refget

Name	refget JSON
Version	0.3.0 JSON
	download
home_page	https://github.com/refgenie/refget
Summary	Python client for refget
upload_time	2024-02-23 17:24:31
maintainer
docs_url	None
author	Nathan Sheffield, Michal Stolarczyk
requires_python
license	BSD2
keywords	genome assembly bioinformatics reference sequence
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # Refget

![Run pytests](https://github.com/pepkit/looper/workflows/Run%20pytests/badge.svg)

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](https://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

1. Load the fasta files from the `test_fasta` folder into your API database.
2. 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
```

            

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