slynx 0.5.1.1 → 0.6.0.0

raw patch · 13 files changed

+183/−634 lines, 13 filesdep −monad-loggerdep ~attoparsecdep ~bytestringdep ~containersPVP ok

version bump matches the API change (PVP)

Dependencies removed: monad-logger

Dependency ranges changed: attoparsec, bytestring, containers, elynx-markov, elynx-seq, elynx-tools, elynx-tree, hmatrix, mwc-random, optparse-applicative, statistics, text, transformers, vector

API changes (from Hackage documentation)

Files

• ChangeLog.md +10/−0
• README.md +27/−412
• slynx.cabal +67/−67
• src/SLynx/Concatenate/Concatenate.hs +2/−4
• src/SLynx/Examine/Examine.hs +2/−4
• src/SLynx/Filter/Filter.hs +10/−15
• src/SLynx/SLynx.hs +9/−29
• src/SLynx/Simulate/Options.hs +2/−2
• src/SLynx/Simulate/Simulate.hs +33/−50
• src/SLynx/SubSample/Options.hs +2/−2
• src/SLynx/SubSample/SubSample.hs +3/−10
• src/SLynx/Tools.hs +11/−31
• src/SLynx/Translate/Translate.hs +5/−8

@@ -5,6 +5,16 @@ ## Unreleased changes  +## Version 0.6.0.0++-   **elynx-tree:** remove parallel folds with layers (`parBranchFoldMapWithLayer`+    too special and slow).+-   **elynx-tree:** fix various tree instances; add zip trees with appropriate+    instances.+-   Remove `monad-logger` dependency and implement lighter alternative.+-   Significant changes to the tool chain.++ ## Version 0.5.1.0  -   **elynx-tree:** new functions `isValidPath`, `isLeaf`, `depth`; add conversion

