taxonomizr (version 0.2.2)

getAccession2taxid: Download accession2taxid files from NCBI

Description

Download a nucl_xxx.accession2taxid.gz from NCBI servers. These can then be used to create a SQLite datanase with read.accession2taxid. Note that if the files already exist in the target directory then this function will not redownload them. Delete the files if a fresh download is desired.

Usage

getAccession2taxid(outDir = ".",
  baseUrl = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/",
  types = c("nucl_gb", "nucl_est", "nucl_gss", "nucl_wgs"))

Arguments

outDir

the directory to put the accession2taxid.gz files in

baseUrl

the url of the directory where accession2taxid.gz files are located

types

the types if accession2taxid.gz files desired where type is the prefix of xxx.accession2taxid.gz. The default is to download all nucl_ accessions. For protein accessions, try types=c('prot').

Value

a vector of file path strings of the locations of the output files

References

ftp://ftp.ncbi.nih.gov/pub/taxonomy/, https://www.ncbi.nlm.nih.gov/Sequin/acc.html

See Also

read.accession2taxid

Examples

# NOT RUN {
  getAccession2taxid()
# }