https://github.com/higlass/higlass-gff-datafetcher
https://github.com/higlass/higlass-gff-datafetcher
Last synced: 24 days ago
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- Host: GitHub
- URL: https://github.com/higlass/higlass-gff-datafetcher
- Owner: higlass
- License: mit
- Created: 2020-08-17T19:05:57.000Z (almost 6 years ago)
- Default Branch: master
- Last Pushed: 2021-01-25T21:36:47.000Z (over 5 years ago)
- Last Synced: 2025-09-13T22:57:36.280Z (9 months ago)
- Language: JavaScript
- Size: 1 MB
- Stars: 2
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# GFF Data Fetcher for HiGlass
Quickly load data from a GFF file to create a gene annotations track in HiGlass.
[](http://higlass.io)
This is the source code for multivec tracks in HiGlass only; for the rest of HiGlass,
see these repositories:
- HiGlass viewer: https://github.com/hms-dbmi/higlass
- HiGlass server: https://github.com/hms-dbmi/higlass-server
- HiGlass docker: https://github.com/hms-dbmi/higlass-docker
## Usage
The live scripts can be found at:
- https://unpkg.com/higlass-gff-datafetcher/dist/higlass-gff-datafetcher.min.js
Configure the track in your view config; you should be all set from here!
```
[...
{
"type": "horizontal-gene-annotations",
"height": 80,
"data": {
"type": "gff",
"url": "https://pkerp.s3.amazonaws.com/public/GCF_001461035.1_ASM146103v1_genomic.gff.gz",
"chromSizesUrl": "https://domain.com/my.chrom.sizes",
"options": {
"namePaths": [
"gene",
"annotationName"
]
}
}
}
]
```
Note that the `chromSizesUrl` option is optional and only needs to be provided if the gff file lacks the `region` entries listing the chromosomes in the assembly.
For an example, see [`src/index.html`](src/index.html).
### Options
**namePaths** - A list (e.g. `['gene', 'annotationName']`) of attributes to look in when choosing the name of the region to display. The fetcher will go through the items in this option and use the first one that is present in the attributes.
**excludeTypes** - A list of types to exclude from the display.
## Development
### Testing
To run the test suite:
```
npm run test-watch
```
### Installation
```bash
$ git clone https://github.com/higlass/higlass-gff-datafetcher
$ cd higlass-gff-datafetcher
$ npm install
```
If you have a local copy of higlass, you can then run this command in the higlass-gff-datafetcher directory:
```bash
npm link higlass
```
### Commands
- **Developmental server**: `npm start`
- **Production build**: `npm run build`