Convert NCBI taxdump to binary formated OBITools taxonomy database

buildOBITaxonomy.py -t <taxdump dir> -d <db name>

Convert an text dump directory of the NCBI Taxonomy database to the binary format used by ecoPCR and many OBITools scripts. An archive corresponding to this directory can be downloaded at the following URL

ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

obitools common options

-h, --help
show this help message and exit
--DEBUG
Set logging in debug mode
--no-psyco
Don’t use psyco even if it installed

example

for building a new taxonomy database named ncbitaxonomy from a taxdump dir

% curl ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz | tar zxf -
% buildOBITaxonomy.py --taxonomy-dump taxdump --database ncbitaxonomy