metacoder (version 0.1.2)

genbank_ex_data: Fungal ITS Genbank refseq

Description

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

Usage

genbank_ex_data

Format

An object of type taxmap

Source

http://www.ncbi.nlm.nih.gov/nuccore

Details

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

Examples

## 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")
# ## End(Not run)

Run the code above in your browser using DataCamp Workspace