metacoder (version 0.1.3)

genbank_ex_data: Fungal ITS Genbank refseq

Description

A dataset containing information for 299 sequences obtained from NCBI using the following query:

Usage

genbank_ex_data

Arguments

Format

An object of type taxmap

Details

(18s[All Fields] AND 28s[All Fields]) AND "basidiomycetes"[porgn] AND (refseq[filter] AND ("700"[SLEN] : "800"[SLEN]))

Examples

Run this code
# NOT RUN {
file_path <- system.file("extdata", "ncbi_basidiomycetes.fasta", package = "metacoder")
sequences <- ape::read.FASTA(file_path)
genbank_ex_data <- extract_taxonomy(sequences,
                                    regex = "^.*\\|(.*)\\|.*\\|(.*)\\|(.*)$",
                                    key = c(gi_no = "obs_info", "obs_id", desc = "obs_info"),
                                    database = "ncbi")
# }

Run the code above in your browser using DataCamp Workspace