https://github.com/bionode/bionode-gff
GFF parser
https://github.com/bionode/bionode-gff
bioinformatics bionode nodejs parser tools
Last synced: 11 months ago
JSON representation
GFF parser
- Host: GitHub
- URL: https://github.com/bionode/bionode-gff
- Owner: bionode
- Created: 2015-09-15T13:44:01.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2022-11-10T06:46:38.000Z (over 3 years ago)
- Last Synced: 2025-04-06T16:41:12.775Z (about 1 year ago)
- Topics: bioinformatics, bionode, nodejs, parser, tools
- Language: JavaScript
- Size: 146 KB
- Stars: 3
- Watchers: 15
- Forks: 3
- Open Issues: 7
-
Metadata Files:
- Readme: README.MD
- Contributing: CONTRIBUTING.md
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
README
# bionode-gff
> Node.js module for parsing gff files
[](http://npmjs.org/package/bionode-gff)
[](https://travis-ci.org/bionode/bionode-gff)
[](http://coveralls.io/r/bionode/bionode-gff)
[](http://david-dm.org/bionode/bionode-gff)
[](https://www.npmjs.com/package/bionode-gff)
[](https://gitter.im/bionode/bionode)
## Install
You need to install the latest Node.JS first, please check [nodejs.org](http://nodejs.org) or do the following:
```bash
# Ubuntu
sudo apt-get install npm
# Mac
brew install node
# Both
npm install -g n
n stable
```
To use `bionode-gff` as a command line tool, you can install it globally with `-g`.
```bash
npm install bionode-gff -g
```
Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the `node_modules` directory by doing the same command **without** `-g`.
```bash
npm i bionode-gff # 'i' can be used as shortcut to 'install'
```
## Usage
If you are using ```bionode-gff``` with Node.js, you can require the module:
```js
var gff = require('bionode-gff')
GFF.read(filePath).on('data',onFeatures).on('end', done);
function onFeature(feature){
console.log(feature.seqid);
console.log(feature.source);
console.log(feature.type);
console.log(feature.start);
console.log(feature.end);
console.log(feature.score || '.');
console.log(feature.strand || '?');
console.log(feature.phase || '.');
console.log(feature.attributes);
}
function done(){
console.log('done');
}
```
## Documentation
Check our documentation at [doc.bionode.io](http://doc.bionode.io) or do:
```bash
bionode-gff --help
```
## Contributing
We welcome all kinds of contributions at all levels of experience, please read the [CONTRIBUTING.md](CONTRIBUTING.md) to get started!
## Communication channels
Don't be shy! Come talk to us :smiley:
* **Email** [mail@bionode.io](mailto:mail@bionode.io)
* **Chat room** [http://gitter.im/bionode/bionode](http://gitter.im/bionode/bionode)
* **IRC** #bionode on Freenode
* **Twitter** [@bionode](http://twitter.com/@bionode)
