elynx-tree 0.3.3 → 0.3.4

raw patch · 7 files changed

+178/−116 lines, 7 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +8/−0
• README.md +45/−48
• elynx-tree.cabal +2/−1
• src/ELynx/Data/Tree/Measurable.hs +4/−6
• src/ELynx/Data/Tree/Phylogeny.hs +67/−56
• src/ELynx/Data/Tree/Supported.hs +10/−5
• test/ELynx/Data/Tree/SupportedSpec.hs +42/−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-tree-version:        0.3.3+version:        0.3.4 synopsis:       Handle phylogenetic trees description:    Examine, compare, and simulate phylogenetic trees in a reproducible way. Please see the README on GitHub at <https://github.com/dschrempf/elynx>. category:       Bioinformatics@@ -101,6 +101,7 @@       ELynx.Data.Tree.PartitionSpec       ELynx.Data.Tree.PhylogenySpec       ELynx.Data.Tree.RootedSpec+      ELynx.Data.Tree.SupportedSpec       ELynx.Export.Tree.NewickSpec       ELynx.Export.Tree.NexusSpec       ELynx.Import.Tree.NewickSpec

@@ -9,6 +9,10 @@ -- Portability :  portable -- -- Creation date: Thu Jan 17 14:16:34 2019.+--+-- Non-negativity of branch lengths is not (yet) ensured. To ensure+-- non-negativity, a newtype wrapper could be used, but this would be a major+-- refactor. module ELynx.Data.Tree.Measurable   ( BranchLength,     Measurable (..),@@ -73,12 +77,6 @@ rootHeight :: Measurable e => Tree e a -> BranchLength rootHeight (Node _ _ []) = 0 rootHeight t = maximum $ concatMap distancesOriginLeaves (forest t)---- -- | The maximum distance between root and leaves.--- ----- -- Does not include the length of the stem, see 'height'.--- rootHeight :: Measurable e => Tree e a -> BranchLength--- rootHeight t = subtract (getStem t) $ height t  -- | Distances from the origin of a tree to the leaves. --

