import of taxdump files

[nick-youngblut]

As far as I can tell from reading the docs & paper on taxa, the package cannot directly import from taxdump files. This would be helpful for importing custom taxdump files created from non-NCBI taxonomies (eg., taxdump files created from the GTDB taxonomy)

[zachary-foster]

Hi @nick-youngblut, thanks for the idea, I will look into it!

[zachary-foster]

After looking into this a bit, I am not sure what file type you mean. I found the following examples:

I see this on GTDB's website:

https://data.ace.uq.edu.au/public/gtdb/data/releases/latest/bac120_taxonomy.tsv

And these from NCBI:

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

https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz

Are one of these the format you were talking about?

[nick-youngblut]

Here's the taxdump that I created from the GTDB: http://ftp.tue.mpg.de/ebio/projects/struo/GTDB_release89/taxdump/

The simple script used to create it can be found at: https://github.com/nick-youngblut/gtdb_to_taxdump