Retrieve Taxonomic Ranks for a List of NCBI Taxonomy Tax IDs in Parallel

Retrieves taxonomy ranks for a list of NCBI Taxonomy Tax IDs using parallel processing. The function queries the NCBI database and can retry fetching taxonomy information multiple times if initial attempts fail.

Usage

parallel_get_tax(
  organisms_taxIDs,
  parse_result = TRUE,
  total_cores = 1L,
  retry_times = 10L,
  verbose = c("silent", "cmd", "output", "full"),
  env_name = "blastr-entrez-env"
)

Arguments

organisms_taxIDs

A character vector of NCBI Taxonomy Tax IDs to retrieve taxonomy information for.

parse_result

Logical indicating whether to parse the taxonomy information into a tibble (TRUE, default) or return the raw output as returned by efetch (FALSE).

total_cores

Integer specifying the number of cores to use for parallel processing. Defaults to 1.

retry_times

Integer specifying the number of times to retry fetching taxonomy information if it fails. Defaults to 10.

verbose

Character string indicating whether to print verbose messages during the process. Default is silent.

env_name

Character string specifying the name of the conda environment where efetch is installed. Default is "blastr-entrez-env".

Value

A tibble containing the taxonomic ranks for the given Tax IDs.

Examples

if (FALSE) { # \dontrun{
# Retrieve taxonomy for multiple Tax IDs using 4 cores
tax_ids <- c("9606", "10090", "10116") # Human, Mouse, Rat
tax_info <- parallel_get_tax(tax_ids, total_cores = 4)

# Retrieve unparsed taxonomy result
tax_info_unparsed <- parallel_get_tax(tax_ids, parse_result = FALSE)

# Increase the number of retry attempts
tax_info <- parallel_get_tax(tax_ids, retry_times = 20)

# Enable verbose output
tax_info <- parallel_get_tax(tax_ids, verbose = "output")
} # }