@@ -31,12 +31,13 @@ -- Note: 'Tree's encoded in Newick format correspond to rooted trees. By -- convention only, a tree parsed from Newick format is usually thought to be -- unrooted, when the root node is multifurcating and has three children. This--- convention is not enforced here. Newick trees are just parsed as they are,--- and a rooted tree is returned.+-- convention is not used here. Newick trees are just parsed as they are, and a+-- rooted tree is returned. ----- The bifurcating root of a tree can be changed with 'roots', or 'rootAt'.+-- The bifurcating root of a tree can be changed with 'rootAt' or 'midpoint'; a+-- list of all rooted trees is returned by 'roots'. ----- Trees with multifurcating root nodes can be properly rooted using 'outgroup'.+-- Trees with multifurcating root nodes can be rooted using 'outgroup'. module ELynx.Data.Tree.Phylogeny   ( -- * Functions     equal,@@ -49,15 +50,16 @@      -- * Branch labels     Phylo (..),+    toPhyloTree,+    measurableToPhyloTree,+    supportedToPhyloTree,     Length (..),     phyloToLengthTree,-    lengthToPhyloTree,     Support (..),     phyloToSupportTree,     phyloToSupportTreeUnsafe,-    PhyloStrict (..),-    toStrictTree,-    fromStrictTree,+    PhyloExplicit (..),+    toExplicitTree,   ) where @@ -122,20 +124,22 @@ bifurcating (Node _ _ [x, y]) = bifurcating x && bifurcating y bifurcating _ = False --- TODO. Adapt for trees with branches.+-- I believe that manual treatment with 'outgroup' is preferable.+ -- -- | Remove multifurcations. -- ----- -- A caterpillar like bifurcating tree is used to resolve all multifurcations on--- -- a tree. The multifurcating nodes are copied.+-- -- A caterpillar like bifurcating structure is used to resolve all+-- -- multifurcations on a tree. -- ----- -- Branch labels are not handled.--- resolve :: Tree e a -> Tree e a+-- -- Multifurcating nodes are copied and branches are 'split'.+-- resolve :: Splittable e => Tree e a -> Tree e a -- resolve t@(Node _ _ []) = t--- resolve (Node _ l [x]) = Node () l [resolve x]--- resolve (Node _ l [x, y]) = Node () l $ map resolve [x, y]--- resolve (Node _ l (x : xs)) = Node () l $ map resolve [x, Node () l xs]+-- resolve (Node br lb [x]) = Node br lb [resolve x]+-- resolve (Node br lb [x, y]) = Node br lb $ map resolve [x, y]+-- resolve (Node br lb (Node brL lbL xsL : xs)) = Node br lb [Node brL' lbL (map resolve xsL), Node brL' lb (map resolve xs)]+--   where brL' = split brL --- | Resolve a multifurcation at the root using an outgroup.+-- | Resolve a multifurcating root using an outgroup. -- -- A bifurcating root node with the provided label is introduced. The affected -- branch is 'split'.@@ -163,11 +167,11 @@     -- Introduce a bifurcating root node.     t' = Node b r [Node (split brO) lbO tsO, Node (split brO) l (tail ts)] --- XXX: The 'midpoint' algorithm is pretty stupid because it calculates all--- rooted trees and then finds the one minimizing the difference between the--- heights of the left and right sub tree. Actually, one just needs to move left--- or right, with the aim to minimize the height difference between the left and--- right sub tree.+-- The 'midpoint' algorithm is pretty stupid because it calculates all rooted+-- trees and then finds the one minimizing the difference between the heights of+-- the left and right sub tree. Actually, one just needs to move left or right,+-- with the aim to minimize the height difference between the left and right sub+-- tree.  -- | Root tree at the midpoint. --@@ -323,6 +327,33 @@  instance FromJSON Phylo +-- | Set all branch length and support values to 'Just' the value.+--+-- Useful to export a tree with branch lengths in Newick format.+toPhyloTree :: (Measurable e, Supported e) => Tree e a -> Tree Phylo a+toPhyloTree = first toPhyloLabel++toPhyloLabel :: (Measurable e, Supported e) => e -> Phylo+toPhyloLabel x = Phylo (Just $ getLen x) (Just $ getSup x)++-- | Set all branch support values to 'Nothing'.+--+-- Useful to export a tree with branch lengths to Newick format.+measurableToPhyloTree :: Measurable e => Tree e a -> Tree Phylo a+measurableToPhyloTree = first measurableToPhyloLabel++measurableToPhyloLabel :: Measurable e => e -> Phylo+measurableToPhyloLabel x = Phylo (Just $ getLen x) Nothing++-- | Set all branch lengths to 'Nothing'.+--+-- Useful to export a tree with branch support to Newick format.+supportedToPhyloTree :: Supported e => Tree e a -> Tree Phylo a+supportedToPhyloTree = first supportedToPhyloLabel++supportedToPhyloLabel :: Supported e => e -> Phylo+supportedToPhyloLabel x = Phylo Nothing (Just $ getSup x)+ -- | Branch length label. -- -- For conversion, see 'phyloToLengthTree' and 'lengthToPhyloTree'.@@ -358,15 +389,6 @@ toLength :: Phylo -> Maybe Length toLength p = Length <$> brLen p --- | Set all branch support values to 'Nothing'.------ Useful, for example, to export a tree with branch lengths in Newick format.-lengthToPhyloTree :: Tree Length a -> Tree Phylo a-lengthToPhyloTree = first fromLengthLabel--fromLengthLabel :: Length -> Phylo-fromLengthLabel (Length b) = Phylo (Just b) Nothing- -- | Branch support label. -- -- For conversion, see 'phyloToSupportTree'.@@ -426,51 +448,40 @@ cleanSupport :: BranchSupport -> Tree Phylo a -> Tree Support a cleanSupport maxSup (Node (Phylo _ s) l xs) = Node (Support $ fromMaybe maxSup s) l $ map (cleanSupport maxSup) xs --- XXX: Probably change name. Strict is reserved for "not lazy".---- | Strict branch label for phylogenetic trees.-data PhyloStrict = PhyloStrict+-- | Explicit branch label for phylogenetic trees.+data PhyloExplicit = PhyloExplicit   { sBrLen :: BranchLength,     sBrSup :: BranchSupport   }   deriving (Read, Show, Eq, Ord, Generic) -instance Semigroup PhyloStrict where-  PhyloStrict bL sL <> PhyloStrict bR sR = PhyloStrict (bL + bR) (min sL sR)+instance Semigroup PhyloExplicit where+  PhyloExplicit bL sL <> PhyloExplicit bR sR = PhyloExplicit (bL + bR) (min sL sR) -instance Measurable PhyloStrict where+instance Measurable PhyloExplicit where   getLen = sBrLen   setLen b l = l {sBrLen = b} -instance Splittable PhyloStrict where+instance Splittable PhyloExplicit where   split l = l {sBrLen = b'}     where       b' = sBrLen l / 2.0 -instance Supported PhyloStrict where+instance Supported PhyloExplicit where   getSup = sBrSup   setSup s l = l {sBrSup = s} -instance ToJSON PhyloStrict+instance ToJSON PhyloExplicit -instance FromJSON PhyloStrict+instance FromJSON PhyloExplicit --- | Conversion to a 'PhyloStrict' tree.+-- | Conversion to a 'PhyloExplicit' tree. -- -- See 'phyloToLengthTree' and 'phyloToSupportTree'.-toStrictTree :: Tree Phylo a -> Either String (Tree PhyloStrict a)-toStrictTree t = do+toExplicitTree :: Tree Phylo a -> Either String (Tree PhyloExplicit a)+toExplicitTree t = do   lt <- first fromLength <$> phyloToLengthTree t   st <- first fromSupport <$> phyloToSupportTree t-  case zipTreesWith PhyloStrict const lt st of-    Nothing -> error "toStrictTree: This is a bug. Can not zip two trees with the same topology."+  case zipTreesWith PhyloExplicit const lt st of+    Nothing -> error "toExplicitTree: This is a bug. Can not zip two trees with the same topology."     Just zt -> return zt---- | Set all branch length and support values to 'Just' the value.------ Useful, for example, to export a tree with branch lengths in Newick format.-fromStrictTree :: Tree PhyloStrict a -> Tree Phylo a-fromStrictTree = first fromStrictLabel--fromStrictLabel :: PhyloStrict -> Phylo-fromStrictLabel (PhyloStrict b s) = Phylo (Just b) (Just s)

