )++maybeMixtureWeights :: Parser (Maybe [Double])+maybeMixtureWeights = optional $ option auto+ ( long "mixture-model-weights"+ <> short 'w'+ <> metavar "\"[DOUBLE,DOUBLE,...]\""+ <> help "Weights of mixture model components" )++maybeGammaParams :: Parser (Maybe GammaRateHeterogeneityParams)+maybeGammaParams = optional $ option auto+ ( long "gamma-rate-heterogeneity"+ <> short 'g'+ <> metavar "\"(NCAT,SHAPE)\""+ <> help "Number of gamma rate categories and shape parameter" )++lengthOpt :: Parser Int+lengthOpt = option auto+ ( long "length"+ <> short 'l'+ <> metavar "NUMBER"+ <> help "Set alignment length to NUMBER" )++-- | The model specification is somewhat complicated, so we need to provide+-- additional help.+simulateFooter :: String+simulateFooter = intercalate "\n" $ sms ++ mms+ where+ sms =+ [ "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{...}"+ ]+ mms =+ [ ""+ , "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."+ ]
+ src/Simulate/PhyloModel.hs view
@@ -0,0 +1,188 @@+{- |+Module : Simulate.PhyloModel+Description : Parse and interpret the model string+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Feb 1 13:32:16 2019.++-}++module Simulate.PhyloModel+ ( getPhyloModel+ ) where++import qualified Data.ByteString.Lazy.Char8 as L+import Data.Maybe+import Data.Void+import Data.Word (Word8)+import Numeric.LinearAlgebra (norm_1, size,+ vector)+import Text.Megaparsec+import Text.Megaparsec.Byte+import Text.Megaparsec.Byte.Lexer++import ELynx.Data.MarkovProcess.AminoAcid+import ELynx.Data.MarkovProcess.CXXModels+import qualified ELynx.Data.MarkovProcess.MixtureModel as M+import ELynx.Data.MarkovProcess.Nucleotide+import qualified ELynx.Data.MarkovProcess.PhyloModel as P+import ELynx.Data.MarkovProcess.RateMatrix+import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S+import ELynx.Import.MarkovProcess.EDMModelPhylobayes (EDMComponent)+import ELynx.Tools.ByteString+import ELynx.Tools.Equality+import ELynx.Tools.InputOutput++type Parser = Parsec Void L.ByteString++bs :: String -> L.ByteString+bs = L.pack++nNuc :: Int+-- nNuc = length (alphabet :: [Nucleotide])+nNuc = 4++nAA :: Int+-- nAA = length (alphabet :: [AminoAcid])+nAA = 20++-- Model parameters between square brackets.+paramsStart :: Word8+paramsStart = c2w '['++paramsEnd :: Word8+paramsEnd = c2w ']'++-- Stationary distribution between curly brackets.+sdStart :: Word8+sdStart = c2w '{'++sdEnd :: Word8+sdEnd = c2w '}'++-- Mixture model components between round brackets.+mmStart :: Word8+mmStart = c2w '('++mmEnd :: Word8+mmEnd = c2w ')'++separator :: Word8+separator = c2w ','++name :: Parser String+name = L.unpack <$>+ takeWhile1P (Just "Model name") (`notElem` [paramsStart, paramsEnd, sdStart, sdEnd, mmStart, mmEnd, separator])++params :: Parser [Double]+params = between (char paramsStart) (char paramsEnd) (sepBy1 float (char separator))++stationaryDistribution :: Parser StationaryDistribution+stationaryDistribution = do+ f <- vector <$> between (char sdStart) (char sdEnd) (sepBy1 float (char separator))+ if nearlyEq (norm_1 f) 1.0+ then return f+ else error $ "Sum of stationary distribution is " ++ show (norm_1 f)+ ++ " but should be 1.0."++assertLength :: StationaryDistribution -> Int -> a -> a+assertLength d n r = if size d /= n+ then error $ "Length of stationary distribution is " ++ show (size d)+ ++ " but should be " ++ show n ++ "."+ else r++-- This is the main function that connects the model string, the parameters and+-- the stationary distribution. It should check that the model is valid.