bionode.io

# bionode-ncbi > Node.js module for working with the NCBI API (aka e-utils).

Install

Install bionode-ncbi with npm:

$ npm install bionode-ncbi

To use it as a command line tool, you can install it globally by adding -g .

Usage

If you are using bionode-ncbi with Node.js, you can require the module:

var ncbi = require('bionode-ncbi')
ncbi.search('sra', 'solenopsis').on('data', console.log)

Please read the documentation for the methods exposed by bionode.

Command line examples

$ bionode-ncbi search taxonomy solenopsis
$ bionode-ncbi search sra human --limit 10 # or just -l
$ bionode-ncbi download assembly solenopsis invicta
$ bionode-ncbi urls sra solenopsis invicta
$ bionode-ncbi link assembly bioproject 244018

Usage with Dat

bionode-ncbi search gds solenopsis | dat import --json

Contributing

To contribute, clone this repo locally and commit your code on a separate branch.

Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:

$ npm test

Please also check for code coverage:

$ npm run coverage

To rebuild the documentation using the comments in the code:

$ npm run build-docs

Check the issues for ways to contribute.

Contributors

Please see the file contributors.md for a list.

Contacts

Bruno Vieira <[email protected]> @bmpvieira

Yannick Wurm (yannick.poulet.org) @yannick__

Licenses

bionode-ncbi is licensed under the MIT license.
Check ChooseALicense.com for details.