Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project provides a combination of a Beacon-protocol based API with additional API services, used as backend and middleware for the Progenetix resource.

bycon has been developed to support Beacon protocol development following earlier implementations of Beacon+ (“beaconPlus”) with now deprected Perl libraries. The work tightly integrates with the ELIXIR Beacon project.

Examples for v2 endpoints

NOTE The Beacon v2 endpoints are currently implemented under https://progenetix.org/beacon/....

The examples for the v2 paths can now be found on the paths page.

For more information see the beaconresponse json documentation.

DEPRECATED v1+ and cutom test examples

• https://beacon.progenetix.org/?datasetIds=progenetix&assemblyId=GRCh38&includeDatasetResponses=ALL&variantType=DUP&filterLogic=AND&geneSymbol=MYC&varMinLength=1000000&varMaxLength=3000000&filters=icdom-80463

• /get-datasetids/
  • dataset retrieval
  • https://bycon.progenetix.org/get-datasetids/

    {
    "datasets": [
        { "id": "progenetix", "name": "progenetix" ...
    

• sample retrieval like “id” query by endpoint
  • This type of query emulates the endpoint based queries above through the parameters
    • scope
    • id
    • response Only providing scope or response without id will only work if other valid query parameters are provided.
  • https://bycon.progenetix.org?id=PGX_AM_BS_GSM253289&datasetIds=progenetix&scope=biosamples
  • https://bycon.progenetix.org?id=PGX_AM_BS_GSM253289&datasetIds=progenetix&scope=biosamples&response=g_variants

The first examples are for “standard” Beacon (v1) queries and may become deprecated/remapped during the ongoing development.

• standard test deletion CNV queries (these may take a minute or so…)
  • https://bycon.progenetix.org/query?datasetIds=progenetix&assemblyId=GRCh38&referenceName=9&variantType=DEL&start=20000000&start=21975097&end=21967753&end=23000000&filters=icdom-94403
  • https://bycon.progenetix.org/query?datasetIds=progenetix&assemblyId=GRCh38&referenceName=9&variantType=DEL&start=18000000&start=21975097&end=21967753&end=26000000&filters=icdom-94403
• retrieving biosamples w/ a given filter code
  • https://bycon.progenetix.org/query?assemblyId=GRCh38&datasetIds=progenetix&filters=NCIT:C3326
• precise variant query together with filter
  • https://bycon.progenetix.org/query?datasetIds=progenetix&assemblyId=GRCh38&start=7577120&referenceBases=G&alternateBases=A&filters=icdot-C71.7

Links

• [www]