SMT#Bioinformatics #VEP #DuckDB
I just got the realization that instead of trying to parse in C ensembl VEP's caches (ridiculous idea given the perl serialization format), duckdb has a mysql reader and i can just load this into duckdb the ensembl DB tables i need ! this make the duckvep project much more manageable and mostly sql kernel work now since we already have variant keys and cgranges udfs in the duckhts extension https://github.com/RGenomicsETL/duckhts
I just got the realization that instead of trying to parse in C ensembl VEP's caches (ridiculous idea given the perl serialization format), duckdb has a mysql reader and i can just load this into duckdb the ensembl DB tables i need ! this make the duckvep project much more manageable and mostly sql kernel work now since we already have variant keys and cgranges udfs in the duckhts extension https://github.com/RGenomicsETL/duckhts
