jsanjak/grape_demog

Simulating and analyzing a theoretical wine grape demography

This project is setup to perform large scale population genetic simulations and perform time-series analysis of the data. A detailed description of the motivation and use of these simulations can be found in Zhou et al. 2017.

Clonal package

clonal is a pybind11 extension module for fwdpy11

clonal dependencies

• Python3
• pybind11
• fwdpy11
• pylibseq
• numpy

Install

In the main repo directory, you can run python3 setup.py install --user

Evolve script

In 'project/' you will see scripts names evolve_.py. These are set up to run simulations in parallel and dump results to 'project/data/'

Recorder class

The recroder class in project/RecordStats.py is a critical piece to this project. It collect's time series data during the simulations. I am currently collecting the following data

• Generation time
• Population size
• Relative load = one minus the mean fitness divided the maximum fitness in the population
• Segregating load = one minus the mean fitness divided the maximum theoretical fitness
• Fixed load = load due to fixations, not considered in other loads
• Number of fixed mutations - neutral and deleterious separately
• Mean number of deleterious mutatiosn per individual
• Sum of derived allele frequencies - neutral and deleterious separately
• Tajima's D at neutral sites
• Tajima's D at all sites
• Heterozygosity (pi) at neutral sites
• Heterozygosity (pi) at all sites
• Fay and Wu's Hprime at neutral sites
• Fay and Wu's Hprime at all sites

Examples

Please see 'project/Example' for shorter example jupyter notebooks or just take a look at any of the notebooks in the main project directory.