SNP_analysis

Code to compare total genetic diversity in Humans vs Wheat

A word of warning

Almost all sequencing data is collected in a different way. I used an Ipython notebook (Data_munging.ipynb) to lightly munge the data before feeding it into a more consistent pipeline.

Analyzing the data

entropy_calculators.py is a set of functions with unit test calculating average entropy for a species with a number of individuals and a number of SNPs. total_data_driver.py uses these functions to calculated the analysis for wheat and humans. The wheat and human data comes in large csv files which must be downloaded separately hereand here

Plotting

swarm_visulization.py makes the pretty swarm plots. Note that it uses an inverse entropy calculation to approximate what a population of individuals with a given entropy score would look like. Granted, a single entropy score has a degenerate number of possible populations that could produce it, so I just found one solution that would work.