taxonomizr (version 0.8.0)

getNamesAndNodes: Download names and nodes files from NCBI

Description

Download a taxdump.tar.gz file from NCBI servers and extract the names.dmp and nodes.dmp files from it. These can then be used to create a SQLite database with read.names.sql and read.nodes.sql. 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

getNamesAndNodes(
  outDir = ".",
  url = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz",
  fileNames = c("names.dmp", "nodes.dmp")
)

Arguments

outDir

the directory to put names.dmp and nodes.dmp in

url

the url where taxdump.tar.gz is located

fileNames

the filenames desired from the tar.gz file

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/Taxonomy/taxonomyhome.html/

See Also

read.nodes.sql, read.names.sql

Examples

# NOT RUN {
  getNamesAndNodes()
# }