Additional file 4 of New molecular diagnostic and surveillance tools for orthotospoviruses and their thrips vectors

Additional file 4: This compressed file (.7z) contains a folder ‘codes’. Python codes showing the programmatic processes of primer design are documented in Jupyter Notebook files (.ipynb) in the folder along with other files (e.g., custom Python functions and sequence files) required for running the codes. The codes relevant to the design of orthtospoviral RdRp primers are in ‘RdRp.ipynb’, those of EF1α primers in ‘EF1a.ipynb’, and those of COX1 primers in ‘COX1.ipynb’. The view-only version of these scripts are files with the same names but have the extension ‘.html’ instead of ‘.ipynb’, and those files can be directly viewed with a web browser. The Conda environment setup used for running the Python scripts is stored in ‘environment.yml’. The files ‘custom_functions.py’ and ‘custom_functions2.py’ contain custom-defined functions required to run the scripts. The FASTA files (.fasta) are sequence or sequence alignment data used as input for the computational analyses. Software, such as Anaconda (installation instructions can be found here: https://docs.anaconda.com/anaconda/install/ ), is required to set up the Conda environment. Instructions on setting up the environment with the supplied .yml file can be found in the following link: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#creating-an-environment-from-an-environment-yml-file . After the environment is set up and activated, Jupyter Notebook can be started by typing ‘jupyter lab’, which will open a browser window that allows the user to navigate to the .ipynb files and execute the Python scripts.