Retrieve genome IDs for each taxon via BV-BRC and DuckDB

Source: R/data_curation.R

Resolves user-provided taxa to taxon IDs, queries BV-BRC per unique taxon ID, and returns distinct genome IDs. Uses a per-selection DuckDB located under: <base_dir>/data/<bug_dir>/.duckdb BV-BRC column names are preserved.

.retrieveQueryIDs(base_dir = ".", user_bacs, overwrite = FALSE, verbose = TRUE)

Arguments

base_dir

Character. Project root directory. Default ".".

user_bacs

Character vector. Mixed inputs of taxon IDs and/or species names.

overwrite

Logical. If FALSE and the DuckDB already exists for this selection, abort. Default: FALSE.

verbose

Logical.

Value

A numeric vector of distinct genome.genome_id, or NULL if none found.