elynx-nexus (empty) → 0.3.0
raw patch · 7 files changed
+1363/−0 lines, 7 filesdep +basedep +bytestringdep +hspec
Dependencies added: base, bytestring, hspec, megaparsec
Files
- ChangeLog.md +24/−0
- LICENSE +674/−0
- README.md +508/−0
- elynx-nexus.cabal +58/−0
- src/ELynx/Export/Nexus.hs +36/−0
- src/ELynx/Import/Nexus.hs +62/−0
- test/Spec.hs +1/−0
+ ChangeLog.md view
@@ -0,0 +1,24 @@++# Changelog for ELynx+++## Version 0.3.1; in development+++## Version 0.3.0++- **`elynx-nexus`:** library to import and export Nexus files.+- **`elynx-tree`:** major refactor and big cleanup; use rose trees with branch+ labels.+- **`elynx-tree`:** provide zippers.+++## Version 0.2.2++- Validation and repetition of previous analyses is finally possible with the+ new `elynx` binary.+- A library `elynx-markov` for running Markov processes along phylogenetic trees+ has been split off `elynx-seq`. This library performs the computations when+ executing `slynx simulate ...`.+- Many other small improvements.+
+ LICENSE view
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+ README.md view
@@ -0,0 +1,508 @@+++# The ELynx Suite++Version: 0.3.0.+Reproducible evolution made easy.++<p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>++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.++The Elynx Suite consists of library packages and executables providing a range+of sub commands.++The library packages are:++- **elynx-nexus:** Nexus file support.+- **elynx-markov:** Simulate multi sequence alignments along phylogenetic trees.+- **elynx-seq:** Handle evolutionary sequences and multi sequence alignments.+- **elynx-tools:** Tools for the provided executables.+- **elynx-tree:** Handle phylogenetic trees.++The executables are:++- **slynx:** Analyze, modify, and simulate evolutionary sequences.+- **tlynx:** Analyze, modify, and simulate phylogenetic trees.+- **elynx:** Validate and redo past analyses.++**ELynx is actively developed. We happily receive comments, ideas, feature+requests, and 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 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 to the+ [PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.+++# Documentation++Documentation is available on [Hackage](https://hackage.haskell.org/).++Libraries:++- [elynx-nexus](https://hackage.haskell.org/package/elynx-nexus)+- [elynx-markov](https://hackage.haskell.org/package/elynx-markov)+- [elynx-seq](https://hackage.haskell.org/package/elynx-seq)+- [elynx-tools](https://hackage.haskell.org/package/elynx-tools)+- [elynx-tree](https://hackage.haskell.org/package/elynx-tree)++Executables:++- [elynx](https://hackage.haskell.org/package/elynx)+- [slynx](https://hackage.haskell.org/package/slynx)+- [tlynx](https://hackage.haskell.org/package/tlynx)+++# SLynx++Handle evolutionary sequences.++ slynx --help | head -n -16++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 pm, UTC.+ + Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] + [-f|--force] 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+ -f,--force Ignore previous analysis and overwrite existing+ output files.+ + Available commands:+ concatenate Concatenate sequences found in input files.+ examine Examine sequences. If data is a multi sequence alignment, additionally analyze columns.+ filter-columns Filter columns of multi sequence alignments.+ filter-rows Filter rows (or sequences) found in input files.+ simulate Simulate multi sequence alignments.+ sub-sample Sub-sample columns from multi sequence alignments.+ translate Translate from DNA to Protein or DNAX to ProteinX.+ + + Available sequence file formats:+ - FASTA+ + Available alphabets:+ - 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)+++## Concatenate++Concatenate multi sequence alignments.++ slynx concatenate --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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`.++ slynx examine --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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`.++ slynx filter-rows --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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`.++ slynx filter-columns --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 pm, UTC.+ + Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE + [--standard-chars DOUBLE]+ Filter columns of 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+ --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++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 pm, UTC.+ + Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] + [-m|--mixture-model MODEL] [-e|--edm-file NAME] + [-p|--siteprofile-files NAMES] + [-w|--mixture-model-weights "[DOUBLE,DOUBLE,...]"] + [-g|--gamma-rate-heterogeneity "(NCAT,SHAPE)"]+ (-l|--length NUMBER) [-S|--seed [INT]]+ Simulate multi sequence alignments.+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -t,--tree-file Name Read tree from Newick 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+ -p,--siteprofile-files NAMES+ File names of site profiles 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, F81, HKY, GTR4.+ For example,+ -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}+ -s GTR4[e_AC,e_AG,e_AT,e_CG,e_CT,e_GT]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}+ where the 'e_XY' are the exchangeabilities from nucleotide X to Y.+ Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom, GTR20.+ MODEL-Custom means that only the exchangeabilities of MODEL are used,+ and a custom stationary distribution is provided.+ For example,+ -s LG+ -s LG-Custom{...}+ -s GTR20[e_AR,e_AN,...]{...}+ the 'e_XY' are the exchangeabilities from amino acid X to Y (alphabetical order).+ Notes: The F81 model for DNA is equivalent to the Poisson-Custom for proteins.+ The GTR4 model for DNA is equivalent to the GTR20 for proteins.