Refget

The refget package provides a Python interface to both remote and local use of the refget protocol.

This package provides clients and functions for both refget sequences and refget sequence collections (seqcol).

Documentation is hosted at refgenie.org/refget.

Testing

Local unit tests of refget package

pytest to test refget package, local unit tests

Compliance testing

Under /test_api are compliance tests for a service implementing the sequence collections API. This will test your collection and comparison endpoints to make sure the comparison function is working.

pytest test_api to tests API compliance
pytest test_api --api_root http://127.0.0.1:8100 to customize the API root URL to test

Load the fasta files from the test_fasta folder into your API database.
Run pytest test_api --api_root <API_URL>, pointing to your URL to test

For example, this will test my remote server instance:

pytest test_api --api_root https://seqcolapi.databio.org

Loading up data into an instance

Starting a demo instance

Use docker to create a local postgres database like this:

docker run --rm --name refget-postgres -p 5432:5432 \
  -e POSTGRES_PASSWORD=postgres \
  -e POSTGRES_USER=postgres \
  -e POSTGRES_DB=postgres \
  postgres:13

Loading files

If you need to load, then you have to install either gc_count (fast) or pyfaidx (slow).

You can load them like:

python load_demo_data.py

Or:

refget add-fasta path/to/fasta.fa

Adding data to production service

Just first source the production credentials, then load the data:

source deployment/seqcolapi.databio.org/production.env
python load_demo_data.py

refgenie/refget