R/make_framebot_tax_table.R

In jfq3/RDPutils: R Utilities for Processing RDPTool Output

make_framebot_tax_table <- function(clstr_machine="match_cluster_machine_name.txt", taxa_machine="match_taxa_machine_names.txt") {
  clstr_machine <- read.table(file=clstr_machine, header = FALSE, stringsAsFactors = FALSE, sep="\t")
  taxa_machine <- read.table(file=taxa_machine, header = FALSE, stringsAsFactors = FALSE, sep="\t")
  colnames(taxa_machine) <- c("strain","machine_name", "nucl_length", "as_length", "%identity")
  taxa_machine[ , 1] <- paste(taxa_machine[ , 1], taxa_machine[ , 5], sep = "_%")
  colnames(clstr_machine) <- c("cluster", "machine_name")
  taxonomy_table <- merge(clstr_machine, taxa_machine, by.x="machine_name", by.y = "machine_name")
  row.names(taxonomy_table) <- taxonomy_table[,"cluster"]
  for (i in 1:nrow(taxonomy_table)) {
    taxonomy_table[i,"genus"] <- strsplit(taxonomy_table[i,"strain"],"_")[[1]][1]
    taxonomy_table[i,"species"] <- strsplit(taxonomy_table[i,"strain"],"_")[[1]][2]
  }
  taxonomy_table <- taxonomy_table[ , c("genus", "species", "strain")]
  colnames(taxonomy_table) <- c("Genus", "Species", "Strain")
  taxonomy_table <- tax_table(as.matrix(taxonomy_table), errorIfNULL = TRUE)
  return(taxonomy_table)
}