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.5.1.0.+Version: 0.6.0.0. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -39,7 +39,7 @@  # Installation -ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [Stack](https://docs.haskellstack.org/en/stable/README/).+ELynx is written in [Haskell](https://www.haskell.org/) and can be installed with [cabal-install](https://cabal.readthedocs.io/en/3.4/cabal-commands.html) or [Stack](https://docs.haskellstack.org/en/stable/README/).  1.  Install Stack with your package manager, or directly from the web     page.@@ -67,15 +67,15 @@     [PATH](https://en.wikipedia.org/wiki/PATH_(variable)) environment variable. Then, they can be used directly.  -# SLynx+# Get help -Handle evolutionary sequences.+For example: -    stack exec slynx -- --help | head -n -16+    slynx --help -    ELynx Suite version 0.5.1.0.+    ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.+    Compiled on September 3, 2021, at 20:56 pm, UTC.          Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME]                   [-f|--force] [--no-elynx-file] COMMAND@@ -84,7 +84,7 @@     Available options:       -h,--help                Show this help text       -V,--version             Show version-      -v,--verbosity VALUE     Be verbose; one of: Quiet Warning Info Debug+      -v,--verbosity VALUE     Be verbose; one of: Quiet Warn Info Debug                                (default: Info)       -o,--output-file-basename NAME                                Specify base name of output file@@ -112,107 +112,33 @@       - Protein (amino acids)       - ProteinX (amino acids; including gaps)       - ProteinS (amino acids; including gaps, and translation stops)---## Concatenate--Concatenate multi sequence alignments.--    stack exec slynx -- concatenate --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE-      Concatenate sequences found in input files.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      -h,--help                Show this help text---## Examine--Examine sequence with `slynx examine`.--    stack exec slynx -- examine --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site]-      Examine sequences. If data is a multi sequence alignment, additionally analyze columns.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      --per-site               Report per site summary statistics-      -h,--help                Show this help text---## Filter--Filter sequences with `filer-rows`.--    stack exec slynx -- filter-rows --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] -                             [--shorter-than LENGTH] [--standard-characters]-      Filter rows (or sequences) found in input files.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      --longer-than LENGTH     Only keep sequences longer than LENGTH-      --shorter-than LENGTH    Only keep sequences shorter than LENGTH-      --standard-characters    Only keep sequences containing at least one standard-                               (i.e., non-IUPAC) character-      -h,--help                Show this help text--Filter columns of multi sequence alignments with `filter-columns`.--    stack exec slynx -- filter-columns --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.+      - ProteinI (amino acids; including gaps, translation stops, and IUPAC codes)+    ELynx+    -----+    A Haskell library and tool set for computational biology. The goal of ELynx is+    reproducible research. Evolutionary sequences and phylogenetic trees can be+    read, viewed, modified and simulated. The command line with all arguments is+    logged consistently, and automatically. Data integrity is verified using SHA256+    sums so that validation of past analyses is possible without the need to+    recompute the result.     -    Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE -                                [--standard-chars DOUBLE]-      Filter columns of multi sequence alignments.+    slynx     Analyze, modify, and simulate evolutionary sequences.+    tlynx     Analyze, modify, and simulate phylogenetic trees.+    elynx     Validate and redo past analyses.     -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      --standard-chars DOUBLE  Keep columns with a proportion standard (non-IUPAC)-                               characters larger than DOUBLE in [0,1]-      -h,--help                Show this help text+    Get help for sub commands:+      slynx examine --help  -## Simulate+## Sub command -Simulate sequences with `slynx simulate`.+The documentation of sub commands can be accessed separately: -    stack exec slynx -- simulate --help+    slynx simulate --help -    ELynx Suite version 0.5.1.0.+    ELynx Suite version 0.6.0.0.     Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.+    Compiled on September 3, 2021, at 20:56 pm, UTC.          Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL]                            [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -281,315 +207,4 @@          LG exchangeabilities with site profiles (Phylobayes) given in FILES.          -m "EDM(LG-Custom)" -p FILES     For special mixture models, mixture weights are optional.---## Sub-sample--Sub-sample columns from multi sequence alignments.--    stack exec slynx -- sub-sample --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE-                            (-n|--number-of-sites INT)-                            (-m|--number-of-alignments INT) [-S|--seed [INT]]-      Sub-sample columns from multi sequence alignments.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      -n,--number-of-sites INT Number of sites randomly drawn with replacement-      -m,--number-of-alignments INT-                               Number of multi sequence alignments to be created-      -S,--seed [INT]          Seed for random number generator; list of 32 bit-                               integers with up to 256 elements (default: random)-      -h,--help                Show this help text-    -    Create a given number of multi sequence alignments, each of which contains a given number of random sites drawn from the original multi sequence alignment.---## Translate--Translate sequences.--    stack exec slynx -- translate --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT)-                           (-u|--universal-code CODE)-      Translate from DNA to Protein or DNAX to ProteinX.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -a,--alphabet NAME       Specify alphabet type NAME-      INPUT-FILE               Read sequences from INPUT-FILE-      -r,--reading-frame INT   Reading frame [0|1|2].-      -u,--universal-code CODE universal code; one of: Standard,-                               VertebrateMitochondrial.-      -h,--help                Show this help text---# TLynx--Handle phylogenetic trees in Newick format.--    stack exec tlynx -- --help | head -n -16--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] -                 [-f|--force] [--no-elynx-file] COMMAND-      Compare, examine, and simulate phylogenetic trees.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -v,--verbosity VALUE     Be verbose; one of: Quiet Warning Info Debug-                               (default: Info)-      -o,--output-file-basename NAME-                               Specify base name of output file-      -f,--force               Ignore previous analysis and overwrite existing-                               output files.-      --no-elynx-file          Do not write data required to reproduce an analysis.-    -    Available commands:-      compare                  Compare two phylogenetic trees (compute distances and branch-wise differences).-      connect                  Connect two phylogenetic trees in all ways (possibly honoring constraints).-      distance                 Compute distances between many phylogenetic trees.-      examine                  Compute summary statistics of phylogenetic trees.-      shuffle                  Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).-      simulate                 Simulate phylogenetic trees using a birth and death or coalescent process.