be-datahive

Python library for the BE-dataHIVE API.

Installation

be_datahive is available on PYPI. Install with pip:

pip install be_datahive

Get Started

Create an api object for interacting with the API:

from be_datahive import be_datahive
api = be_datahive()

Obtain efficiency & bystander data:

efficiency_data = api.get_efficiency()
bystander_data = api.get_bystander()

Convert efficiency & bystander data into machine-ready arrays:

ef_features, ef_target, variable_info = api.get_efficiency_ml_arrays(efficiency_data, target_col = "efficiency_full_grna_reported", encoding='hilbert-curve', clean=True, flatten=True)
by_features, by_target, variable_info = api.get_bystander_ml_arrays(bystander_data, encoding='one-hot', bystander_type = 'edited', clean=True, flatten=True)

API Documentation

The Python wrapper uses the BE-dataHive API which is accessible at the endpoint (https://be-server.herokuapp.com). The detailed API documentation, describing all endpoints, query parameters, and response schema, can be viewed here.

Troubleshooting

If you encounter any issues while using the be_datahive library, please refer to the common issues listed below:

1. Installation issues: Make sure you have the latest version of pip and Python installed. Use pip install --upgrade pip to upgrade pip if necessary.
2. API Connection Errors: Check your internet connection and ensure that the API endpoint (https://be-server.herokuapp.com) is reachable.
3. Data Retrieval Issues: Ensure that you are using the correct function names and parameters as outlined in the documentation.

If your issue is not listed here or you need further assistance, please open an issue on GitHub or reach out directly.

Reporting Issues

If you have any problems, you can open an issue on GitHub in the following format:

Title: [Brief description of the issue]

Description:

1. Summary: A detailed description of the issue.
2. Steps to Reproduce: Step-by-step instructions to reproduce the issue.
3. Expected Result: What you expected to happen.
4. Actual Result: What actually happened.
5. Software: Operating system and Python version.
6. Additional Information: Any other information that may help us resolve the issue.

Alternatively, you can reach out directly to Lucas Schneider at lucas.schneider@cs.ox.ac.uk.

Citation

When using the BE-dataHIVE API, please cite our paper as outlined below.

@article{Schneider.2023,
    title = "BE-dataHIVE: a Base Editing Database",
    author = "Lucas Schneider, Peter Minary",
    year = "2024",
}