Import GTDB Output — import

Import GTDB output (from file or data frame) and parse the species name into a microorganism recognised by AMR package. AMR mo code and species name will be added to the data frame.

Usage

import_gtdb(file = NULL, tbl = NULL, species_column = "Species")

Arguments

file: File path to GTDB output file (tab-separated). If not given, tbl must be given.
tbl: Data frame containing GTDB output. If not given, file must be given.
species_column: Name of column containing the species call (default "Species").

Value

tbl Data frame containing GTDB output with AMR-parsed microorganism code (gtdb.mo) and species name (gtdb.species) appended.

Examples

if (FALSE) { # \dontrun{
import_gtdb(tbl = data.frame(Species = c(
  "Pseudomonas_E piscis",
  "Haemophilus_D parainfluenzae_A",
  "Acinetobacter calcoaceticus_C"
)))
} # }