Scripts to analyse the dataset from Funk et al. 2022
These scripts are meant to be used with a sorted dataset like the one provided alongside the article. Data has to be sorted by subtype as well as splitting variable(s) (region and species in this case). The script will produce graphs taking only the terrestrial poultry and wild aquatic bird files into account.
The script provided to generate an interactive figure contains all the analyses performed in the article and was used to generate the interactive HTML figure S3. Two scripts are provided to generate static figures (PDF format): the tribasic site mutational analysis script and the adenine stretch mutational analysis script. The code for the analysis is identical to that used in the interactive figure script and to generate Figures 6, 7 and S3 of the article.
For all scripts the folder containing the data, i.e., the subfolders split by region and species, has to be provided. See the readmes in each folder. The scripts require the data to be organized in the same way as the dataset from the article, i.e.,
<data folder>
└── by_region-species
├── america-ans_cha
│ └── fasta files in 'america-ans_cha_hX_unique_CSregion.fasta' format
├── america-poultry
│ └── fasta files in 'america-poultry_hX_unique_CSregion.fasta' format
├── eurasia-ans_cha
│ └── fasta files in 'eurasia-ans_cha_hX_unique_CSregion.fasta' format
└── eurasia-poultry
└── fasta files in 'eurasia-poultry_hX_unique_CSregion.fasta' format