read.GB: Download sequences from Genbank with metadata.

In spider: Species Identity and Evolution in R

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".

Author(s)

Samuel Brown <[e-mail]>

See Also

read.GenBank.

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)

Example output

sh: 1: cannot create /dev/null: Permission denied
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 
Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4
Warning message:
'read.GB' is deprecated. Please use the 'rentrez', 'traits' or 'ape' packages. 
Warning message:
'read.GB' is deprecated. Please use the 'rentrez', 'traits' or 'ape' packages. 
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spider documentation built on May 2, 2019, 5:16 p.m.