spider (version 1.5.1)

read.GB: 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
)

Value

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

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.

Warning

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

Author

Samuel Brown <[e-mail]>

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.

See Also

read.GenBank.

Examples

if (FALSE) {
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")}