+assembleSubstitutionModel :: String -> Maybe S.Params -> Maybe StationaryDistribution+ -> Either String S.SubstitutionModel+-- DNA models.+assembleSubstitutionModel "JC" Nothing Nothing = Right jc+assembleSubstitutionModel "HKY" (Just [k]) (Just d) = Right $ assertLength d nNuc $ hky k d+-- Protein models.+assembleSubstitutionModel "LG" Nothing Nothing = Right lg+assembleSubstitutionModel "LG-Custom" Nothing (Just d) = Right $ assertLength d nAA $ lgCustom Nothing d+assembleSubstitutionModel "WAG" Nothing Nothing = Right wag+assembleSubstitutionModel "WAG-Custom" Nothing (Just d) = Right $ assertLength d nAA $ wagCustom Nothing d+assembleSubstitutionModel "Poisson" Nothing Nothing = Right poisson+assembleSubstitutionModel "Poisson-Custom" Nothing (Just d) = Right $ assertLength d nAA $ poissonCustom Nothing d+-- Ohterwisse, we cannot assemble the model.+assembleSubstitutionModel n mps mf = Left $ unlines+ [ "Cannot assemble substitution model. "+ , "Name: " ++ show n+ , "Parameters: " ++ show mps+ , "Stationary distribution: " ++ show mf ]++parseSubstitutionModel :: Parser S.SubstitutionModel+parseSubstitutionModel = do+ n <- name+ mps <- optional params+ mf <- optional stationaryDistribution+ let esm = assembleSubstitutionModel n mps mf+ case esm of+ Left err -> fail err+ Right sm -> return sm++edmModel :: [EDMComponent] -> Maybe [M.Weight] -> Parser M.MixtureModel+edmModel cs mws = do+ _ <- chunk (bs "EDM")+ _ <- char mmStart+ n <- name+ mps <- optional params+ _ <- char mmEnd+ let sms = map (\c -> assembleSubstitutionModel n mps (Just $ snd c)) cs+ edmName = "EDM" ++ show (length cs)+ ws = fromMaybe (map fst cs) mws+ errs = [ e | (Left e) <- sms ]+ if not $ null errs+ then fail $ head errs+ else return $ M.MixtureModel edmName+ [ M.Component w sm | (w, Right sm) <- zip ws sms ]++cxxModel :: Maybe [M.Weight] -> Parser M.MixtureModel+cxxModel mws = do+ _ <- char (c2w 'C')+ n <- decimal :: Parser Int+ case cxx n mws of+ Nothing -> fail "Only 10, 20, 30, 40, 50, and 60 components are supported."+ Just m -> return m++standardMixtureModel :: [M.Weight] -> Parser M.MixtureModel+standardMixtureModel ws = do+ _ <- chunk (bs "MIXTURE")+ _ <- char mmStart+ sms <- parseSubstitutionModel `sepBy1` char separator+ _ <- char mmEnd+ return $ M.MixtureModel "MIXTURE"+ [ M.Component w sm | (w, sm) <- zip ws sms]++mixtureModel :: Maybe [EDMComponent] -> Maybe [M.Weight] -> Parser M.MixtureModel+mixtureModel Nothing Nothing = try (cxxModel Nothing) <|> fail "No weights provided."+mixtureModel Nothing mws@(Just ws) = try (cxxModel mws) <|> standardMixtureModel ws+mixtureModel (Just cs) mws = edmModel cs mws++-- | Parse the phylogenetic model string. The argument list is somewhat long,+-- but models can have many parameters and we have to check for redundant+-- parameters.+--+-- @+-- getPhyloModel maybeSubstitutionModelString maybeMixtureModelString maybeEDMComponents+-- @+getPhyloModel :: Maybe String -> Maybe String -> Maybe [M.Weight] -> Maybe [EDMComponent]+ -> Either String P.PhyloModel+getPhyloModel Nothing Nothing _ _ =+ Left "No model was given. See help."+getPhyloModel (Just _) (Just _) _ _ =+ Left "Both, substitution and mixture model string given; use only one."+getPhyloModel (Just s) Nothing Nothing Nothing =+ Right $ P.SubstitutionModel $ parseStringWith "Substitution model string" parseSubstitutionModel s+getPhyloModel (Just _) Nothing (Just _) _ =+ Left "Weights given; but cannot be used with substitution model."+getPhyloModel (Just _) Nothing _ (Just _) =+ Left "Empirical distribution mixture model components given; but cannot be used with substitution model."+getPhyloModel Nothing (Just m) mws mcs =+ Right $ P.MixtureModel $ parseStringWith "Mixture model string" (mixtureModel mcs mws) m
