helminth selection

Scripts for exploring selection on helminths in multiple populations. Specifically in regards to Redman 2015 in PLoS NTDs an H. contortus.

fasta2pylibset.py

• Script accepts a fasta file and parses it for stats using pylibseq modules

helminth_figs1AB.py

• Main script for creating figures 1A and 1B in the manuscript. You will have to change the path to msms in the code.

fixplotHelminth1B.py

• A mistake in how I was coding resistant haplotypes. This script should be run on the output csv of helminth_figs1AB.py

ms2stats.py

• Script accepts a ms-formatted file and parses it for use with pylibseq modules

permuteFst.py

• Simple script that takes as input a ms-formatted file and outputs FST calculations as well as p-values based on permutation test. I implemented this after some issues with the current version of msstats and FST calculation from stdin. Probably become deprecated when pylibset and pymsstats is updated.

helminth_models.txt

• Text version of some of the models.

helminthSelection.Rmd

• Markdown for plotting output data