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)
}
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