slynx 0.6.0.0 → 0.6.1.0

raw patch · 19 files changed

+96/−32 lines, 19 filesdep +aesonPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: aeson

API changes (from Hackage documentation)

Files

• ChangeLog.md +7/−0
• README.md +12/−6
• slynx.cabal +3/−2
• src/SLynx/Concatenate/Concatenate.hs +2/−1
• src/SLynx/Concatenate/Options.hs +3/−1
• src/SLynx/Examine/Examine.hs +3/−1
• src/SLynx/Examine/Options.hs +3/−1
• src/SLynx/Filter/Filter.hs +7/−1
• src/SLynx/Filter/Options.hs +3/−1
• src/SLynx/Options.hs +6/−8
• src/SLynx/SLynx.hs +2/−1
• src/SLynx/Simulate/Options.hs +4/−1
• src/SLynx/Simulate/PhyloModel.hs +2/−1
• src/SLynx/Simulate/Simulate.hs +22/−1
• src/SLynx/SubSample/Options.hs +4/−1
• src/SLynx/SubSample/SubSample.hs +4/−1
• src/SLynx/Tools.hs +2/−1
• src/SLynx/Translate/Options.hs +4/−2
• src/SLynx/Translate/Translate.hs +3/−1

@@ -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`

@@ -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] 

@@ -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 <https://github.com/dschrempf/elynx>. 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

@@ -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 

@@ -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 

@@ -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

@@ -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 

@@ -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

@@ -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 

@@ -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 

@@ -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

@@ -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.

@@ -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,

@@ -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]

@@ -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 

@@ -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

@@ -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.

@@ -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 

@@ -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