dogsheep / genome-to-sqlite

Import your genome into a SQLite database

genome-to-sqlite

Import your genome into a SQLite database.

How to install

$ pip install genome-to-sqlite

How to use

First, export your genome. This tool has only been tested against 23andMe so far. You can request an export of your genome from https://you.23andme.com/tools/data/download/

Now you can convert the resulting export.zip file to SQLite like so:

$ genome-to-sqlite export.zip genome.db

A progress bar will be displayed. You can disable this using --silent.

Importing genome  [#----------------]    5%  00:01:33

You can explore the resulting data using Datasette like this:

$ datasette genome.db --config facet_time_limit_ms:1000

Bumping up the facet time limit is useful in order to enable faceting by chromosome:

http://127.0.0.1:8001/genome/genome?_facet=chromosome&_sort=position

genome-to-sqlite's Issues

Yak shave

Just a quick note... The 23andme data is not exactly your genome, but a SNP chip of your genome. It's "some of your genotypes." Or about 0.1% of your genome. Nice work in any case! It deserves to be liberated!!!!!

Figure out some interesting example SQL queries

My knowledge of genetics has left me short here. I'd love to be able to provide some interesting example SELECT queries - maybe one that spots if you are likely to have red hair?