diff --git a/ChangeLog.md b/ChangeLog.md
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -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
diff --git a/README.md b/README.md
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
# The ELynx Suite
-Version: 0.5.1.0.
+Version: 0.6.0.0.
Reproducible evolution made easy.
@@ -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
diff --git a/app/Main.hs b/app/Main.hs
--- a/app/Main.hs
+++ b/app/Main.hs
@@ -174,8 +174,8 @@
runRedo :: RedoArguments -> IO ()
runRedo a = do
let fp = rElynxFile a
- let f = rForce a
- when (f == Force False) $ do
+ let f = rExecutionMode a
+ when (f == Fail) $ do
putStrLn "Validate ELynx reproduction file before reanalysis."
putStrLn "Use the --force (-f) option to skip this test."
runValidate (ValidateArguments fp)
@@ -190,12 +190,14 @@
else return as
withProgName (getELynxProgName repr) $ withArgs as' $ redo repr
-setForce :: Arguments a -> Arguments a
-setForce (Arguments g l) = Arguments g {forceReanalysis = Force True} l
+setExecutionMode :: Arguments a -> Arguments a
+setExecutionMode (Arguments g l) = Arguments g' l
+ where
+ g' = g {executionMode = Overwrite}
redo :: AllReproductions -> IO ()
-redo (S x) = slynx $ setForce $ reproducible x
-redo (T x) = tlynx $ setForce $ reproducible x
+redo (S x) = slynx $ setExecutionMode $ reproducible x
+redo (T x) = tlynx $ setExecutionMode $ reproducible x
main :: IO ()
main = do
diff --git a/app/Options.hs b/app/Options.hs
--- a/app/Options.hs
+++ b/app/Options.hs
@@ -54,12 +54,12 @@
data RedoArguments = RedoArguments
{ rElynxFile :: FilePath,
- rForce :: Force
+ rExecutionMode :: ExecutionMode
}
deriving (Eq, Show, Generic)
redoArguments :: Parser RedoArguments
-redoArguments = RedoArguments <$> inFileArg <*> forceOpt
+redoArguments = RedoArguments <$> inFileArg <*> executionModeOpt
redoDsc :: [String]
redoDsc = ["Redo an ELynx analysis"]
diff --git a/elynx.cabal b/elynx.cabal
--- a/elynx.cabal
+++ b/elynx.cabal
@@ -1,44 +1,41 @@
-cabal-version: 2.2
-name: elynx
-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: Validate and (optionally) redo ELynx analyses
-description:
- Please see the README on GitHub at .
+cabal-version: 2.2
+name: elynx
+version: 0.6.0.0
+synopsis: Validate and (optionally) redo ELynx analyses
+description: Please see the README on GitHub at .
+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
executable elynx
- main-is: Main.hs
- hs-source-dirs: app
- other-modules:
- Options
- Paths_elynx
-
- autogen-modules: Paths_elynx
- default-language: Haskell2010
- ghc-options:
- -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N
-
- build-depends:
- aeson >=1.5.6.0,
- base >=4.7 && <5,
- bytestring >=0.10.12.0,
- elynx-tools >=0.5.1.1,
- optparse-applicative >=0.16.1.0,
- slynx >=0.5.1.1,
- tlynx >=0.5.1.1
+ main-is: Main.hs
+ other-modules:
+ Options
+ Paths_elynx
+ autogen-modules:
+ Paths_elynx
+ hs-source-dirs: app
+ ghc-options: -Wall -Wunused-packages -threaded -rtsopts -with-rtsopts=-N
+ build-depends:
+ aeson
+ , base >=4.7 && <5
+ , bytestring
+ , elynx-tools
+ , optparse-applicative
+ , slynx
+ , tlynx
+ default-language: Haskell2010