diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -5,6 +5,14 @@ ## Unreleased changes +## Version 0.3.4 + +- Improve `slynx examine`; show hamming distance; show constant sites. +- PhyloStrict -> PhyloExplicit; and some conversion functions were changed. +- `tlynx coalesce` was merged into `tlynx simulate`, the syntax has changed; see + `tlynx simulate --help`. + + ## Version 0.3.3 - Fix test suites. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ # The ELynx Suite -Version: 0.3.3. +Version: 0.3.4. Reproducible evolution made easy.

@@ -90,9 +90,9 @@ slynx --help | head -n -16 - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -136,9 +136,9 @@ slynx concatenate --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx concatenate (-a|--alphabet NAME) INPUT-FILE Concatenate sequences found in input files. @@ -157,9 +157,9 @@ slynx examine --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx examine (-a|--alphabet NAME) INPUT-FILE [--per-site] Examine sequences. If data is a multi sequence alignment, additionally analyze columns. @@ -179,9 +179,9 @@ slynx filter-rows --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx filter-rows (-a|--alphabet NAME) INPUT-FILE [--longer-than LENGTH] [--shorter-than LENGTH] [--standard-characters] @@ -202,9 +202,9 @@ slynx filter-columns --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx filter-columns (-a|--alphabet NAME) INPUT-FILE [--standard-chars DOUBLE] @@ -226,9 +226,9 @@ slynx simulate --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx simulate (-t|--tree-file Name) [-s|--substitution-model MODEL] [-m|--mixture-model MODEL] [-e|--edm-file NAME] @@ -305,9 +305,9 @@ slynx sub-sample --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx sub-sample (-a|--alphabet NAME) INPUT-FILE (-n|--number-of-sites INT) @@ -335,9 +335,9 @@ slynx translate --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: slynx translate (-a|--alphabet NAME) INPUT-FILE (-r|--reading-frame INT) (-u|--universal-code CODE) @@ -360,9 +360,9 @@ tlynx --help | head -n -16 - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: tlynx [-v|--verbosity VALUE] [-o|--output-file-basename NAME] [-f|--force] COMMAND @@ -379,13 +379,12 @@ 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). + simulate Simulate phylogenetic trees using a birth and death or coalescent process. Available tree file formats: @@ -399,9 +398,9 @@ tlynx compare --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: tlynx compare [-n|--normalize] [-b|--bipartitions] [-t|--intersect] [-f|--newick-format FORMAT] NAMES @@ -428,9 +427,9 @@ tlynx examine --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: tlynx examine INPUT-FILE [-f|--newick-format FORMAT] Compute summary statistics of phylogenetic trees. @@ -452,37 +451,35 @@ tlynx simulate --help - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, 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). + 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 (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 + -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 - 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 + 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 @@ -491,9 +488,9 @@ elynx --help | head -n -16 - ELynx Suite version 0.3.3. + ELynx Suite version 0.3.4. Developed by Dominik Schrempf. - Compiled on August 18, 2020, at 08:07 am, UTC. + Compiled on August 21, 2020, at 09:40 am, UTC. Usage: elynx COMMAND Validate and redo past ELynx analyses diff --git a/elynx-seq.cabal b/elynx-seq.cabal --- a/elynx-seq.cabal +++ b/elynx-seq.cabal @@ -1,6 +1,6 @@ cabal-version: 2.2 name: elynx-seq -version: 0.3.3 +version: 0.3.4 synopsis: Handle molecular sequences description: Examine, modify, and simulate molecular sequences in a reproducible way. Please see the README on GitHub at . category: Bioinformatics @@ -45,6 +45,7 @@ ELynx.Data.Character.NucleotideX ELynx.Data.Sequence.Alignment ELynx.Data.Sequence.Defaults + ELynx.Data.Sequence.Distance ELynx.Data.Sequence.Sequence ELynx.Data.Sequence.Translate ELynx.Export.Sequence.Fasta diff --git a/src/ELynx/Data/Sequence/Alignment.hs b/src/ELynx/Data/Sequence/Alignment.hs --- a/src/ELynx/Data/Sequence/Alignment.hs +++ b/src/ELynx/Data/Sequence/Alignment.hs @@ -24,6 +24,8 @@ join, concat, concatAlignments, + filterColsConstant, + filterColsConstantSoft, filterColsOnlyStd, filterColsStd, filterColsNoGaps, @@ -203,6 +205,20 @@ filterColsWith p a = a {matrix = m'} where m' = M.fromColumns . filter p . M.toColumns $ matrix a + +-- | Only keep constant columns. +filterColsConstant :: Alignment -> Alignment +filterColsConstant = filterColsWith (\v -> V.all (== V.head v) v) + +-- | Only keep constant columns, and constant columns with at least one standard +-- character as well as any number of gaps or unknowns. +filterColsConstantSoft :: Alignment -> Alignment +filterColsConstantSoft a = filterColsWith f a + where + al = alphabet a + f v = case V.find (A.isStd al) v of + Nothing -> False + Just c -> V.all (\x -> x == c || (A.isGap al) x || (A.isUnknown al) x) v -- | Only keep columns with standard characters. Alignment columns with IUPAC -- characters are removed. diff --git a/src/ELynx/Data/Sequence/Distance.hs b/src/ELynx/Data/Sequence/Distance.hs new file mode 100644 --- /dev/null +++ b/src/ELynx/Data/Sequence/Distance.hs @@ -0,0 +1,33 @@ +-- | +-- Module : ELynx.Data.Sequence.Distance +-- Description : Distance functions between sequences +-- Copyright : (c) Dominik Schrempf, 2020 +-- License : GPL-3.0-or-later +-- +-- Maintainer : dominik.schrempf@gmail.com +-- Stability : unstable +-- Portability : portable +-- +-- Creation date: Fri Aug 21 15:09:58 2020. +module ELynx.Data.Sequence.Distance + ( hamming, + ) +where + +import qualified Data.Vector.Unboxed as V +import ELynx.Data.Sequence.Sequence + +countFalses :: (Int -> Bool -> Int) +countFalses n False = succ n +countFalses n True = n + +-- | Compute hamming distance between two sequences. +hamming :: Sequence -> Sequence -> Either String Int +hamming l r + | alphabet l /= alphabet r = Left "hamming: Alphabets of sequences differ." + | V.length csL /= V.length csR = Left "hamming: Sequence lengths differ." + | V.null csL || V.null csR = Left "hamming: Empty sequence encountered." + | otherwise = Right $ V.foldl' countFalses 0 $ V.zipWith (==) (characters l) (characters r) + where + csL = characters l + csR = characters r