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Signal Service

A graphql service that does the following:

  • Reads data from Trackhubs
  • Reads data from BigWig and BigBed files in batches.
  • Reads signal data from 2-bit files.
  • Reads BAM indexes and data

BigWig / BigBed / 2bit

Request

For BigWig / BigBed /2bit data, use the /big POST endpoint

The body of the request must be a json formatted list of "BigRequests"

Each BigRequest contains a URL and a genomic region consisting of chr1, start, chr2 (optional), end. An optional zoomLevel field is also available to get zoomed data from BigWig and BigBed files.

The following is a complete example request body for batching big file and 2-bit file requests:

Variables will look like this:

[
    { "url": "http://localhost/sample.bigwig", "chr1": "chr14", "start": 19485000, "end": 20000100 },
    { "url": "http://localhost/sample.bigwig", "chr1": "chr2", "start": 0, "chr2": "chr6", "end": 1000, "zoomLevel": 100 },
    { "url": "http://localhost/sample.bigwig", "chr1": "chr2", "start": 0, "end": 1000000, "zoomLevel": 1000 },
    { "url": "http://localhost/sample.bigbed", "chr1": "chr21", "start": 10000000, "chr2": "chr21", "end": 20000000 },
    { "url": "http://localhost/sample.2bit", "chr1": "chr22", "start": 1000000, "end": 1001000 }
]

Response

The response is streamed back and multiplexed. Chunks of data are added in the order they are received. As such, each chunk of data starts with the index of it's request. Similar signals are used for indicating the end for a stream or error for a single file.

  • BigWig, BigBed, and Zoom data chunks will be in JSON format (See src/models/bigwigModel.ts).
  • 2bit data chunks will be strings.
0:DATA:{"chr": "chr14", "start": 19_485_969, "end": 19_485_974, "value": 1}
2:DATA:{...}
1:DATA:AAAACTCAG...
...
1:END
0:DATA:{...}
0:END
2:ERROR:Some error message

Trackhubs

Trackhub Requests use the /graphql endpoint

query trackHubRequests($url: trackHubUrl!) {
    trackHubRequests(trackhuburl: $url)  {
        trackhubname
        ... on TrackHubGenomes {          
            genomes{
                trackDb
                defaultPos
                genome
            }
        }  
        ... on TrackHub {
            trackHubContent
        }
   }
}

and corresponding variables json

{
    "url": { "trackHubUrl": "http://localhost:8001/hub.txt", "hubUrl": true }
}

BAMs

BAMs work a little differently. Since BAM indexes are only useful if read in their entirety, we have created a separate request for bam index data (for a single chromosome). Then, using the bigwig-reader library, use the index to find a file block use when requesting BAM data.

BAM Header Request

First, in order to get reference IDs needed in BAM Index and BAM Data requests, we need to make a BAM Header request.

Use a POST on /bamHeader with a JSON formatted body similar to { "bamUrl": "http://someUrl/test.bam" }

The response will be a json object containing a map of chromosome names to reference ids called chromToId

BAM Index Request

Next, we will request the raw index data for a single chromosome (by referenceId).

Use a POST on /bamIndex with a json formatted body similar to { "baiUrl": "http://someUrl/test.bai", "refId": 1 }

The response will be raw binary bai data. You can use the bigwig-reader library to parse it using the provided parseRawIndexRefData function.

BAM Data Request

Finally, we will request bam data for a genomic region.

Use a POST on /bam with a JSON formatted body similar to the following

{
    "bamUrl": "http://someUrl/test.bam", 
    "refId": 1, 
    "chr": "chr14", 
    "start": 100000, 
    "end": 100100,
    "chunks": ...
}

In the example above, chunks is a set of file locations we get from the index. You can use the bigwig-reader library's function blocksForRange to get these values.

For a complete example of using the bam interface, see test/bam.test.ts

For contributors

Building

  • Run yarn install to install dependencies.
  • Run yarn build to compile typescript
  • scripts/build.sh SOME_VERSION to build docker image and tag it with SOME_VERSION.

Testing

You must have Node.js and docker-compose installed.

  • scripts/test.sh to spin up dependences and run automated tests.
  • yarn test to run tests without spinning up dependencies.
  • scripts/run-dependencies.sh to stand up a web server to host static sample BigWig and BigBed files. scripts/test.sh runs this for you.
  • scripts/stop-dependencies.sh to stop bring down the server.

Deploying

  • scripts/push-image.sh SOME_VERSION to push docker image tagged with SOME_VERSION to Google Container Registry.
  • scripts/deploy.sh staging SOME_VERSION to deploy the docker image tagged with SOME_VERSION in GCR to kubernetes in staging environment. A list of options will be provided if the second argument is left blank.