ericmjl / influenza-global-reassortment

Jupyter notebooks and data - reproducible analysis from reassortment paper

influenza-global-reassortment

Jupyter notebooks and data - reproducible analysis from reassortment paper.

To re-run these analyses, run the code in the following notebooks:

• Make Figure - Known Transmission Patterns.ipynb
• Make Figure - Proportion Reassortant.ipynb
• Make Figure - PWI Histogram.ipynb
• Make Supplementary Data - Edge List and Node List.ipynb

For a tutorial on how to run Jupyter notebooks, see the Jupyter project website.

Software requirements:

• Python 3.4 (minimum)
• networkx
• pandas
• numpy
• seaborn
• matplotlib
• biopython
• joblib
• python-Levenshtein

To visualize lineage traces of the 2009 H1N1 or 2013 H7N9 viruses, do the following:

1. Clone the repository to disk.
2. Navigate to the directory supp_data/viz
3. Start a web server in the directory. One option is to use python -m http.server 8000. This starts a local web server in the directory with port 8000.
4. In your browser, type: localhost:8000/h1n1.html. Replace the port number accordingly; to visualize H7N9, use h7n9.html instead.