Rebuild for Julia 1.0, 1.1, and 1.2

get loglikelihood calculation running

forgot to save on code re-locate causing function overwriting

Manifest

Sequence generation for a defined phylogenetic tree

update manifest

custom travis script

Nice registry functionality limited to >v1.1.0

remove Manifest?

remove Manifest?

update .gitignore - Manifest removed for dependency version flexibility needed for Julia-1.0 support

README update

.gitignore

@@ -3,3 +3,5 @@
 *.jl.mem
 .ipynb_checkpoints
 testfile.jl
+.DS_Store
+Manifest.toml

.travis.yml

@@ -4,11 +4,23 @@ os:
   - linux
   - osx
 julia:
-  - 0.5
+  - 1.0
+  - 1.1
+  - 1.2
   - nightly
 notifications:
-  email: false
+  email: true
 matrix:
   allow_failures:
     - julia: nightly
   fast_finish: true
+script:
+    - julia -e 'using Pkg;
+                if VERSION >= v"1.1.0";
+                  Registry.add(Registry.RegistrySpec(url = "https://github.com/JuliaRegistries/General.git"));
+                  Registry.add(Registry.RegistrySpec(url = "https://github.com/BioJulia/BioJuliaRegistry.git"));
+                  Pkg.build(verbose = true);
+                else;
+                  Pkg.build();
+                end;
+                Pkg.test(coverage=true)'

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 Justin Angevaare
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Project.toml

@@ -0,0 +1,19 @@
+name = "PhyloModels"
+uuid = "6465ae08-de3a-5dbe-bda8-3920f6a01ab7"
+authors = ["Justin Angevaare <[email protected]>"]
+version = "0.3.0"
+
+[deps]
+GeneticBitArrays = "5d6f8c34-7f74-4dab-a49b-48b3414fbfce"
+PhyloTrees = "4c47b132-0681-5a5d-b498-3afcf53fd314"
+SubstitutionModels = "8365b1bb-bd83-58ee-a267-f2965fc81c73"
+
+[compat]
+GeneticBitArrays = "≥ 0.2.1"
+julia = "≥ 1.0.0"
+
+[extras]
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["Test"]

README.md

@@ -1,47 +1,23 @@
 # PhyloModels.jl
-
+[![Latest Release](https://img.shields.io/github/release/jangevaare/PhyloModels.jl.svg)](https://github.com/jangevaare/PhyloModels.jl/releases/latest)
+[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/jangevaare/PhyloModels.jl/blob/master/LICENSE)
 [![Build Status](https://travis-ci.org/jangevaare/PhyloModels.jl.svg?branch=master)](https://travis-ci.org/jangevaare/PhyloModels.jl)
 
-PhyloModels.jl is a package for performing phylogenetic simulation and inference in Julia. This package is no longer being developed or maintained in favour of [BioJulia/SubstitutionModels.jl](https://github.com/BioJulia/SubstitutionModels.jl) and related bioinformatics packages in the [BioJulia](https://github.com/BioJulia) Ecosystem.
-
-
-### Simulation
-Genetic sequences can be simulated from phylogenetic trees by defining a root sequence, site rates, and a nucleotide substitution model. The following nucleotide substitution models are currently available: `JC69`, `K80`, `F81`, `F84`, `HKY85`, `TN93`, and `GTR`.
-
-
-### Inference
-The log likelihood of phylogenetic trees can be calculated when genetic sequences have been observed at all leaves, and a nucleotide substitution model has been specified by using the `loglikelihood` function. Below is an example from *Molecular Evolution: A Statistical Approach*
+PhyloModels.jl is a package for performing genetic sequence simulation from specified phylogenetic trees (using [PhyloTrees.jl](https://github.com/jangevaare/PhyloTrees.jl) for phylogenetic tree specification, and [SubstitutionModels.jl](https://github.com/BioJulia/SubstitutionModels.jl) for nucleic acid substitution model specification), and for loglikelihood calculation of phylogenetic trees using Felsenstein's tree pruning algorithm¹.
 
-    > using PhyloTrees, PhyloModels
-    >
-    > # Build tree
-    > tree = Tree()
-    > addnodes!(tree, 9)
-    > addbranch!(tree, 9, 6, 0.1)
-    > addbranch!(tree, 9, 8, 0.1)
-    > addbranch!(tree, 6, 7, 0.1)
-    > addbranch!(tree, 6, 3, 0.2)
-    > addbranch!(tree, 7, 1, 0.2)
-    > addbranch!(tree, 7, 2, 0.2)
-    > addbranch!(tree, 8, 4, 0.2)
-    > addbranch!(tree, 8, 5, 0.2)
+¹ Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. *Journal of molecular evolution, 17*(6), 368-376.
 