-    -    -    Available tree file formats:-      - Newick Standard: Branch support values are stored in square brackets after branch lengths.-      - Newick IqTree:   Branch support values are stored as node names after the closing bracket of forests.-      - Newick RevBayes: Key-value pairs is provided in square brackets after node names as well as branch lengths. XXX: Key value pairs are ignored at the moment.---## Compare--Compute distances between phylogenetic trees.--    stack exec tlynx -- compare --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] -                         [-f|--newick-format FORMAT] NAMES-      Compare two phylogenetic trees (compute distances and branch-wise differences).-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -n,--normalize           Normalize trees before comparison-      -b,--bipartitions        Print and plot common and missing bipartitions-      -t,--intersect           Compare intersections; i.e., before comparison, drop-                               leaves that are not present in the other tree-      -f,--newick-format FORMAT-                               Newick tree format: Standard, IqTree, or RevBayes;-                               default: Standard; for detailed help, see 'tlynx-                               --help'-      NAMES                    Tree files-      -h,--help                Show this help text---## Connect--Connect two phylogenetic tree in all ways (possibly honoring constraints).--    stack exec tlynx -- connect --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx connect [-f|--newick-format FORMAT] [-c|--contraints CONSTRAINTS]-                         TREE-FILE-A TREE-FILE-B-      Connect two phylogenetic trees in all ways (possibly honoring constraints).-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -f,--newick-format FORMAT-                               Newick tree format: Standard, IqTree, or RevBayes;-                               default: Standard; for detailed help, see 'tlynx-                               --help'-      -c,--contraints CONSTRAINTS-                               File containing one or more Newick trees to be used-                               as constraints-      TREE-FILE-A              File containing the first Newick tree-      TREE-FILE-B              File containing the second Newick tree-      -h,--help                Show this help text---## Distancce--Compute distances between many phylogenetic trees.--    stack exec tlynx -- distance --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx distance (-d|--distance MEASURE) [-n|--normalize] [-t|--intersect] -                          [-s|--summary-statistics] -                          [-m|--master-tree-file MASTER-TREE-File] -                          [-f|--newick-format FORMAT] [INPUT-FILES]-      Compute distances between many phylogenetic trees.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -d,--distance MEASURE    Type of distance to calculate (available distance-                               measures are listed below)-      -n,--normalize           Normalize trees before distance calculation; only-                               affect distances depending on branch lengths-      -t,--intersect           Compare intersections; i.e., before comparison, drop-                               leaves that are not present in the other tree-      -s,--summary-statistics  Report summary statistics only-      -m,--master-tree-file MASTER-TREE-File-                               Compare all trees to the tree in the master tree-                               file.-      -f,--newick-format FORMAT-                               Newick tree format: Standard, IqTree, or RevBayes;-                               default: Standard; for detailed help, see 'tlynx-                               --help'-      INPUT-FILES              Read tree(s) from INPUT-FILES; if more files are-                               given, one tree is expected per file-      -h,--help                Show this help text-    -    Distance measures:-      symmetric                Symmetric distance (Robinson-Foulds distance).-      incompatible-split[VAL]  Incompatible split distance. Collapse branches with (normalized)-                               support less than 0.0<=VAL<=1.0 before distance calculation;-                               if, let's say, VAL>0.7, only well supported differences contribute-                               to the total distance.-      branch-score             Branch score distance.---## Examine--Compute summary statistics of phylogenetic trees.--    stack exec tlynx -- examine --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT]-      Compute summary statistics of phylogenetic trees.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      INPUT-FILE               Read trees from INPUT-FILE-      -f,--newick-format FORMAT-                               Newick tree format: Standard, IqTree, or RevBayes;-                               default: Standard; for detailed help, see 'tlynx-                               --help'-      -h,--help                Show this help text---## Shuffle--Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and-leaves).--    stack exec tlynx -- shuffle --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx shuffle [-f|--newick-format FORMAT] [-n|--replicates N] TREE-FILE -                         [-S|--seed [INT]]-      Shuffle a phylogenetic tree (keep coalescent times, but shuffle topology and leaves).-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -f,--newick-format FORMAT-                               Newick tree format: Standard, IqTree, or RevBayes;-                               default: Standard; for detailed help, see 'tlynx-                               --help'-      -n,--replicates N        Number of trees to generate-      TREE-FILE                File containing a Newick tree-      -S,--seed [INT]          Seed for random number generator; list of 32 bit-                               integers with up to 256 elements (default: random)-      -h,--help                Show this help text---## Simulate--Simulate phylogenetic trees using birth and death processes.--    stack exec tlynx -- simulate --help--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: tlynx simulate (-t|--nTrees INT) (-n|--nLeaves INT) PROCESS -                          [-u|--sub-sample DOUBLE] [-s|--summary-statistics] -                          [-S|--seed [INT]]-      Simulate phylogenetic trees using a birth and death or coalescent process.-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-      -t,--nTrees INT          Number of trees-      -n,--nLeaves INT         Number of leaves per tree-      -u,--sub-sample DOUBLE   Perform sub-sampling; see below.-      -s,--summary-statistics  For each branch, print length and number of children-      -S,--seed [INT]          Seed for random number generator; list of 32 bit-                               integers with up to 256 elements (default: random)-      -h,--help                Show this help text-    -    Available processes:-      birthdeath               Birth and death process-      coalescent               Coalescent process-    -    See, for example, 'tlynx simulate birthdeath --help'.-    Sub-sample with probability p:-      1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;-      2. Randomly sample sub-trees with n leaves.-      (With p=1.0, the same tree is reported over and over again.)---# ELynx--Validate and (optionally) redo past ELynx analyses.--    stack exec elynx -- --help | head -n -16--    ELynx Suite version 0.5.1.0.-    Developed by Dominik Schrempf.-    Compiled on June 12, 2021, at 14:54 pm, UTC.-    -    Usage: elynx COMMAND-      Validate and redo past ELynx analyses-    -    Available options:-      -h,--help                Show this help text-      -V,--version             Show version-    -    Available commands:-      validate                 Validate an ELynx analysis-      redo                     Redo an ELynx analysis 

