Retrieve AMR or Microtrait metadata from BV-BRC and store in DuckDB

Source: R/data_curation.R

Queries BV-BRC for AMR or microtrait metadata for genomes corresponding to user inputs. Results are written to a per-selection DuckDB at: <base_dir>/data/<bug_dir>/.duckdb Tables written:

  • amr_phenotype

  • genome_data

  • metadata (inner join on genome ID field names as returned by BV-BRC)

retrieveMetadata(
  user_bacs,
  filter_type = "AMR",
  base_dir = ".",
  abx = "All",
  overwrite = FALSE,
  image = "danylmb/bvbrc:5.3",
  verbose = TRUE
)

Arguments

user_bacs

Character vector. Mixed taxon IDs and/or species strings (used for naming).

filter_type

Character. "AMR" or "microTraits". Default "AMR".

base_dir

Character. Project root. Default "results/" in legacy scripts; now default ".".

abx

Character or vector. Antibiotic filter. "All" for all antibiotics, else names.

overwrite

Logical. If FALSE and DuckDB exists already, abort. Default FALSE.

image

Character. Docker image. Default "danylmb/bvbrc:5.3".

verbose

Logical. If TRUE, prints concise messages.

Value

A list with:

  • duckdbConnection: live DBI connection to the created DuckDB

  • table_name: "metadata"