lisaiceland / ezancestry

Visualize your genotype data with streamlit

ezancestry

One Thousand Genomes Project -- Population Visualizations using Streamlit

ezancestry is an interactive visualization app built in Python with Streamlit and deployed on Heroku.

Visualize you genotypes at http://ezancestry.herokuapp.com/

Local Installation and Usage

ezancestry can be installed locally:

1. Download ezancestry

2. Change into the ezancestry directory:

   $ cd ezancestry
   

3. Create a virtual environment:

   $ python -m venv .venv
   

4. Activate the virtual environment:

   $ source .venv/bin/activate
   

5. Install required packages:

   (.venv) $ pip install -r requirements.txt
   

   If issues installing cyvcf2, see here. Setting these environment variables might work (if openssl installed with MacPorts):

   export LDFLAGS="-L/opt/local/include"
   export PKG_CONFIG_PATH="/opt/local/include"
   export CPPFLAGS="-I/opt/local/include"
   

6. Run ezancestry:

   (.venv) $ streamlit run app.py
   

   You will then be presented with a URL to use the app in a browser.

7. Ctrl-C to stop the web server

8. Deactivate the virtual environment:

   (.venv) $ deactivate
   

Run ezancestry on openSNP data!

Thanks to Andrew Riha, it's easy to predict the ancestries for all of the openSNP samples:

1. Download the data to the data directory. It's a large zipped directory!
2. Follow steps 1-5 above.
3. Run python opensnp_ancestry.py and wait for the results.