Allow export of trees

[richardreeve]

Closes #84

• Function to write newick tree
• Function to write nexus trees
• Easy to write out
• Add testing
• Add docs

[richardreeve]

@KYQiu21 - please test the newick export if you like. Phylo.outputtree!() does the work, with the third argument being the file type, in this case Phylo.Newick(). I'll improve it, export the functionality and document it once I'm happy with it, but it seems to work at the moment - it would be helpful to have someone else look at it though! It's in this branch, so you can load it using pkg> add Phylo#rr/output. @mkborregaard, your input would obviously be v helpful too!

(Phylo) pkg> activate --temp
  Activating new project at `/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_5AJEJR`

(jl_5AJEJR) pkg> add Phylo#rr/output
     Cloning git-repo `https://github.com/EcoJulia/Phylo.jl.git`
    Updating git-repo `https://github.com/EcoJulia/Phylo.jl.git`
   Resolving package versions...
    Updating `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_5AJEJR/Project.toml`
  [aea672f4] + Phylo v0.5.0 `https://github.com/EcoJulia/Phylo.jl.git#rr/output`
    Updating `/private/var/folders/fv/1rqrvwq14ssggm_gc_x4v1cw0000gq/T/jl_5AJEJR/Manifest.toml`
[...]
  [3f19e933] + p7zip_jll v17.4.0+0
Precompiling project...
  ✓ Phylo
  1 dependency successfully precompiled in 4 seconds. 79 already precompiled.
julia> using Phylo

julia> tree = open(parsenewick, Phylo.path("H1N1.newick"))
RootedTree with 507 tips and 1 root. Leaf names are 227, 294, 295, 110, 390, ... [501 omitted] ... and 418

1013 nodes: [RecursiveNode{OneRoot} 'Node 1013', a root node with 2 outbound connections (branches [1011, 1012]), RecursiveNode{OneRoot} 'Node 1011', an internal node with 1 inbound and 2 outbound connections (branches 1011 and [1009, 1010]), RecursiveNode{OneRoot} 'Node 1009', an internal node with 1 inbound and 2 outbound connections (branches 1009 and [1007, 1008]), RecursiveNode{OneRoot} 'Node 1008', an internal node with 1 inbound and 2 outbound connections (branches 1007 and [1005, 1006]), RecursiveNode{OneRoot} 'Node 1004', an internal node with 1 inbound and 2 outbound connections (branches 1005 and [1001, 1002]) ... 1007 missing ... RecursiveNode{OneRoot} '418', a leaf with an incoming connection (branch 1012)]

1012 branches: [RecursiveBranch{OneRoot} 1, from node 'Node 5' to node '294' (length 0.2559376385188), RecursiveBranch{OneRoot} 2, from node 'Node 5' to node '295' (length 1.255937638519), RecursiveBranch{OneRoot} 3, from node 'Node 7' to node '227' (length 3.093983613629), RecursiveBranch{OneRoot} 4, from node 'Node 7' to node 'Node 5' (length 4.83804597511), RecursiveBranch{OneRoot} 5, from node 'Node 11' to node '104' (length 0.4902870119746) ... 1006 missing ... RecursiveBranch{OneRoot} 1012, from node 'Node 1013' to node '418' (length 13.87884773144)]

Node records: "Node 1013" => Dict{String, Any}("length" => 0.0, "height" => 84.94613266277547, "height/95%/HPD" => [75.00016004016078, 100.9885305644122], "height/median" => 82.87499084796832, "posterior" => 1.0, "height/range" => [75.00016004016078, 151.06404614035887]) ... "418" => Dict{String, Any}("length/range" => [0.000160040160921, 76.06404614036], "height/median" => 75.00000000000021, "rate" => 0.00287656620693594, "rate/95%/HPD" => [0.00032906282418212297, 0.00668807772865533], "rate/median" => 0.002350371083836891, "length/median" => 7.87499084797, "length" => 9.946132662775383, "height" => 74.99999999999999, "height/95%/HPD" => [74.99999999999359, 75.0000000000068], "length/95%/HPD" => [0.000160040160921, 25.98853056441]…)

julia> open("out.newick", "w") do io
       Phylo.outputtree!(io, tree, Phylo.Newick())
       end

ulia> t2 = open(parsenewick, "out.newick")
RootedTree with 507 tips and 1 root. Leaf names are 227, 294, 295, 110, 390, ... [501 omitted] ... and 418

1013 nodes: [RecursiveNode{OneRoot} 'Node 1013', a root node with 2 outbound connections (branches [1011, 1012]), RecursiveNode{OneRoot} 'Node 1011', an internal node with 1 inbound and 2 outbound connections (branches 1011 and [1009, 1010]), RecursiveNode{OneRoot} 'Node 1009', an internal node with 1 inbound and 2 outbound connections (branches 1009 and [1007, 1008]), RecursiveNode{OneRoot} 'Node 1008', an internal node with 1 inbound and 2 outbound connections (branches 1007 and [1005, 1006]), RecursiveNode{OneRoot} 'Node 1004', an internal node with 1 inbound and 2 outbound connections (branches 1005 and [1001, 1002]) ... 1007 missing ... RecursiveNode{OneRoot} '418', a leaf with an incoming connection (branch 1012)]

