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simulation-ratevariation's Issues

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Which versions of SiPhyNetwork and of ape are you using? (or which commit for SiPhyNetwork)?

When I tried to run your jupyter notebook, I couldn't use SiPhyNetwork, so I upgraded my version of R and RStudio... which led me to several hours trying to compile packages. I was finally able to re-install SiPhyNetwork. And now your jupyter notebook throws me an error, which traces back to R"write.net(net, tol=1e-12)" .

calcPatternCounts in calcD.jl MethodError

I'm trying the following example that we use in the docstrings and getting a MethodError:

> file = "scripts/examples/tinyexample.fasta"
> calcPatternCounts(file, ["P2","P5","P3","P1"])
MethodError: Cannot `convert` an object of type LongAA to an object of type String
Closest candidates are:
  convert(::Type{String}, ::String) at essentials.jl:210
  convert(::Type{String}, ::WeakRefStrings.WeakRefString) at /Users/laurenfrankel/.julia/packages/WeakRefStrings/AN9bY/src/WeakRefStrings.jl:81
  convert(::Type{String}, ::FilePathsBase.AbstractPath) at /Users/laurenfrankel/.julia/packages/FilePathsBase/qgXdE/src/path.jl:117
  ...

Stacktrace:
 [1] calcPatternCounts(file::String, taxa::Vector{String}, nsites_perlocus::Nothing; ambig::Symbol)
   @ Main ~/Desktop/Ane/simulation-ratevariation/scripts/calcD.jl:86
 [2] calcPatternCounts (repeats 2 times)
   @ ~/Desktop/Ane/simulation-ratevariation/scripts/calcD.jl:78 [inlined]
 [3] top-level scope
   @ In[2]:2
 [4] eval
   @ ./boot.jl:360 [inlined]
 [5] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
   @ Base ./loading.jl:1116

Seems to be an error in line 86 of calcD.jl: alg[i] = LongDNASeq(convert(String, alg[i])) while trying to Convert. Perhaps due to me upgrading packages in the last week?

I try with other fastas that I've simulated and it seems to work so I'm not sure what the deal is.

> calcPatternCounts("output/fourtaxa_sequence.fasta", ["t1", "t2", "t7", "t4"])
([1000], [28], [25], [25])

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