@@ -1,77 +1,77 @@-cabal-version:      2.2-name:               slynx-version:            0.5.1.1-license:            GPL-3.0-or-later-license-file:       LICENSE-copyright:          Dominik Schrempf (2021)-maintainer:         dominik.schrempf@gmail.com-author:             Dominik Schrempf-homepage:           https://github.com/dschrempf/elynx#readme-bug-reports:        https://github.com/dschrempf/elynx/issues-synopsis:           Handle 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>.+cabal-version:  2.2+name:           slynx+version:        0.6.0.0+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+homepage:       https://github.com/dschrempf/elynx#readme+bug-reports:    https://github.com/dschrempf/elynx/issues+author:         Dominik Schrempf+maintainer:     dominik.schrempf@gmail.com+copyright:      Dominik Schrempf (2021)+license:        GPL-3.0-or-later+license-file:   LICENSE+build-type:     Simple -category:           Bioinformatics-build-type:         Simple extra-source-files:     README.md     ChangeLog.md  source-repository head-    type:     git-    location: https://github.com/dschrempf/elynx+  type: git+  location: https://github.com/dschrempf/elynx  library-    exposed-modules:-        SLynx.Concatenate.Concatenate-        SLynx.Concatenate.Options-        SLynx.Examine.Examine-        SLynx.Examine.Options-        SLynx.Filter.Filter-        SLynx.Filter.Options-        SLynx.Options-        SLynx.Simulate.Options-        SLynx.Simulate.PhyloModel-        SLynx.Simulate.Simulate-        SLynx.SLynx-        SLynx.SubSample.Options-        SLynx.SubSample.SubSample-        SLynx.Tools-        SLynx.Translate.Options-        SLynx.Translate.Translate--    hs-source-dirs:   src-    other-modules:    Paths_slynx-    autogen-modules:  Paths_slynx-    default-language: Haskell2010-    ghc-options:      -Wall -Wunused-packages-    build-depends:-        attoparsec >=0.13.2.5,-        base >=4.7 && <5,-        bytestring >=0.10.12.0,-        containers >=0.6.2.1,-        elynx-markov >=0.5.1.1,-        elynx-seq >=0.5.1.1,-        elynx-tools >=0.5.1.1,-        elynx-tree >=0.5.1.1,-        hmatrix >=0.20.2,-        monad-logger >=0.3.36,-        mwc-random >=0.15.0.1,-        optparse-applicative >=0.16.1.0,-        statistics >=0.15.2.0,-        text >=1.2.4.1,-        transformers >=0.5.6.2,-        vector >=0.12.3.0+  exposed-modules:+      SLynx.Concatenate.Concatenate+      SLynx.Concatenate.Options+      SLynx.Examine.Examine+      SLynx.Examine.Options+      SLynx.Filter.Filter+      SLynx.Filter.Options+      SLynx.Options+      SLynx.Simulate.Options+      SLynx.Simulate.PhyloModel+      SLynx.Simulate.Simulate+      SLynx.SLynx+      SLynx.SubSample.Options+      SLynx.SubSample.SubSample+      SLynx.Tools+      SLynx.Translate.Options+      SLynx.Translate.Translate+  other-modules:+      Paths_slynx+  autogen-modules:+      Paths_slynx+  hs-source-dirs: src+  ghc-options: -Wall -Wunused-packages+  build-depends:+      attoparsec+    , base >=4.7 && <5+    , bytestring+    , containers+    , elynx-markov+    , elynx-seq+    , elynx-tools+    , elynx-tree+    , hmatrix+    , mwc-random+    , optparse-applicative+    , statistics+    , text+    , transformers+    , vector+  default-language: Haskell2010  executable slynx-    main-is:          Main.hs-    hs-source-dirs:   app-    other-modules:    Paths_slynx-    default-language: Haskell2010-    ghc-options:-        -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N--    build-depends:-        base >=4.7 && <5,-        slynx -any+  main-is: Main.hs+  other-modules:+      Paths_slynx+  autogen-modules:+      Paths_slynx+  hs-source-dirs: app+  ghc-options: -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N+  build-depends:+      base >=4.7 && <5+    , slynx+  default-language: Haskell2010

