pyentrez 0.1.0

pyEntrez tool suite wrapped in pyCUI TUI

pyEntrez

pyEntrez aims to be a user-friendly suite of Biopython’s Entrez tools that may be accessed from either the commandline in a script/arg function, or from a persistent Text User Interface (TUI). The current implementation will extend to the full use of Entrez for publication browsing, and will offer features to automatically send query results to a database of the user’s choice as well as facilitate database manipulation.

Planned features include data interpretation with toolsets such as Pandas. As well as incorporating text analysis and machine learning to flag abstracts that are pertinent to the research conducted by the user.

Unplanned, but interesting, features would be to incorporate the rest of the tools offered by Biopython in a one-stop shop.

The current implementation has been developed in Python 3 Win10 but should work with Linux based OS (maybe with minor modifications in terms of printing and error handling.)

Motivation

As a novice programmer in the medical science realm, I wanted to see if I could implement a suite of tools that could pull all of the Entrez functionality together under one script, as well as manipulate the data pulled. I envision this script allowing for a much more rapid acquisition of relevant data for systemic reviews and meta-analysis, which is a process limited by the amount of research assistants and hours available to scrape and read abstracts.

Code style

Installation

API Reference

How to use?

Credits

Powered by: py_CUI Python Command Line UI library: https://github.com/jwlodek/py_cui Docs: https://jwlodek.github.io/py_cui-docs

Biopython library: https://github.com/biopython/biopython Docs: https://biopython.org

License

MIT © William Slattery 2020