The _Translator class defines a beacon string format which has no known relationship to the Beacon standard but apparently mimics a non-codified use in the query fields of some front-end implementations (but does not conform to any Beacon definition):
r"(?P<chr>[^-]+)\s*:\s*(?P<pos>\d+)\s*(?P<ref>\w+)\s*>\s*(?P<alt>\w+)"
The Beacon specification allows the definition of genomic variations as
- $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation
- $ref: '#/$defs/LegacyVariation'
... where a LegacyVariation is an object with properties location (i.e. .../vrs/1.3/vrs.json#/definitions/Location), variantType, referenceBases and alternateBases.
Recommendation
- rename the misleading
beacon translator to beacon-legacy
- define an appropriate input format, preferably as an object using the Beacon v2 definition (or a stringified/list version of this) and integrate it with the appropriate method
- coordinate with/ the Beacon developers :-)
The
_Translatorclass defines abeaconstring format which has no known relationship to the Beacon standard but apparently mimics a non-codified use in the query fields of some front-end implementations (but does not conform to any Beacon definition):The Beacon specification allows the definition of genomic variations as
... where a
LegacyVariationis an object with propertieslocation(i.e..../vrs/1.3/vrs.json#/definitions/Location),variantType,referenceBasesandalternateBases.Recommendation
beacontranslator tobeacon-legacy