@@ -17,8 +17,7 @@   ) where -import Control.Monad.Logger-import Control.Monad.Trans.Reader (ask)+import Control.Monad.Trans.Reader import qualified ELynx.Data.Sequence.Sequence as S import ELynx.Export.Sequence.Fasta import ELynx.Tools@@ -28,8 +27,7 @@ -- | Concatenate sequences. concatenateCmd :: ELynx ConcatenateArguments () concatenateCmd = do-  (ConcatenateArguments al fps) <- local <$> ask-  $(logInfo) "Command: Concatenate sequences."+  (ConcatenateArguments al fps) <- reader localArguments   sss <- mapM (readSeqs al) fps   let result = sequencesToFasta $ S.concatSequences sss   out "concatenated multi sequence alignment " result ".fasta"

@@ -18,8 +18,7 @@   ) where -import Control.Monad.Logger-import Control.Monad.Trans.Reader (ask)+import Control.Monad.Trans.Reader import qualified Data.ByteString.Lazy.Char8 as BL import qualified Data.Set as S import qualified Data.Vector.Unboxed as V@@ -157,8 +156,7 @@ -- | Examine sequences. examineCmd :: ELynx ExamineArguments () examineCmd = do-  (ExamineArguments al inFile perSiteFlag) <- local <$> ask-  $(logInfo) "Command: Examine sequences."+  (ExamineArguments al inFile perSiteFlag) <- localArguments <$> ask   ss <- readSeqs al inFile   let result = examine perSiteFlag ss   out "result of examination" result ".out"

@@ -19,11 +19,9 @@ where  import Control.Monad (when)-import Control.Monad.Logger-import Control.Monad.Trans.Reader (ask)+import Control.Monad.Trans.Reader import qualified Data.ByteString.Lazy.Char8 as BL import Data.Maybe (fromMaybe)-import qualified Data.Text as T import qualified ELynx.Data.Sequence.Alignment as M import qualified ELynx.Data.Sequence.Sequence as S import ELynx.Export.Sequence.Fasta@@ -41,22 +39,21 @@ -- | Filter sequences. filterRowsCmd :: ELynx FilterRowsArguments () filterRowsCmd = do-  (FilterRowsArguments al inFile long short std) <- local <$> ask-  $(logInfo) "Command: Filter sequences of a list of sequences."+  (FilterRowsArguments al inFile long short std) <- localArguments <$> ask   maybe     (return ())     ( \val ->-        $(logInfo) $ T.pack $ "  Keep sequences longer than " <> show val <> "."+        logInfoS $ "  Keep sequences longer than " <> show val <> "."     )     long   maybe     (return ())     ( \val ->-        $(logInfo) $ T.pack $ "  Keep sequences shorter than " <> show val <> "."+        logInfoS $ "  Keep sequences shorter than " <> show val <> "."     )     short   when std $-    $(logInfo)+    logInfoS       "  Keep sequences containing at least one standard (i.e., non-IUPAC) character."   ss <- readSeqs al inFile   let result = filterRows long short std ss@@ -71,16 +68,14 @@ -- | Filter columns. filterColsCmd :: ELynx FilterColsArguments () filterColsCmd = do-  (FilterColsArguments al inFile standard) <- local <$> ask-  $(logInfo) "Command: Filter columns of a multi sequence alignment."+  (FilterColsArguments al inFile standard) <- localArguments <$> 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-            ++ "."+      logInfoS $+        "  Keep columns with a proportion of standard (non-IUPAC) characters larger than "+          ++ show p+          ++ "."   ss <- readSeqs al inFile   let result = filterCols standard ss   out "filtered sequences" result ".fasta"