+ src/Simulate/Simulate.hs view
@@ -0,0 +1,158 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Simulate.Simulate+Description : Simulate multiple sequence alignments+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Mon Jan 28 14:12:52 2019.++-}++module Simulate.Simulate+ ( simulateCmd )+where++import Control.Concurrent+import Control.Concurrent.Async+import Control.Lens+import Control.Monad.IO.Class+import Control.Monad.Logger+import Control.Monad.Trans.Class+import Control.Monad.Trans.Reader+import qualified Data.ByteString.Lazy as L+import qualified Data.ByteString.Lazy.Char8 as LC+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 Data.Tree+import qualified Data.Vector.Unboxed as V+import Numeric.LinearAlgebra hiding ((<>))+import System.Random.MWC++import Simulate.Options+import Simulate.PhyloModel++import ELynx.Data.Alphabet.Alphabet as A+import ELynx.Data.MarkovProcess.GammaRateHeterogeneity+import qualified ELynx.Data.MarkovProcess.MixtureModel as M+import qualified ELynx.Data.MarkovProcess.PhyloModel as P+import qualified ELynx.Data.MarkovProcess.SubstitutionModel as S+import ELynx.Data.Sequence.MultiSequenceAlignment+import ELynx.Data.Sequence.Sequence hiding (name)+import ELynx.Data.Tree.MeasurableTree+import ELynx.Data.Tree.NamedTree+import ELynx.Data.Tree.Tree+import ELynx.Export.Sequence.Fasta+import ELynx.Import.MarkovProcess.EDMModelPhylobayes hiding (Parser)+import ELynx.Import.Tree.Newick hiding (name)+import ELynx.Simulate.MarkovProcessAlongTree++import ELynx.Tools.ByteString+import ELynx.Tools.Concurrent+import ELynx.Tools.InputOutput+import ELynx.Tools.Misc++-- Simulate a 'MultiSequenceAlignment' for a given phylogenetic model,+-- phylogenetic tree, and alignment length.+simulateMSA :: (Measurable a, Named a)+ => P.PhyloModel -> Tree a -> Int -> GenIO+ -> IO MultiSequenceAlignment+simulateMSA pm t n g = do+ c <- getNumCapabilities+ gs <- splitGen c g+ let chunks = getChunks c n+ leafStatesS <- case pm of+ P.SubstitutionModel sm -> mapConcurrently+ (\(num, gen) -> simulateAndFlattenNSitesAlongTree num d e t gen) (zip chunks gs)+ where d = sm ^. S.stationaryDistribution+ e = sm ^. S.exchangeabilityMatrix+ P.MixtureModel mm -> mapConcurrently+ (\(num, gen) -> simulateAndFlattenNSitesAlongTreeMixtureModel num ws ds es t gen) (zip chunks gs)+ where+ ws = vector $ M.getWeights mm+ ds = map (view S.stationaryDistribution) $ M.getSubstitutionModels mm+ es = map (view S.exchangeabilityMatrix) $ M.getSubstitutionModels mm+ -- XXX: The horizontal concatenation might be slow. If so, 'concatenateSeqs'+ -- or 'concatenateMSAs' can be used, which directly appends vectors.+ let leafStates = horizontalConcat leafStatesS+ leafNames = map getName $ leaves t+ code = P.getAlphabet pm+ -- XXX: Probably use type safe stuff here?+ alph = A.all $ alphabetSpec code+ sequences = [ Sequence sName code (V.fromList $ map (`Set.elemAt` alph) ss) |+ (sName, ss) <- zip leafNames leafStates ]+ return $ either error id $ fromSequenceList sequences++-- Summarize EDM components; line to be printed to screen or log.