#' Read mothur formatted ...0.03.cons.taxonomy file
#'
#' This function allows to read and reformat the output taxonomy file from mothur to a data frame
#' @param tax.file is a taxonomy output file from mothur i.e. ends in "..0.03.cons.taxonomy"
#' @keywords mothur , igraph, taxonomy
#' @export
#' @examples
#' tax <- read.mothur.taxonomy(Sys.glob("data/*taxonomy"))
read.mothur.taxonomy <- function(tax.file) {
tbl <- read.delim(tax.file, header = FALSE, row.names = 1) %>%
.[2:nrow(.),]
split <- strsplit(as.character(tbl$V3), ";", fixed = TRUE)
kingdom <- sapply(split, "[", 1) %>% sub("\\([0-9.]+\\)", "", .)
phylum <- sapply(split, "[", 2) %>% sub("\\([0-9.]+\\)", "", .)
class <- sapply(split, "[", 3) %>% sub("\\([0-9.]+\\)", "", .)
order <- sapply(split, "[", 4) %>% sub("\\([0-9.]+\\)", "", .)
family <- sapply(split, "[", 5) %>% sub("\\([0-9.]+\\)", "", .)
genus <- sapply(split, "[", 6) %>% sub("\\([0-9.]+\\)", "", .)
species<- sapply(split, "[", 7) %>% sub("\\([0-9.]+\\)", "", .)
tax_df <- data.frame(Count= tbl$V2, Kingdom=kingdom, Phylum = phylum, Class = class, Order = order, Family = family,
Genus = genus, Species = species) %>% `rownames<-`(rownames(tbl))
return(tax_df)
}
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