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kr-colab / greatapes_sims

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ploidy being set as 1 #3

Closed mufernando closed 4 years ago

mufernando commented 4 years ago

see https://github.com/mufernando/greatapes_sims/commit/cc6c9cd0c24c53b42e70aade88612e38edf95e28

because we can have more than one subpopulation per tree sequence and we want to calculate some stats to each subpop individually, I need to subset my genotype matrix. it is possible to get the indices belonging to a population for each haploid genome using tskit with ts.samples(population=i), but not for diploid genomes. If I were to treat the genotype matrix with ploidy=2, I wouldn't be able to do the subsetting this way.

ploidy should not matter for the stats we are using so far (pi and dxy), but could be an issue with other stats.

petrelharp commented 4 years ago

Well, let's see:

ind_pops = np.array([i.population for i in ts.individuals()])

gives you the population for each individual - is that what you need?

mufernando commented 4 years ago

solved. see commit 380068157345bdd0e444ec81a85fd3de6a638708