+summarizeEDMComponents :: [EDMComponent] -> L.ByteString+summarizeEDMComponents cs = LC.pack+ $ "Empiricial distribution mixture model with "+ ++ show (length cs) ++ " components."++-- XXX. Maybe provide human readable model file. But then, why is this+-- necessary. A human readable summary is reported anyways, and for Protein+-- models the exchangeabilities are too many.+reportModel :: Maybe FilePath -> P.PhyloModel -> Simulate ()+reportModel outFn m = do+ let modelFn = (<> ".model") <$> outFn+ io "model definition (machine readable)" (bsShow m <> "\n") modelFn++-- | Simulate sequences.+simulateCmd :: Maybe FilePath -> Simulate ()+simulateCmd outFn = do+ a <- lift ask+ $(logInfo) "Read tree."+ let treeFile = argsTreeFile a+ tree <- liftIO $ parseFileWith newick treeFile+ $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ summarize tree++ let edmFile = argsEDMFile a+ edmCs <- case edmFile of+ Nothing -> return Nothing+ Just edmF -> do+ $(logInfo) "Read EDM file."+ liftIO $ Just <$> parseFileWith phylobayes edmF+ maybe (return ()) ($(logInfo) . LT.toStrict . LT.decodeUtf8 . summarizeEDMComponents) edmCs++ $(logInfo) "Read model string."+ let ms = argsSubstitutionModelString a+ mm = argsMixtureModelString a+ mws = argsMixtureWeights a+ eitherPhyloModel' = getPhyloModel ms mm mws edmCs+ phyloModel' <- case eitherPhyloModel' of+ Left err -> lift $ error err+ Right pm -> return pm++ let maybeGammaParams = argsGammaParams a+ phyloModel <- case maybeGammaParams of+ Nothing -> do+ $(logInfo) $ LT.toStrict $ LT.decodeUtf8+ $ LC.unlines $ P.summarize phyloModel'+ return phyloModel'+ Just (n, alpha) -> do+ $(logInfo) $ LT.toStrict $ LT.decodeUtf8+ $ LC.unlines $ P.summarize phyloModel' ++ summarizeGammaRateHeterogeneity n alpha+ return $ expand n alpha phyloModel'+ reportModel outFn phyloModel++ $(logInfo) "Simulate alignment."+ let alignmentLength = argsLength a+ $(logInfo) $ T.pack $ "Length: " <> show alignmentLength <> "."+ let maybeSeed = argsMaybeSeed a+ gen <- case maybeSeed of+ Nothing -> $(logInfo) "Seed: random"+ >> liftIO createSystemRandom+ Just s -> $(logInfo) (T.pack ("Seed: " <> show s <> "."))+ >> liftIO (initialize (V.fromList s))+ msa <- liftIO $ simulateMSA phyloModel tree alignmentLength gen+ let output = (sequencesToFasta . toSequenceList) msa+ outFile = (<> ".fasta") <$> outFn+ io "simulated multi sequence alignment" output outFile
+ src/SubSample/Options.hs view
@@ -0,0 +1,69 @@+{- |+Module : SubSample.Options+Description : ELynxSeq argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++-}++module SubSample.Options+ ( SubSampleArguments (..)+ , SubSample+ , subSampleArguments+ ) where++import Control.Applicative+import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Data.Word+import Options.Applicative++import Tools++import ELynx.Data.Alphabet.Alphabet+import ELynx.Tools.Options++-- | Data structure holding the Command line arguments.+data SubSampleArguments = SubSampleArguments+ { ssAlphabet :: Alphabet+ , ssInFile :: Maybe FilePath+ , ssNSites :: Int+ , ssNAlignments :: Int+ , ssMbSeed :: Maybe [Word32] }++-- | The sub sample command can log stuff and read necessary arguments.+type SubSample = LoggingT (ReaderT SubSampleArguments IO)++-- | Sub command parser.+subSampleArguments :: Parser SubSampleArguments+subSampleArguments = SubSampleArguments+ <$> alphabetOpt+ <*> optional filePathArg+ <*> subSampleNSitesOpt+ <*> subSampleNAlignmentsOpt+ <*> seedOpt++subSampleNSitesOpt :: Parser Int+subSampleNSitesOpt = option auto $+ long "number-of-sites" <>+ short 'n' <>+ metavar "INT" <>+ help "Number of sites randomly drawn with replacement"++subSampleNAlignmentsOpt :: Parser Int+subSampleNAlignmentsOpt = option auto $+ long "number-of-alignments" <>+ short 'm' <>+ metavar "INT" <>+ help "Number of multi sequence alignments to be created"++filePathArg :: Parser FilePath+filePathArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read sequences from INPUT-FILE"
