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

import_gtdb(tbl = data.frame(Species = c("Pseudomonas_E piscis","Haemophilus_D parainfluenzae_A", "Acinetobacter calcoaceticus_C")))
#> Error in mutate(., gtdb.mo = gtdb.mo(tbl[[species_column]]), gtdb.species = mo_name(gtdb.mo,     keep_synonyms = TRUE)): ℹ In argument: `gtdb.mo = gtdb.mo(tbl[[species_column]])`.
#> Caused by error:
#> ! could not find function "mo_cleaning_regex"