read.GB: Download sequences from GenBank with metadata.
In boopsboops/spider: Species Identity and Evolution in R

read.GB

R Documentation

Download sequences from GenBank with metadata.

Description

Downloads sequences associated with the given accession numbers into a ‘DNAbin’ class.

Usage

read.GB(
  access.nb,
  seq.names = access.nb,
  species.names = TRUE,
  gene = TRUE,
  access = TRUE,
  as.character = FALSE
)

Arguments

`access.nb`	A character vector giving the GenBank accession numbers to download.
`seq.names`	A character vector giving the names to give to each sequence. Defaults to "accession number \| species name".
`species.names`	Logical. Should species names be downloaded? Default of TRUE.
`gene`	Logical. Should the name of the gene region be downloaded? Default of TRUE.
`access`	Logical. Should the accession number be downloaded? Default of TRUE.
`as.character`	Logical. Should the sequences be returned as character vector? Default of FALSE, function returns sequences as a ‘DNAbin’ object.

Details

This function is a modification of read.GenBank to include metadata with each sequence. Additional data currently implemented are the species names and the gene region from which sequences were derived.

Value

A 'DNAbin' object with the following attributes: "species", "gene", and "accession_num".

Warning

15 Feb 2018: 'read.GB' is deprecated. Please use the rOpenSci packages 'rentrez' and 'traits', or 'ape' for better functionality.

Author(s)

Samuel Brown <s_d_j_brown@hotmail.com>

Examples


## Not run: 
read.GB("AY059961")

#Download the sequences making data(anoteropsis) from GenBank
nums <- 59961:59993
seqs <- paste("AY0", nums, sep="")
dat <- read.GB(seqs)

attr(dat, "species")
attr(dat, "gene")
attr(dat, "accession_num")
## End(Not run)

boopsboops/spider documentation built on June 2, 2025, 7:28 a.m.