pull_PATRIC_genomes: Automated download of genomes from PATRIC database

In MIC: Analysis of Antimicrobial Minimum Inhibitory Concentration Data

Automated download of genomes from PATRIC database

Description

Automated download of genomes from PATRIC database

Usage

pull_PATRIC_genomes(
  output_directory,
  taxonomic_name = NULL,
  database = patric_ftp_path,
  filter = "MIC",
  n_genomes = 0
)

Arguments

output_directory	local directory to save to
taxonomic_name	character of taxonomic bacterial name to download
database	local or ftp path to PATRIC database, or loaded database using load_patric_db()
filter	"MIC" or "disk" or "all" phenotypes
n_genomes	number of genomes (0 = all)

Value

The number of failed downloads (i.e., 0 if all attempted downloads were successful).

Examples

pull_PATRIC_genomes(tempdir(),
                    taxonomic_name = "Escherichia coli",
                    filter = "MIC",
                    n_genomes = 10)

MIC documentation built on April 12, 2025, 2:26 a.m.