+ + Mixture models:+ -m "MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2[PARAMETERS]{STATIONARY_DISTRIBUTION},...)"+ 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 or -p option.+ For example,+ LG exchangeabilities with stationary distributions given in FILE.+ -m "EDM(LG-Custom)" -e FILE+ 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.++ slynx sub-sample --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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.++ slynx translate --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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.++ tlynx --help | head -n -16++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 pm, UTC.+ + Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] + [-f|--force] 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.+ + Available commands:+ coalesce Simulate phylogenetic trees using the coalescent processes (see also the 'simulate' command for simulations using the birth and death process).+ 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 birth and death processes (see also the 'coalesce' command for simulations using the 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.+++## Compare++Compute distances between phylogenetic trees.++ tlynx compare --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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+++## Examine++Compute summary statistics of phylogenetic trees.++ tlynx examine --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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+++## Simulate++Simulate phylogenetic trees using birth and death processes.++ tlynx simulate --help++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 pm, UTC.+ + 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 phylogenetic trees using birth and death processes (see also the 'coalesce' command for simulations using the coalescent process).+ + Available options:+ -h,--help Show this help text+ -V,--version Show version+ -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.+ 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+++# ELynx++Validate and (optionally) redo past ELynx analyses.++ elynx --help | head -n -16++ ELynx Suite version 0.3.0.+ Developed by Dominik Schrempf.+ Compiled on July 30, 2020, at 12:40 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+
+ elynx-nexus.cabal view
@@ -0,0 +1,58 @@+cabal-version: 2.2++-- This file has been generated from package.yaml by hpack version 0.34.2.+--+-- see: https://github.com/sol/hpack+--+-- hash: 9c674ee4c190e6ed28b942de7dd8ded7fdc03eb4fb5b0fbcdbc6560f57bcba4a++name: elynx-nexus+version: 0.3.0+synopsis: Import and export Nexus files+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+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 (2020)+license: GPL-3.0-or-later+license-file: LICENSE+build-type: Simple+extra-source-files:+ README.md+ ChangeLog.md++source-repository head+ type: git+ location: https://github.com/dschrempf/elynx++library+ exposed-modules:+ ELynx.Export.Nexus+ ELynx.Import.Nexus+ other-modules:+ Paths_elynx_nexus+ autogen-modules:+ Paths_elynx_nexus+ hs-source-dirs:+ src+ ghc-options: -Wall -fllvm+ build-depends:+ base >=4.7 && <5+ , bytestring+ , megaparsec+ default-language: Haskell2010++test-suite seq-test+ type: exitcode-stdio-1.0+ main-is: Spec.hs+ other-modules:+ Paths_elynx_nexus+ hs-source-dirs:+ test+ ghc-options: -Wall -fllvm+ build-depends:+ base >=4.7 && <5+ , hspec+ default-language: Haskell2010
+ src/ELynx/Export/Nexus.hs view
@@ -0,0 +1,36 @@+{-# LANGUAGE OverloadedStrings #-}++-- |+-- Module : ELynx.Export.Nexus+-- Description : Nexus types and classes+-- Copyright : (c) Dominik Schrempf 2020+-- License : GPL-3+--+-- Maintainer : dominik.schrempf@gmail.com+-- Stability : unstable+-- Portability : portable+--+-- Creation date: Tue Apr 28 17:10:05 2020.+module ELynx.Export.Nexus+ ( toNexus,+ )+where++import Data.ByteString.Lazy.Char8 (ByteString)+import qualified Data.ByteString.Lazy.Char8 as L++-- This has to be refined. Like this, only one block can be parsed, and the+-- block type has to be known beforehand.++-- | Create nexus file with block name and block body.+toNexus :: ByteString -> [ByteString] -> ByteString+toNexus n b = L.unlines $ [start, begin n] <> b <> [end]++start :: ByteString+start = "#NEXUS"++begin :: ByteString -> ByteString+begin n = "BEGIN " <> n <> ";"++end :: ByteString+end = "END;"
+ src/ELynx/Import/Nexus.hs view
@@ -0,0 +1,62 @@+{-# LANGUAGE OverloadedStrings #-}++-- |+-- Module : ELynx.Import.Nexus+-- Description : Nexus types and classes+-- Copyright : (c) Dominik Schrempf 2020+-- License : GPL-3+--+-- Maintainer : dominik.schrempf@gmail.com+-- Stability : unstable+-- Portability : portable+--+-- Creation date: Tue Apr 28 17:10:05 2020.+module ELynx.Import.Nexus+ ( Parser,+ Block (..),+ nexus,+ )+where++import Control.Monad (void)+import Data.ByteString.Internal (c2w)+import Data.ByteString.Lazy.Char8 (ByteString)+import Data.Void (Void)+import Text.Megaparsec+import Text.Megaparsec.Byte++-- | Megaparsec shortcut.+type Parser = Parsec Void ByteString++-- | A Nexus block has a name (e.g., TREES), and parser for the entry.+data Block a = Block+ { name :: ByteString,+ parser :: Parser a+ }++-- This has to be refined. Like this, only one block can be parsed, and the+-- block type has to be known beforehand.++-- | Parse a Nexus file with a given 'Block'.+nexus :: Block a -> Parser a+nexus b = start *> block b++start :: Parser ()+start = void $ string "#NEXUS" <* space++block :: Block a -> Parser a+block b = between (begin $ name b) end (parser b)++begin :: ByteString -> Parser ()+begin n = do+ _ <- string "BEGIN"+ _ <- space+ _ <- string n+ _ <- char (c2w ';')+ _ <-+ space+ <?> "block-begin"+ return ()++end :: Parser ()+end = void $ string "END;" <* space
+ test/Spec.hs view
@@ -0,0 +1,1 @@+{-# OPTIONS_GHC -F -pgmF hspec-discover #-}