@@ -27,35 +27,15 @@ -- | Run SLynx with given arguments. slynx :: Arguments CommandArguments -> IO () slynx c = case local c of-  Concatenate _ ->-    eLynxWrapper-      c-      (\(Arguments g (Concatenate l)) -> Arguments g l)-      concatenateCmd-  Examine _ ->-    eLynxWrapper c (\(Arguments g (Examine l)) -> Arguments g l) examineCmd-  FilterCols _ ->-    eLynxWrapper-      c-      (\(Arguments g (FilterCols l)) -> Arguments g l)-      filterColsCmd-  FilterRows _ ->-    eLynxWrapper-      c-      (\(Arguments g (FilterRows l)) -> Arguments g l)-      filterRowsCmd-  Simulate _ ->-    eLynxWrapper c (\(Arguments g (Simulate l)) -> Arguments g l) simulateCmd-  SubSample _ ->-    eLynxWrapper-      c-      (\(Arguments g (SubSample l)) -> Arguments g l)-      subSampleCmd-  Translate _ ->-    eLynxWrapper-      c-      (\(Arguments g (Translate l)) -> Arguments g l)-      translateCmd+  Concatenate l -> eLynxWrapper g l Concatenate concatenateCmd+  Examine l -> eLynxWrapper g l Examine examineCmd+  FilterCols l -> eLynxWrapper g l FilterCols filterColsCmd+  FilterRows l -> eLynxWrapper g l FilterRows filterRowsCmd+  Simulate l -> eLynxWrapper g l Simulate simulateCmd+  SubSample l -> eLynxWrapper g l SubSample subSampleCmd+  Translate l -> eLynxWrapper g l Translate translateCmd+  where+    g = global c  -- | Run SLynx, parse arguments from command line. rSLynx :: IO ()

@@ -60,7 +60,7 @@     argsMixtureWeights :: Maybe [Double],     argsGammaParams :: Maybe GammaRateHeterogeneityParams,     argsLength :: Int,-    argsSeed :: Seed+    argsSeed :: SeedOpt   }   deriving (Eq, Show, Generic) @@ -70,7 +70,7 @@     (maybeToList (argsEDMFile a) ++ fromMaybe [] (argsSiteprofilesFiles a))   outSuffixes _ = [".model.gz", ".fasta"]   getSeed = Just . argsSeed-  setSeed a s = a {argsSeed = Fixed s}+  setSeed a s = a {argsSeed = s}   parser = simulateArguments   cmdName = "simulate"   cmdDsc = ["Simulate multi sequence alignments."]

