In grunwaldlab/metacoder: Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reproduce error

devtools::install_github("grunwaldlab/metacoder@59c6555")

library(metacoder)
file_path <- system.file("extdata", "unite_general_release.fasta", package = "metacoder")
sequences <- ape::read.FASTA(file_path)
unite_ex_data_3 <- extract_taxonomy(sequences,
                                    regex = "^(.*)\\|(.*)\\|(.*)\\|.*\\|(.*)$",
                                    key = c(seq_name = "obs_info", seq_id = "obs_info",
                                            other_id = "obs_info", "class"),
                                    class_regex = "^(.*)_not_here_(.*)$",
                                    class_key = c(unite_rank = "taxon_info", "name"),
                                    class_sep = ";")

Verify fix

grunwaldlab/metacoder documentation built on Feb. 22, 2024, 3:47 a.m.