diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,6 +5,13 @@ ## Unreleased changes +## Version 0.6.1.0 + +- Split `ELynx.Tools` into separate modules because the package will be reduced. +- Remove the following modules from `ELynx.Tools`: `Concurrent`, + `LinearAlgebra`, `List`, `Misc`, and `Numeric`. + + ## Version 0.6.0.0 - **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer` diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -69,13 +69,13 @@ # Get help -For example: - - slynx --help + cabal exec slynx -- --help + # OR: stack exec slynx -- --help + # OR: slynx --help ELynx Suite version 0.6.0.0. Developed by Dominik Schrempf. - Compiled on September 3, 2021, at 20:56 pm, UTC. + Compiled on September 4, 2021, at 12:58 pm, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] [--no-elynx-file] COMMAND @@ -113,6 +113,7 @@ - ProteinX (amino acids; including gaps) - ProteinS (amino acids; including gaps, and translation stops) - 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 @@ -126,6 +127,9 @@ tlynx Analyze, modify, and simulate phylogenetic trees. elynx Validate and redo past analyses. + Get help for commands: + slynx --help + Get help for sub commands: slynx examine --help @@ -134,11 +138,13 @@ The documentation of sub commands can be accessed separately: - slynx simulate --help + cabal exec slynx -- simulate --help + # OR: stack exec slynx -- simulate --help + # OR: slynx simulate --help ELynx Suite version 0.6.0.0. Developed by Dominik Schrempf. - Compiled on September 3, 2021, at 20:56 pm, UTC. + Compiled on September 4, 2021, at 12:58 pm, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] diff --git a/slynx.cabal b/slynx.cabal --- a/slynx.cabal +++ b/slynx.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: slynx -version: 0.6.0.0 +version: 0.6.1.0 synopsis: Handle molecular sequences description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at . category: Bioinformatics @@ -46,7 +46,8 @@ hs-source-dirs: src ghc-options: -Wall -Wunused-packages build-depends: - attoparsec + aeson + , attoparsec , base >=4.7 && <5 , bytestring , containers diff --git a/src/SLynx/Concatenate/Concatenate.hs b/src/SLynx/Concatenate/Concatenate.hs --- a/src/SLynx/Concatenate/Concatenate.hs +++ b/src/SLynx/Concatenate/Concatenate.hs @@ -20,7 +20,8 @@ import Control.Monad.Trans.Reader import qualified ELynx.Data.Sequence.Sequence as S import ELynx.Export.Sequence.Fasta -import ELynx.Tools +import ELynx.Tools.ELynx +import ELynx.Tools.Environment import SLynx.Concatenate.Options import SLynx.Tools diff --git a/src/SLynx/Concatenate/Options.hs b/src/SLynx/Concatenate/Options.hs --- a/src/SLynx/Concatenate/Options.hs +++ b/src/SLynx/Concatenate/Options.hs @@ -18,8 +18,10 @@ where import Control.Applicative +import Data.Aeson import ELynx.Data.Alphabet.Alphabet -import ELynx.Tools +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Tools diff --git a/src/SLynx/Examine/Examine.hs b/src/SLynx/Examine/Examine.hs --- a/src/SLynx/Examine/Examine.hs +++ b/src/SLynx/Examine/Examine.hs @@ -27,7 +27,9 @@ import qualified ELynx.Data.Sequence.Alignment as M import qualified ELynx.Data.Sequence.Distance as D import qualified ELynx.Data.Sequence.Sequence as Seq -import ELynx.Tools +import ELynx.Tools.ByteString +import ELynx.Tools.ELynx +import ELynx.Tools.Environment import SLynx.Examine.Options import SLynx.Tools import qualified Statistics.Sample as Sm diff --git a/src/SLynx/Examine/Options.hs b/src/SLynx/Examine/Options.hs --- a/src/SLynx/Examine/Options.hs +++ b/src/SLynx/Examine/Options.hs @@ -17,8 +17,10 @@ ) where +import Data.Aeson import ELynx.Data.Alphabet.Alphabet -import ELynx.Tools +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Tools diff --git a/src/SLynx/Filter/Filter.hs b/src/SLynx/Filter/Filter.hs --- a/src/SLynx/Filter/Filter.hs +++ b/src/SLynx/Filter/Filter.hs @@ -25,9 +25,15 @@ import qualified ELynx.Data.Sequence.Alignment as M import qualified ELynx.Data.Sequence.Sequence as S import ELynx.Export.Sequence.Fasta -import ELynx.Tools +import ELynx.Tools.ELynx +import ELynx.Tools.Environment +import ELynx.Tools.Logger import SLynx.Filter.Options import SLynx.Tools + +-- Chain a list of functions together. See https://wiki.haskell.org/Compose. +compose :: [a -> a] -> a -> a +compose = foldl (flip (.)) id filterRows :: Maybe Int -> Maybe Int -> Bool -> [S.Sequence] -> BL.ByteString filterRows ml ms std ss = sequencesToFasta $ compose filters ss diff --git a/src/SLynx/Filter/Options.hs b/src/SLynx/Filter/Options.hs --- a/src/SLynx/Filter/Options.hs +++ b/src/SLynx/Filter/Options.hs @@ -20,8 +20,10 @@ where import Control.Applicative +import Data.Aeson import ELynx.Data.Alphabet.Alphabet -import ELynx.Tools +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Tools diff --git a/src/SLynx/Options.hs b/src/SLynx/Options.hs --- a/src/SLynx/Options.hs +++ b/src/SLynx/Options.hs @@ -11,15 +11,13 @@ -- Portability : portable -- -- Creation date: Sat Sep 7 18:55:03 2019. -module SLynx.Options - ( Arguments (..), - CommandArguments (..), - parseArguments, - ) -where +module SLynx.Options (CommandArguments (..)) where +import Data.Aeson import ELynx.Data.Alphabet.Alphabet -import ELynx.Tools +import ELynx.Tools.Options +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Concatenate.Options import SLynx.Examine.Options @@ -88,7 +86,7 @@ where toListItem = (" - " ++) fs = map toListItem ["FASTA"] - as = map (toListItem . alphabetDescription) (allValues :: [Alphabet]) + as = map (toListItem . alphabetDescription) ([minBound ..] :: [Alphabet]) instance FromJSON CommandArguments diff --git a/src/SLynx/SLynx.hs b/src/SLynx/SLynx.hs --- a/src/SLynx/SLynx.hs +++ b/src/SLynx/SLynx.hs @@ -15,7 +15,8 @@ ) where -import ELynx.Tools +import ELynx.Tools.ELynx +import ELynx.Tools.Options import SLynx.Concatenate.Concatenate import SLynx.Examine.Examine import SLynx.Filter.Filter diff --git a/src/SLynx/Simulate/Options.hs b/src/SLynx/Simulate/Options.hs --- a/src/SLynx/Simulate/Options.hs +++ b/src/SLynx/Simulate/Options.hs @@ -40,11 +40,14 @@ ) where +import Data.Aeson import Data.Maybe ( fromMaybe, maybeToList, ) -import ELynx.Tools +import ELynx.Tools.Options +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative -- | Number of gamma rate categories and alpha parameter. diff --git a/src/SLynx/Simulate/PhyloModel.hs b/src/SLynx/Simulate/PhyloModel.hs --- a/src/SLynx/Simulate/PhyloModel.hs +++ b/src/SLynx/Simulate/PhyloModel.hs @@ -33,7 +33,8 @@ import ELynx.Import.MarkovProcess.EDMModelPhylobayes ( EDMComponent, ) -import ELynx.Tools +import ELynx.Tools.Equality +import ELynx.Tools.InputOutput import Numeric.LinearAlgebra ( norm_1, size, diff --git a/src/SLynx/Simulate/Simulate.hs b/src/SLynx/Simulate/Simulate.hs --- a/src/SLynx/Simulate/Simulate.hs +++ b/src/SLynx/Simulate/Simulate.hs @@ -44,13 +44,30 @@ import ELynx.Import.MarkovProcess.EDMModelPhylobayes import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes import ELynx.Simulate.MarkovProcessAlongTree -import ELynx.Tools +import ELynx.Tools.ByteString +import ELynx.Tools.Definitions +import ELynx.Tools.ELynx +import ELynx.Tools.Environment +import ELynx.Tools.InputOutput +import ELynx.Tools.Logger +import ELynx.Tools.Options +import ELynx.Tools.Reproduction import ELynx.Tree +import qualified Numeric.LinearAlgebra as L import SLynx.Simulate.Options import SLynx.Simulate.PhyloModel import System.Random.MWC import Text.Printf +-- Display a vector with given precision. +dispv :: Int -> VS.Vector L.R -> String +dispv p v = head $ tail $ lines $ L.dispf p (L.asRow v) + +-- Display a matrix with given precision and indent. +dispmi :: Int -> Int -> L.Matrix L.R -> String +dispmi p i m = + intercalate "\n" $ map (replicate i ' ' ++) $ tail $ lines $ L.dispf p m + getDistLine :: Int -> MR.StationaryDistribution -> BB.Builder getDistLine i d = BB.intDec i @@ -156,6 +173,10 @@ h = height t h' = sum (distancesOriginLeaves t) / fromIntegral n b = totalBranchLength t + +-- Round double to a given precision. +roundN :: Int -> Double -> Double +roundN n v = fromInteger (round $ v * (10 ^ n)) / (10.0 ^^ n) -- Summarize a substitution model; lines to be printed to screen or log. summarizeSM :: MS.SubstitutionModel -> [BL.ByteString] diff --git a/src/SLynx/SubSample/Options.hs b/src/SLynx/SubSample/Options.hs --- a/src/SLynx/SubSample/Options.hs +++ b/src/SLynx/SubSample/Options.hs @@ -18,12 +18,15 @@ ) where +import Data.Aeson 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 ELynx.Data.Alphabet.Alphabet -import ELynx.Tools +import ELynx.Tools.Options +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Tools diff --git a/src/SLynx/SubSample/SubSample.hs b/src/SLynx/SubSample/SubSample.hs --- a/src/SLynx/SubSample/SubSample.hs +++ b/src/SLynx/SubSample/SubSample.hs @@ -22,7 +22,10 @@ import Control.Monad.Trans.Reader (ask) import qualified ELynx.Data.Sequence.Alignment as M import ELynx.Export.Sequence.Fasta -import ELynx.Tools +import ELynx.Tools.ELynx +import ELynx.Tools.Environment +import ELynx.Tools.Logger +import ELynx.Tools.Reproduction import SLynx.SubSample.Options import SLynx.Tools import System.Random.MWC diff --git a/src/SLynx/Tools.hs b/src/SLynx/Tools.hs --- a/src/SLynx/Tools.hs +++ b/src/SLynx/Tools.hs @@ -25,7 +25,8 @@ import ELynx.Data.Alphabet.Alphabet import ELynx.Data.Sequence.Sequence import ELynx.Import.Sequence.Fasta -import ELynx.Tools +import ELynx.Tools.InputOutput +import ELynx.Tools.Logger import Options.Applicative -- | Read sequences of given alphabet from file or standard input. diff --git a/src/SLynx/Translate/Options.hs b/src/SLynx/Translate/Options.hs --- a/src/SLynx/Translate/Options.hs +++ b/src/SLynx/Translate/Options.hs @@ -17,10 +17,12 @@ ) where +import Data.Aeson import Data.List import ELynx.Data.Alphabet.Alphabet import ELynx.Data.Character.Codon -import ELynx.Tools +import ELynx.Tools.Reproduction +import GHC.Generics import Options.Applicative import SLynx.Tools @@ -69,7 +71,7 @@ <> help ("universal code; one of: " ++ codeStr ++ ".") where - codes = allValues :: [UniversalCode] + codes = [minBound ..] :: [UniversalCode] codeWords = map show codes codeStr = intercalate ", " codeWords diff --git a/src/SLynx/Translate/Translate.hs b/src/SLynx/Translate/Translate.hs --- a/src/SLynx/Translate/Translate.hs +++ b/src/SLynx/Translate/Translate.hs @@ -22,7 +22,9 @@ import ELynx.Data.Sequence.Sequence import ELynx.Data.Sequence.Translate import ELynx.Export.Sequence.Fasta -import ELynx.Tools +import ELynx.Tools.ELynx +import ELynx.Tools.Environment +import ELynx.Tools.Logger import SLynx.Tools import SLynx.Translate.Options