@@ -20,7 +20,6 @@ import Control.Applicative ((<|>)) import Control.Monad import Control.Monad.IO.Class-import Control.Monad.Logger import Control.Monad.Trans.Class import Control.Monad.Trans.Reader (ask) import qualified Data.ByteString.Builder as BB@@ -28,9 +27,6 @@ import Data.List import Data.Maybe 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 qualified Data.Vector as V import qualified Data.Vector.Storable as VS import qualified Data.Vector.Unboxed as U@@ -66,7 +62,7 @@ writeSiteDists :: [Int] -> V.Vector MR.StationaryDistribution -> ELynx SimulateArguments () -- writeSiteDists is ds = out "site distributions of distribution mixture model" output ".sitedists" writeSiteDists componentIs ds = do-  mbn <- outFileBaseName . global <$> ask+  mbn <- outFileBaseName . globalArguments <$> ask   case mbn of     Nothing -> return ()     Just bn -> liftIO $ BL.writeFile (bn <> ".sitedists") output@@ -85,7 +81,7 @@   GenIO ->   ELynx SimulateArguments () simulateAlignment pm t' n g = do-  let t = fromLength . getLen <$> toTreeBranchLabels t'+  let t = fromLength . getLength <$> toTreeBranchLabels t'   leafStates <- case pm of     MP.SubstitutionModel sm -> liftIO $ simulateAndFlattenPar n d e t g       where@@ -110,7 +106,7 @@           | (sName, ss) <- zip leafNames leafStates         ]       output = sequencesToFasta sequences-  $(logInfo) ""+  logInfoS ""   out "simulated multi sequence alignment" output ".fasta"  -- Summarize EDM components; line to be printed to screen or log.@@ -123,19 +119,19 @@  reportModel :: MP.PhyloModel -> ELynx SimulateArguments () reportModel m = do-  as <- global <$> ask+  as <- globalArguments <$> ask   if writeElynxFile as     then       ( do           let bn = outFileBaseName as           case bn of             Nothing ->-              $(logInfo)+              logInfoS                 "No output file provided; omit writing machine-readable phylogenetic model."             Just _ ->               out "model definition (machine readable)" (BL.pack (show m) <> "\n") ".model.gz"       )-    else $(logInfo) "No elynx file required; omit writing machine-readable phylogenetic model."+    else logInfoS "No elynx file required; omit writing machine-readable phylogenetic model."  pretty :: Length -> String pretty = printf "%.5f" . fromLength@@ -220,46 +216,45 @@ -- | Simulate sequences. simulateCmd :: ELynx SimulateArguments () simulateCmd = do-  l <- local <$> ask+  l <- localArguments <$> ask   let treeFile = argsTreeFile l-  $(logInfo) ""-  $(logInfo) $ T.pack $ "Read tree from file '" ++ treeFile ++ "'."+  logInfoS ""+  logInfoS $ "Read tree from file '" ++ treeFile ++ "'."   tree <- liftIO $ parseFileWith (newick Standard) treeFile-  let t' = either error id $ phyloToLengthTree tree-  $(logInfo) $ T.pack $ "Number of leaves: " ++ show (length $ leaves t')-  $(logInfo) $ LT.toStrict $ LT.decodeUtf8 $ summarizeLengths t'+  let t' = either error id $ toLengthTree tree+  logInfoS $ "Number of leaves: " ++ show (length $ leaves t')+  logInfoB $ summarizeLengths t'   let edmFile = argsEDMFile l   let sProfileFiles = argsSiteprofilesFiles l-  $(logInfo) ""-  $(logDebug) "Read EDM file or siteprofile files."+  logInfoS ""+  logDebugS "Read EDM file or siteprofile files."   when (isJust edmFile && isJust sProfileFiles) $     error "Got both: --edm-file and --siteprofile-files."   edmCs <- case edmFile of     Nothing -> return Nothing     Just edmF -> do-      $(logInfo) "Read EDM file."+      logInfoS "Read EDM file."       liftIO $ Just <$> parseFileWith phylobayes edmF   maybe     (return ())-    ($(logInfo) . LT.toStrict . LT.decodeUtf8 . summarizeEDMComponents)+    (logInfoB . summarizeEDMComponents)     edmCs   sProfiles <- case sProfileFiles of     Nothing -> return Nothing     Just fns -> do-      $(logInfo) $-        T.pack $-          "Read siteprofiles from "-            ++ show (length fns)-            ++ " file(s)."-      $(logDebug) $ T.pack $ "The file names are:" ++ show fns+      logInfoS $+        "Read siteprofiles from "+          ++ show (length fns)+          ++ " file(s)."+      logDebugS $ "The file names are:" ++ show fns       xs <- liftIO $ mapM (parseFileWith siteprofiles) fns       return $ Just $ concat xs   maybe     (return ())-    ($(logInfo) . LT.toStrict . LT.decodeUtf8 . summarizeEDMComponents)+    (logInfoB . summarizeEDMComponents)     sProfiles   let edmCsOrSiteprofiles = edmCs <|> sProfiles-  $(logInfo) "Read model string."+  logInfoS "Read model string."   let ms = argsSubstitutionModelString l       mm = argsMixtureModelString l       mws = argsMixtureWeights l@@ -270,31 +265,19 @@   let maybeGammaParams = argsGammaParams l   phyloModel <- case maybeGammaParams of     Nothing -> do-      $(logInfo) $-        LT.toStrict $-          LT.decodeUtf8 $-            BL.unlines $-              summarizePM-                phyloModel'+      logInfoB $ BL.unlines $ summarizePM phyloModel'       return phyloModel'     Just (n, alpha) -> do-      $(logInfo) $-        LT.toStrict $-          LT.decodeUtf8 $-            BL.intercalate "\n" $-              summarizePM phyloModel'-      $(logInfo) ""-      $(logInfo) $-        LT.toStrict $-          LT.decodeUtf8 $-            BL.intercalate "\n" $-              summarizeGammaRateHeterogeneity n alpha+      logInfoB $ BL.intercalate "\n" $ summarizePM phyloModel'+      logInfoS ""+      logInfoB $ BL.intercalate "\n" $ summarizeGammaRateHeterogeneity n alpha       return $ expand n alpha phyloModel'   reportModel phyloModel-  $(logInfo) "Simulate alignment."+  logInfoS "Simulate alignment."   let alignmentLength = argsLength l-  $(logInfo) $ T.pack $ "Length: " <> show alignmentLength <> "."-  gen <- case argsSeed l of-    Random -> error "simulateCmd: seed not available; please contact maintainer."-    Fixed s -> liftIO $ initialize s+  logInfoS $ "Length: " <> show alignmentLength <> "."+  gen <- liftIO <$> initialize $ case argsSeed l of+    RandomUnset -> error "simulateCmd: seed not available; please contact maintainer."+    RandomSet s -> s+    Fixed s -> s   simulateAlignment phyloModel t' alignmentLength gen