1012 branches: [RecursiveBranch{OneRoot} 1, from node 'Node 5' to node '294' (length 0.2559376385188), RecursiveBranch{OneRoot} 2, from node 'Node 5' to node '295' (length 1.255937638519), RecursiveBranch{OneRoot} 3, from node 'Node 7' to node '227' (length 3.093983613629), RecursiveBranch{OneRoot} 4, from node 'Node 7' to node 'Node 5' (length 4.83804597511), RecursiveBranch{OneRoot} 5, from node 'Node 18' to node '390' (length 0.2307062432264) ... 1006 missing ... RecursiveBranch{OneRoot} 1012, from node 'Node 1013' to node '418' (length 13.87884773144)]

Node records: "Node 1013" => Dict{String, Any}("length" => 0.0, "height" => 84.94613266277547, "height/95%/HPD" => [75.00016004016078, 100.9885305644122], "height/median" => 82.87499084796832, "posterior" => 1.0, "height/range" => [75.00016004016078, 151.06404614035887]) ... "418" => Dict{String, Any}("length/range" => [0.000160040160921, 76.06404614036], "height/median" => 75.00000000000021, "rate" => 0.00287656620693594, "rate/95%/HPD" => [0.00032906282418212297, 0.00668807772865533], "rate/median" => 0.002350371083836891, "length/median" => 7.87499084797, "length" => 9.946132662775383, "height" => 74.99999999999999, "height/95%/HPD" => [74.99999999999359, 75.0000000000068], "length/95%/HPD" => [0.000160040160921, 25.98853056441]…)

[mkborregaard]

Sorry for being slow here, I'm drowning in finalizing the year before christmas

[richardreeve]

No problem at all @mkborregaard. I've pretty much finished this now I think, and the docs are here:

https://docs.ecojulia.org/Phylo.jl/previews/PR88/man/io/

If you want to have a look / try it out. The format is just:

julia> using Phylo

julia> tree = open(parsenewick, Phylo.path("H1N1.newick"))
RootedTree with 507 tips and 1 root. Leaf names are 227, 294, 295, 110, 390, ... [501 omitted] ... and 418

1013 nodes: [RecursiveNode{OneRoot} 'Node 1013', a root node with 2 outbound connections (branches [1011, 1012]), RecursiveNode{OneRoot} 'Node 1011', an internal node with 1 inbound and 2 outbound connections (branches 1011 and [1009, 1010]), RecursiveNode{OneRoot} 'Node 1009', an internal node with 1 inbound and 2 outbound connections (branches 1009 and [1007, 1008]), RecursiveNode{OneRoot} 'Node 1008', an internal node with 1 inbound and 2 outbound connections (branches 1007 and [1005, 1006]), RecursiveNode{OneRoot} 'Node 1004', an internal node with 1 inbound and 2 outbound connections (branches 1005 and [1001, 1002]) ... 1007 missing ... RecursiveNode{OneRoot} '418', a leaf with an incoming connection (branch 1012)]

1012 branches: [RecursiveBranch{OneRoot} 1, from node 'Node 5' to node '294' (length 0.2559376385188), RecursiveBranch{OneRoot} 2, from node 'Node 5' to node '295' (length 1.255937638519), RecursiveBranch{OneRoot} 3, from node 'Node 7' to node '227' (length 3.093983613629), RecursiveBranch{OneRoot} 4, from node 'Node 7' to node 'Node 5' (length 4.83804597511), RecursiveBranch{OneRoot} 5, from node 'Node 11' to node '104' (length 0.4902870119746) ... 1006 missing ... RecursiveBranch{OneRoot} 1012, from node 'Node 1013' to node '418' (length 13.87884773144)]

Node records: "Node 1013" => Dict{String, Any}("length" => 0.0, "height" => 84.94613266277547, "height/95%/HPD" => [75.00016004016078, 100.9885305644122], "height/median" => 82.87499084796832, "posterior" => 1.0, "height/range" => [75.00016004016078, 151.06404614035887]) ... "418" => Dict{String, Any}("length/range" => [0.000160040160921, 76.06404614036], "height/median" => 75.00000000000021, "rate" => 0.00287656620693594, "rate/95%/HPD" => [0.00032906282418212297, 0.00668807772865533], "rate/median" => 0.002350371083836891, "length/median" => 7.87499084797, "length" => 9.946132662775383, "height" => 74.99999999999999, "height/95%/HPD" => [74.99999999999359, 75.0000000000068], "length/95%/HPD" => [0.000160040160921, 25.98853056441]…)


julia> Phylo.write("test.newick", tree)

Phylo.write() uses newick format by default for single trees and nexus by default for sets of trees, but you can choose to use nexus always by adding a keyword (format = Nexus()) argument. I don't really know if that's a good setup, but it seemed like a good idea at the time! I'll merge it later today if no-one has any comments...