EditURL = "doc/README.jl"
Translation of currocam's slim_wrap.py to Julia.
Workflow example with SlimWrap + PyCall
using SlimWrap
using PyCall
tskit = pyimport("tskit")
pyslim = pyimport("pyslim")
msprime = pyimport("msprime")PyObject <module 'msprime' from '/home/arzwa/.local/lib/python3.10/site-packages/msprime/__init__.py'>
Define and run the SLiM simulation
M = SLiMModel(templates.wf)
params = Dict(
"POPSIZE"=>100,
"CHRSIZE"=>1_000_000,
"RECRATE"=>1e-8,
"NGEN" =>1000,
"OUTFILE"=>tempname())
run(M, constants=params)Process(`slim -s 6563984953498643476 -l 2 -d "SLIM_WRAP_PARAMS = Dictionary(readFile('/tmp/jl_cJCHGD2DQv'))" -p -d "POPSIZE=SLIM_WRAP_PARAMS.getValue('POPSIZE');" -d "NGEN=SLIM_WRAP_PARAMS.getValue('NGEN');" -d "CHRSIZE=SLIM_WRAP_PARAMS.getValue('CHRSIZE');" -d "RECRATE=SLIM_WRAP_PARAMS.getValue('RECRATE');" -d "OUTFILE=SLIM_WRAP_PARAMS.getValue('OUTFILE');" /home/arzwa/dev/SlimWrap/src/templates/wf.slim`, ProcessExited(0))
Load and simplify the tree sequence
ts = tskit.load(params["OUTFILE"])
alive = pyslim.individuals_alive_at(ts, 0) .+ 1
sts = ts.simplify(
ts.individuals_nodes[alive],
keep_input_roots=true)
demography = msprime.Demography.from_tree_sequence(sts)
rts = pyslim.recapitate(
sts, random_seed=11,
demography=demography,
ploidy=2,
recombination_rate=params["RECRATE"]
);Simulate neutral mutations
mts = msprime.sim_mutations(
ts, random_seed=11,
rate=1e-8,
keep=false
);Get coalescence times
tmrca = mts.diversity(mts.samples(population=1),
mode="branch", windows=0:100_000:params["CHRSIZE"]) / 210-element Vector{Float64}:
202.50725526130654
204.2841005829146
190.5178457778894
167.17291633165817
175.7796540577888
220.64733668341697
220.88865190251246
221.7803015075376
221.3815927698492
223.83476951557773
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