higlass-gff-datafetcher

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

Changelog

v0.3.1

• Fixed bug related to collapsed regions
• Dont' display "region" annotations