taxdata2taxflat

Converts an NCBI taxonomy dump ("taxdata") to a flat tsv file with columns for recognized ranks.

How to run the program

The program is a Ruby script, requiring a reasonably recent version of Ruby. I think anything from 1.9 and up will work. (The default options system changed in 1.9.)

Clone the repository and place a symlink to the src/ruby/taxdata2taxflat script in a directory in your PATH variable.

Input files to the script are the nodes.dmp and names.dmp which can be downloaded from NCBI's ftp site as part of the taxdump.tar.gz:

$ wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz

After you've unpacked the tar ball somewhere, you generate the flat taxonomy file like this:

$ taxdata2taxflat --verbose nodes.dmp names.dmp > taxflat.tsv

You can get help from the program:

$ taxdata2taxflat --help