simulateInMSPrime: Simulates a given msprime function in msprime
In JesseGarcia562/psmc2msprime:

Description Usage Arguments Value Examples

given a function that defines the simulation of a population in msprime, this funtion executes the function and returns the resulting msprime.trees.TreeSequence

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simulateInMSPrime(msprimeFunctionPath, mutationRate = 1.5e-08, phi = 2e-08,
  length = 10000, sampleHowManyHaploidGenomes = 2, debug = FALSE,
  seed = 30)

`msprimeFunctionPath`	The path to the python (.py) function that defines an msprime model.
`mutationRate`	The mutation rate in mutations/bp/gen. This is the same mutation rate that one would use to scale results to real time and population sizes. See https://github.com/stschiff/msmc/blob/master/guide.md for more help.
`phi`	The recombination rate in recombinations/bp/gen.
`length`	The total amount of sequence to simulate.
`debug`	If True this parameter evokes msprime's demography debugger.
`seed`	formsprime simulation.
`sampleHowManyHaploidGeneomes`	The number of haploid genomes in the output. For PSMC' you need 1 diploid indidividual. Therefore, you'd need to sample 2 haploid genomes. I don't know what happens when this number is not 2.

msprime.trees.TreeSequence

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readMSMCInference(pathOfMSMCOutFinal = "../data/msprimeMultiHetSep/simulatedMsprime.oak.msmc.out.final.txt", mutationRate = 1e-8)
simulation<-simulateInMSPrime(msprimeFunctionPath = "../code/msmc2msprime_Feb1.py")