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README.md

Snip

Snip is a an API service to link your raw 23&Me data, with a slim version of DbSNP, to return JSON data containing:

  1. Diseases pertaining to your SNPs, and their ClinVar clinical significance labels.
  2. PubMed IDs that support DbSNP's data.
  3. Frequency Studies (i.e. GWAS) that identify how rare the SNP in sample populations (% of study population).

I gave Lightning talk on this API at PyCon2018...you can find it on youtube here

Your data will be uploaded to a PostgreSQL database in AWS, and only accessible with your username, password and application secret. Requests are authenticated at the app-level with a JWT. User-sensitive information (i.e. 23&Me SNP data) is stored in a table with separate permissions from the rest of the database, and only accessible from 1 endpoint.

Open to ideas on how to build interface(s) for this API, and how to leverage the data collected in an open-source, privacy-friendly fashion!

To install:

python3.6 -m venv env
source env/bin/activate
pip install -r requirements.txt

To upload and get your Snip data:

  1. Download your 23&Me data from their website
  2. Move your 23&Me data file to this directory.
  3. Set the SNIP_API_EMAIL and SNIP_API_PASSWORD env variables to define your credentials. (These will be used in the script below to create an account, and to authorize when you request to get your results)
export SNIP_API_EMAIL='<your email>'
export SNIP_API_PASSWORD='<your password>'
  1. Run the upload client, passing the name of your 23&me file as the first arg:
python upload_23_and_me.py <23_and_me_file.txt>
  1. Open the file 23_and_me.json to see your results.

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Accessing the Snip REST API with JWT Auth.

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