easy-entrez 0.2.2

Python REST API for Entrez E-Utilities: stateless, easy to use, reliable.

Python REST API for Entrez E-Utilities, aiming to be easy to use and reliable.

Previously published entrezpy implements stateful API extensions (queries with history) which is error-prone and led me (and others) to obtain misleading results.

This implementation:

• avoids the problem altogether by not using such stateful API,

• makes common tasks easy thanks to simple Pythonic API,

• is typed and integrates well with mypy,

• tested on Windows, Mac and Linux across Python 3.6, 3.7, and 3.8,

• is limited in scope, allowing to focus on the reliability of the core code.

Stats: beta (pending tutorial write-up and documentation improvements before official release).

from easy_entrez import EntrezAPI

entrez_api = EntrezAPI(
    'your-tool-name',
    '[e-mail]',
    # optional
    return_type='json'
)

# find up to 10 000 results for cancer in human
result = entrez_api.search('cancer AND human[organism]', max_results=10_000)

# data will be populated with JSON or XML (depending on the `return_type` value)
result.data

See more in the Demo notebook and documentation.

Installation

Requires Python 3.6+. Install with:

pip install easy-entrez

If you wish to enable (optional, tqdm-based) progress bars use:

pip install easy-entrez[with_progress_bars]

Alternatives:

You might want to try:

• biopython.Entrez - biopython is a heavy dependency, but probably good choice if you already use it

• pubmedpy - provides interesting utilities for parsing the responses

• entrez - appears to have a comparable scope but quite different API

I have tried and do not recommend:

• entrezpy - in addition to the history problems, watch out for documentation issues and basically no reaction to pull requests.