elynx-seq 0.3.3 → 0.3.4

raw patch · 5 files changed

+104/−49 lines, 5 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• ChangeLog.md +8/−0
• README.md +45/−48
• elynx-seq.cabal +2/−1
• src/ELynx/Data/Sequence/Alignment.hs +16/−0
• src/ELynx/Data/Sequence/Distance.hs +33/−0

@@ -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.

@@ -2,7 +2,7 @@  # The ELynx Suite -Version: 0.3.3.+Version: 0.3.4. Reproducible evolution made easy.  <p align="center"><img src="https://travis-ci.org/dschrempf/elynx.svg?branch=master"/></p>@@ -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

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

@@ -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.

@@ -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