higlass-gff-datafetcher
v0.3.1
Published
GFF Data Fetcher for HiGlass
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6
Readme
GFF Data Fetcher for HiGlass
Quickly load data from a GFF file to create a gene annotations track in HiGlass.
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
.
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
$ 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:
npm link higlass
Commands
- Developmental server:
npm start
- Production build:
npm run build