-    Phylogenetic tree with 9 nodes and 8 branches
+## Installation
 
-    > # Set state of leaf nodes
-    > node_data = Dict{Int64, Sequence}()
-    > node_data[1] = Sequence("T")
-    > node_data[2] = Sequence("C")
-    > node_data[3] = Sequence("A")
-    > node_data[4] = Sequence("C")
-    > node_data[5] = Sequence("C")
-    >
-    > # Parametrize substitution model
-    > model = K80([2.])
+Julia 1.0.x, 1.1.x, and 1.2.x are currently supported. The current release can be installed
+from the Julia REPL:
 
-    Kimura 1980 substitution model
+```julia
+pkg> add PhyloModels
+```
 
-    > # Calculate log likelihood
-    > loglikelihood(tree, model, node_data)
+The development version (master branch) can be installed as:
 
-    -7.5814075725577
+```julia
+pkg> add PhyloModels#master
+```

src/PhyloModels.jl

@@ -1,67 +1,31 @@
-__precompile__()
-
 module PhyloModels
 
-# Dependencies
-using
-  PhyloTrees,
-  Distributions
+  using PhyloTrees,
+        SubstitutionModels,
+        GeneticBitArrays
+
+  import SubstitutionModels._π
+  import Base.rand
 
-# Methods expanded
-import
-  Base.show,
-  Base.push!,
-  Base.append!,
-  Base.length,
-  Base.getindex,
-  Base.rand,
-  Base.copy,
-  Base.deleteat!,
-  StatsBase.loglikelihood
+  # Re-export all of PhyloTrees, SubstitutionModels, and GeneticBitArrays
+  for name in names(PhyloTrees)
+    @eval export $(name)
+  end
 
-export
-  # Sequences
-  Sequence,
+  for name in names(SubstitutionModels)
+    @eval export $(name)
+  end
 
-  # Substitution Models
-  SubstitutionModel,
-  SubstitutionModelPrior,
-  JC69,
-  K80,
-  F81,
-  F84,
-  HKY85,
-  TN93,
-  GTR,
-  JC69Prior,
-  K80Prior,
-  F81Prior,
-  F84Prior,
-  HKY85Prior,
-  TN93Prior,
-  GTRPrior,
-  Q,
-  P,
-  logprior,
+  for name in names(GeneticBitArrays)
+    @eval export $(name)
+  end
 
-  # Simulation
-  simulate,
-  simulate!,
+  const NodeDNA = Dict{Int64, DNASeq}
+  const NodeRNA = Dict{Int64, RNASeq}
 
-  # Loglikelihoods
-  loglikelihood
+  include("loglikelihood.jl")
+  include("simulate.jl")
 
-  # Package files
-  include("sequences.jl")
-  include("substitution_models/abstract.jl")
-  include("substitution_models/jc69.jl")
-  include("substitution_models/k80.jl")
-  include("substitution_models/f81.jl")
-  include("substitution_models/f84.jl")
-  include("substitution_models/hky85.jl")
-  include("substitution_models/tn93.jl")
-  include("substitution_models/gtr.jl")
-  include("simulation.jl")
-  include("loglikelihoods.jl")
+  export NodeDNA, NodeRNA, siimulate!, simulate, rand, loglikelihood
 
 end # module

src/loglikelihoods.jl → src/loglikelihood.jl

@@ -1,15 +1,7 @@
-"""
-loglikelihood(tree::Tree,
-              mod::SubstitutionModel,
-              node_data::Dict{Int64, Sequence},
-              output_calculations::Bool=false)
-
-Calculates the log likelihood of a tree with sequences observed at all leaves
-"""
 function loglikelihood(tree::Tree,
-                       mod::SubstitutionModel,
-                       node_data::Dict{Int64, Sequence},
-                       output_calculations::Bool=false)
+                       mod::T,
+                       node_data::N;
+                       output_calculations::Bool=false) where {T <: NASM, N <: Union{NodeDNA, NodeRNA}}
   # Error checking
   if !all(map(x -> x in keys(node_data), findleaves(tree)))
     error("Some leaves are missing sequence data")
@@ -19,11 +11,12 @@ function loglikelihood(tree::Tree,
 
   # Create a Dict to store likelihood calculations
   calculations = Dict{Int64, Array{Float64, 2}}()
+
   # Find node visit order for postorder traversal
   visit_order = postorder(tree)
   for i in visit_order
     if isleaf(tree, i)
-      calculations[i] = node_data[i].nucleotides
+      calculations[i] = node_data[i].data
     else
       branches = tree.nodes[i].out
       for j in branches
@@ -39,8 +32,8 @@ function loglikelihood(tree::Tree,
     end
   end
   if output_calculations
-    return sum(log.(mod.π' * calculations[visit_order[end]])), calculations, visit_order
+    return sum(log.(_π(mod)' * calculations[visit_order[end]])), calculations, visit_order
   else
-    return sum(log.(mod.π' * calculations[visit_order[end]]))
+    return sum(log.(_π(mod)' * calculations[visit_order[end]]))
   end
 end