gpha-mscape-taxaplease

What is this?

taxaPlease: A CLI utility and importable python module for wrangling NCBI taxids.

Installation?

## pip install straight from the github repo
pip install git+https://github.com/ukhsa-collaboration/gpha-mscape-taxaplease.git

When first instantiated, an NCBI taxonomy database will be downloaded. This only happens once.

What can it do?

For a given taxid, we can:

• get metadata (taxa name, rank, parent taxid)
• get the parent taxid
• find the corresponding species-level taxid
• find the corresponding genus-level taxid
• given two taxids, find the common parent taxid
• given two taxids, how many levels ("ranks") are between:
  • those two taxids (sum of the below)
  • each of those taxids and their common parent taxa
• given a taxid, is it:
  • Archaea?
  • Eukaryota?
  • Bacteria?
  • Virus?

How do I use it?

To use it in your code, have a look at demo.iypnb or just jump in and from taxaplease import TaxaPlease.

If you just want a commandline tool, try taxaplease -h to see what it can do.

Realistically, you're probably trying to do one of the following:

## get a record given a taxid
## >> {"taxid": 1337, "name": "Streptococcus hyointestinalis", "rank": "species", "parent_taxid": 1301}
taxaplease record --record 1337

## get a parent taxid
## >> 1301
taxaplease taxid --parent 1337

Each subcommand also has -h help information.

Where did that database come from?

From NCBI plus some wrangling.

The code for generating it is in database_generation/generate_database.py

Do you really need to include taxa like wolves and aloe vera?

Maybe not, but they're in there for now.

Where is the database stored?

In your home directory, in a .taxaplease folder. To recreate the database, you can just delete this folder.