Genetic analysis of the Zika epidemic in Colombia

Scripts for data wrangling and plotting

This repo contains jupyter notebooks for making the input dataset and plotting figures. Note that these scripts should be run inside the colombia-python2 environment specified in envs/colombia.python2.yaml.

To run this environment you will need to have conda or miniconda installed. Instructions can be found here.

Once you have conda installed, you will need to create the environment. To do so, in a terminal run conda env create --file <path/to/envs/colombia.python2.yaml>.

To load the environment, run conda activate colombia-python2.

Once the environment is loaded, from that terminal window run jupyter notebook. That will ensure your notebook is using that environment.

curate-dataset.ipynb is the notebook that does data wrangling. This notebook takes a batch download from nextstrain-fauna and removes sequences that shouldn’t be included in our analysis (e.g. Singapore sequences, sequences without permissions etc.)

plot-figures.ipynb is the notebook that plots the map with sampling locations and the epi curve.