ncbitax

Utilities to navigate NCBI taxonomy dump files.

This package is part of the taxonomy namespace:

from taxonomy import ncbitax

Data files

The package needs NCBI's taxdump.tar.gz (~70 MB) and builds parquet and pickle caches from it (~180 MB more). None of this ships in the wheel, so ncbitax resolves a data directory at import time, in this order:

1. $NCBITAX_DATA_DIR, if set.
2. resources/ in the source checkout, when running from a git clone or an editable install.
3. $XDG_CACHE_HOME/ncbitax, defaulting to ~/.cache/ncbitax.

If the dump is not in that directory, it is downloaded from https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz the first time it is needed. Set NCBITAX_AUTO_DOWNLOAD=0 to turn that off; a missing dump then raises TaxdumpNotFoundError instead.

To fetch the dump ahead of time, for instance in a container build or CI step:

from taxonomy.ncbitax import download_taxdump

download_taxdump()

taxonomy.ncbitax.DATA_DIR reports the resolved directory.