parse_silva_tax: Split single SILVA taxonomic annotation to taxonomic ranks.

View source: R/parse_silva.R

parse_silva_taxR Documentation

Split single SILVA taxonomic annotation to taxonomic ranks.

Description

Split single SILVA taxonomic annotation to taxonomic ranks.

Usage

parse_silva_tax(x, db)

Arguments

x

Character string with taxonomic annotation from BLAST.

db

Data frame with rank designations for all taxonomic paths in the SILVA taxonomy.

Details

This function will split the taxonomic annotation based on the SILVA database and assign a corresponding taxonomic rank to the obtained parts.

Value

Named charcter vector with taxonomic annotation (names = rank designations).

See Also

parse_silva_tax_batch

Examples

# Download taxonomic rank designations for all taxonomic paths used in the SILVA taxonomies
tax.db <- read.delim("https://www.arb-silva.de/fileadmin/silva_databases/release_128/Exports/taxonomy/tax_slv_ssu_128.txt", header = F, stringsAsFactors = F)
colnames(tax.db) <- c("path", "taxid", "rank", "remark", "release")

x <- "Eukaryota;SAR;Alveolata;Ciliophora;Intramacronucleata;Conthreep;Oligohymenophorea;Peritrichia;Telotrochidium;uncultured eukaryote"
parse_silva_tax(x, tax.db)


vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.