@@ -33,7 +33,7 @@     ssInFile :: FilePath,     ssNSites :: Int,     ssNAlignments :: Int,-    ssMbSeed :: Seed+    ssMbSeed :: SeedOpt   }   deriving (Eq, Show, Generic) @@ -55,7 +55,7 @@   inFiles = pure . ssInFile   outSuffixes a = getOutSuffixes (ssNAlignments a) "fasta"   getSeed = Just . ssMbSeed-  setSeed a s = a {ssMbSeed = Fixed s}+  setSeed a s = a {ssMbSeed = s}   parser = subSampleArguments   cmdName = "sub-sample"   cmdDsc = ["Sub-sample columns from multi sequence alignments."]

@@ -19,9 +19,7 @@  import Control.Monad import Control.Monad.IO.Class-import Control.Monad.Logger import Control.Monad.Trans.Reader (ask)-import qualified Data.Text as T import qualified ELynx.Data.Sequence.Alignment as M import ELynx.Export.Sequence.Fasta import ELynx.Tools@@ -32,14 +30,9 @@ -- | Sub sample sequences. subSampleCmd :: ELynx SubSampleArguments () subSampleCmd = do-  (SubSampleArguments al inFile nSites nAlignments (Fixed s)) <- local <$> ask-  $(logInfo) "Command: Sub sample from a multi sequence alignment."-  $(logInfo) $ T.pack $ "  Sample " <> show nSites <> " sites."-  $(logInfo) $-    T.pack $-      "  Sample "-        <> show nAlignments-        <> " multi sequence alignments."+  (SubSampleArguments al inFile nSites nAlignments (Fixed s)) <- localArguments <$> ask+  logInfoS $ "  Sample " <> show nSites <> " sites."+  logInfoS $ "  Sample " <> show nAlignments <> " multi sequence alignments."   ss <- readSeqs al inFile   gen <- liftIO $ initialize s   let a = either error id (M.fromSequences ss)

@@ -22,45 +22,25 @@ where  import Control.Monad.IO.Class-import Control.Monad.Logger-import qualified Data.Text as T import ELynx.Data.Alphabet.Alphabet import ELynx.Data.Sequence.Sequence import ELynx.Import.Sequence.Fasta import ELynx.Tools import Options.Applicative --- -- | 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- -- | Read sequences of given alphabet from file or standard input.-readSeqs :: (MonadIO m, MonadLogger m) => Alphabet -> FilePath -> m [Sequence]+readSeqs ::+  (HasLock e, HasLogHandles e, HasVerbosity e) =>+  Alphabet ->+  FilePath ->+  Logger e [Sequence] readSeqs a fp = do-  $(logInfo) $-    T.pack $-      "Read sequences from file "-        <> fp-        <> "; alphabet "-        <> show a-        <> "."+  logInfoS $+    "Read sequences from file "+      <> fp+      <> "; alphabet "+      <> show a+      <> "."   liftIO $ parseFileWith (fasta a) fp  -- | Command line option to specify the alphabet. Used by various commands.

@@ -17,9 +17,7 @@   ) where -import Control.Monad.Logger-import Control.Monad.Trans.Reader (ask)-import qualified Data.Text as T+import Control.Monad.Trans.Reader import ELynx.Data.Character.Codon import ELynx.Data.Sequence.Sequence import ELynx.Data.Sequence.Translate@@ -34,11 +32,10 @@ -- | Translate sequences. translateCmd :: ELynx TranslateArguments () translateCmd = do-  (TranslateArguments al inFile rf uc) <- local <$> ask-  $(logInfo) "Command: Translate sequences to amino acids."-  $(logInfo) $ T.pack $ "  Universal code: " <> show uc <> "."-  $(logInfo) $ T.pack $ "  Reading frame: " <> show rf <> "."-  $(logInfo) ""+  (TranslateArguments al inFile rf uc) <- localArguments <$> ask+  logInfoS $ "  Universal code: " <> show uc <> "."+  logInfoS $ "  Reading frame: " <> show rf <> "."+  logInfoS ""   ss <- readSeqs al inFile   let result = sequencesToFasta $ translateSeqs rf uc ss   out "translated sequences" result "fasta"