@@ -9,6 +9,10 @@ -- Portability :  portable -- -- Creation date: Thu Jun 13 14:06:45 2019.+--+-- Non-negativity of branch support values is not (yet) ensured. To ensure+-- non-negativity, a newtype wrapper could be used, but this would be a major+-- refactor. module ELynx.Data.Tree.Supported   ( BranchSupport,     Supported (..),@@ -41,9 +45,6 @@   where     m = bimaximum $ bimap getSup (const 0) t --- TODO: Something was wrong here. @collapse 1.0 t@ should be a star tree but it--- was a leaf. Is this still so?- -- | Collapse branches with support lower than given value. -- -- The branch and node labels of the collapsed branches are discarded.@@ -52,10 +53,14 @@   let tr' = collapse' th tr    in if tr == tr' then tr else collapse th tr' +-- A leaf has full support.+highP :: Supported e => Double -> Tree e a -> Bool+highP _  (Node _ _ []) = True+highP th (Node br _ _) = getSup br >= th+ -- See 'collapse'. collapse' :: Supported e => BranchSupport -> Tree e a -> Tree e a-collapse' _ t@(Node _ _ []) = t collapse' th (Node br lb ts) = Node br lb $ map (collapse' th) (highSupport ++ lowSupportForest)   where-    (highSupport, lowSupport) = partition ((>= th) . getSup . branch) ts+    (highSupport, lowSupport) = partition (highP th) ts     lowSupportForest = concatMap forest lowSupport

@@ -0,0 +1,42 @@+{-# LANGUAGE OverloadedStrings #-}++-- |+-- Module      :  ELynx.Data.Tree.SupportedSpec+-- Description :  Unit tests for ELynx.Data.Tree.SupportedSpec+-- 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 14:20:09 2020.+module ELynx.Data.Tree.SupportedSpec+  ( spec,+  )+where++import qualified Data.ByteString.Char8 as BS+import ELynx.Data.Tree+import ELynx.Import.Tree.Newick+-- import ELynx.Export.Tree.Newick+import ELynx.Tools+import Test.Hspec++collapseTree :: Tree Phylo BS.ByteString+collapseTree = parseByteStringWith (oneNewick IqTree) "((a,b),(c,d));"++collapseStarTree :: Tree Phylo BS.ByteString+collapseStarTree = parseByteStringWith (oneNewick Standard) "(a[1.0],b[1.0],c[1.0],d[1.0])[1.0];"++spec :: Spec+spec = do+  describe "collapse" $ do+    it "creates a star tree for 1.0" $ do+      let t = phyloToSupportTreeUnsafe collapseTree+          s = phyloToSupportTreeUnsafe collapseStarTree+      collapse 0 t `shouldBe` t+      collapse 0.01 t `shouldBe` t+      collapse 0.99 t `shouldBe` t+      collapse 1.0 t `shouldBe` t+      collapse 1.1 t `shouldBe` s