This repository contains datasets and code which were used to generate the results reported in the main manuscript. To use the code, you may need to update the paths located in each file. If there are issues or you need help using the code, please contact Joe Rudar at [email protected].
SCoV2_Table_1_2_Supp1_10.py - This file runs the generalization performance analysis and will produce data for Tables 1 and 2, and Supplementary Tables 1 to 10.
SCoV2_Selection_All_Features.py - This file will return a metadata file and a file of amino acid, SNP, and structural variants for each sample. The output of this file is used later to generate figures and analyze the FUBAR/Triglav data.
SCoV2_Triglav.py - This file will run the Triglav analysis and return a CSV file containing data on which features were selected across all Triglav runs.
SCoV2 Triglav Stats Subset.py - This file will run the analysis which looks at how well Triglav performed w.r.t the rejected features and generate data to produce Figures 1 to 5.
SCoV2_TreeOrdination.py - This file runs the TreeOrdination/NN Search and will generate data to produce Figure 8.
R_Clustermap.txt - This file contains and example of the R code used to generate Figures 1, 2, 3, 6, and 8.
Tanglegram_by_clade/host.Rmd - This file contains the code used to generate Figure 7a and 7b. The trees used are found in the "Selection Analysis" directory.
Deer_GISAID - This directory contains the raw data used for this analysis (sequences, GFF file, etc.).
Final_Results - This directory is used to store the output files. Currently, it only contains data which was used to generate the results reported in the manuscript.
Selection_Results - This directory contains the data and trees used to generate Figures 6 and 7.