+ src/SubSample/SubSample.hs view
@@ -0,0 +1,70 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Analyze.Analyze+Description : Parse sequence file formats and analyze them+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Oct 5 08:41:05 2018.++-}++module SubSample.SubSample+ ( subSampleCmd+ )+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.Text as T+import qualified Data.Text.Lazy as LT+import qualified Data.Text.Lazy.Builder as LT+import qualified Data.Text.Lazy.Builder.Int as LT+import qualified Data.Vector as V+import System.Random.MWC++import SubSample.Options+import Tools++import ELynx.Data.Sequence.MultiSequenceAlignment+import ELynx.Export.Sequence.Fasta+import ELynx.Tools.InputOutput++-- | Get a given number of output file names with provided suffix.+--+-- > getOutFilePaths "BasePath" 11 "fasta"+--+-- Will result in @BasePath.00.fasta@ up to @BasePath.10.fasta@.+getOutFilePaths :: String -> Int -> String -> [FilePath]+getOutFilePaths file n suffix = [ file ++ "." ++ digitStr i ++ "." ++ suffix+ | i <- [0 .. n-1] ]+ where nDigits = ceiling $ logBase (10 :: Double) (fromIntegral n)+ digitStr i = T.unpack $ T.justifyRight nDigits '0' (LT.toStrict $ LT.toLazyText $ LT.decimal i)++-- | Sub sample sequences.+subSampleCmd :: Maybe FilePath -- ^ Output file base name+ -> SubSample ()+subSampleCmd outFileBaseName = do+ SubSampleArguments al inFile nSites nAlignments seed <- lift ask+ $(logInfo) "Command: Sub sample from a multi sequence alignment."+ $(logInfo) $ T.pack $ " Sample " <> show nSites <> " sites."+ $(logInfo) $ T.pack $ " Sample " <> show nAlignments <> " multi sequence alignments."+ ss <- readSeqs al inFile+ gen <- liftIO $ maybe createSystemRandom (initialize . V.fromList) seed+ let msa = either error id (fromSequenceList ss)+ samples <- lift $ replicateM nAlignments $ randomSubSample nSites msa gen+ let results = map (sequencesToFasta . toSequenceList) samples+ outFilePaths <- case outFileBaseName of+ Nothing -> return $ repeat Nothing+ Just fn -> return $ Just <$> getOutFilePaths fn nAlignments "fasta"+ zipWithM_ (io "sub sampled multi sequence alignments") results outFilePaths+
+ src/Tools.hs view
@@ -0,0 +1,53 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Tools+Description : Common tools for sequence lynx+Copyright : (c) Dominik Schrempf 2019+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sat Sep 7 06:24:22 2019.++-}++module Tools+ ( -- * Tools+ readSeqs+ -- * Options+ , alphabetOpt+ ) where++import Control.Monad.IO.Class+import Control.Monad.Logger+import qualified Data.Text as T+import Options.Applicative++import ELynx.Data.Alphabet.Alphabet+import ELynx.Data.Sequence.Sequence+import ELynx.Import.Sequence.Fasta+import ELynx.Tools.InputOutput++-- | Read sequences of given alphabet from file or standard input.+readSeqs :: (MonadIO m, MonadLogger m) => Alphabet -> Maybe FilePath -> m [Sequence]+readSeqs a mfp = do+ case mfp of+ Nothing -> $(logInfo) $ T.pack+ $ "Read sequences from standard input; alphabet "+ <> show a <> "."+ Just fp -> $(logInfo) $ T.pack+ $ "Read sequences from file "+ <> fp <> "; alphabet" <> show a <> "."+ liftIO $ parseFileOrIOWith (fasta a) mfp++-- | Command line option to specify the alphabet. Used by various commands.+alphabetOpt :: Parser Alphabet+alphabetOpt = option auto $+ long "alphabet" <>+ short 'a' <>+ metavar "NAME" <>+ help "Specify alphabet type NAME"
