A repo containing the scripts to perform the convergence analysis on GEA results. What you need is a set of WZA results. These files are assumed to be in
The first to do is to add the orthogroup info to each file. I do that using the bin/annotateWZAfiles.py script. This is a vitally important step.
This script can be used like this, for example:
python ../bin/annotateWZAfiles.py --anno Orthogroups.tsv --wza JP_all_wza_tc.txt --species Pi --output JP_all_wza_tc_OG.txt
Where, Orthogroups.tsv - is the output from Orthofinder; JP_all_wza_tc.txt - is the WZA output file; Pi - is the species-code for the pine pan-genome; P_all_wza_tc_OG.txt - is the name of the output script
Once you've run that, you'll have a set of files with both the Zw scores from the WZA as well as orthogroup information for each species. We'll put that into the script analysing convergent evolution.
The script bin/convergenceAnalysis.py implements both multi-species tests for convergent evolution as well as pairwise tests. You'll have to take care which species you are providing to the program.
The script has help info accessed via python bin/convergenceAnalysis.py --help if you want to take a look at the list of arguments it takes.
Here's an example of how you might use the convergence script:
python bin/convergenceAnalysis.py -i species_1.ENV.csv species_2.ENV.csv species_3.ENV.csv species_4.ENV.csv -o ENV.convergence --alpha_1 0.01 --alpha_2 0.05 -v --allPairs
That command will run the script on data for species 1, 2, 3, 4 using alpha_1 = 0.01 and alpha_2 = 0.05. The -v is for verbose mode, so the script will tell you what it's doing. --allPairs runs the analysis using the multi-species test as well as on all pair wie comparisons.