+ src/Translate/Options.hs view
@@ -0,0 +1,71 @@+{- |+Module : Translate.Options+Description : ELynxSeq argument parsing+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Sun Oct 7 17:29:45 2018.++-}++module Translate.Options+ ( TranslateArguments (..)+ , Translate+ , translateArguments+ ) where++import Control.Applicative+import Control.Monad.Logger+import Control.Monad.Trans.Reader+import Data.List+import Options.Applicative++import Tools++import ELynx.Data.Alphabet.Alphabet+import ELynx.Data.Character.Codon+import ELynx.Tools.Misc++-- | Arguments needed to translate sequences.+data TranslateArguments = TranslateArguments+ { trAlphabet :: Alphabet+ , trInFile :: Maybe FilePath+ , trReadingFrame :: Int+ , trUniversalCode :: UniversalCode }++-- | Logger and Reader type.+type Translate = LoggingT (ReaderT TranslateArguments IO)++-- | Command line parser.+translateArguments :: Parser TranslateArguments+translateArguments = TranslateArguments <$>+ alphabetOpt <*>+ optional inFileArg <*>+ readingFrameOpt <*>+ universalCodeOpt++readingFrameOpt :: Parser Int+readingFrameOpt = option auto $+ long "reading-frame" <>+ short 'r' <>+ metavar "INT" <>+ help "Reading frame [0|1|2]."++universalCodeOpt :: Parser UniversalCode+universalCodeOpt = option auto $+ long "universal-code" <>+ short 'u' <>+ metavar "CODE" <>+ help ("universal code; one of: " ++ codeStr ++ ".")+ where codes = allValues :: [UniversalCode]+ codeWords = map show codes+ codeStr = intercalate ", " codeWords++inFileArg :: Parser FilePath+inFileArg = strArgument $+ metavar "INPUT-FILE" <>+ help "Read sequences from INPUT-FILE"
+ src/Translate/Translate.hs view
@@ -0,0 +1,51 @@+{-# LANGUAGE OverloadedStrings #-}+{-# LANGUAGE TemplateHaskell #-}++{- |+Module : Analyze.Analyze+Description : Parse sequence file formats and analyze them+Copyright : (c) Dominik Schrempf 2018+License : GPL-3++Maintainer : dominik.schrempf@gmail.com+Stability : unstable+Portability : portable++Creation date: Fri Oct 5 08:41:05 2018.++-}++module Translate.Translate+ ( translateCmd+ )+ where++import Control.Monad.Logger+import Control.Monad.Trans.Class+import Control.Monad.Trans.Reader+import qualified Data.Text as T++import Tools+import Translate.Options++import ELynx.Data.Character.Codon+import ELynx.Data.Sequence.Sequence+import ELynx.Data.Sequence.Translate+import ELynx.Export.Sequence.Fasta+import ELynx.Tools.InputOutput++translateSeqs :: Int -> UniversalCode -> [Sequence] -> [Sequence]+translateSeqs rf uc = map (translateSeq uc rf)++-- | Translate sequences.+translateCmd :: Maybe FilePath -> Translate ()+translateCmd outFileBaseName = do+ $(logInfo) "Command: Translate sequences to amino acids."+ TranslateArguments al inFile rf uc <- lift ask+ $(logInfo) $ T.pack $ " Universal code: " <> show uc <> "."+ $(logInfo) $ T.pack $ " Reading frame: " <> show rf <> "."+ $(logInfo) ""+ ss <- readSeqs al inFile+ let result = sequencesToFasta $ translateSeqs rf uc ss+ let outFilePath = (++ ".fasta") <$> outFileBaseName+ io "translated sequences" result outFilePath