ncbi-baltimore

Gets the Baltimore ranks (if applicable) from NCBI taxa IDs

Requirements

Requires:

If you're using Sunbeam, these requirements are already met, so I'd suggest simply switching to the sunbeam conda environment to run.

Step 1 Get a list of NCBI Taxonomy IDs, one per line.

If you're using Sunbeam, these can be found in the classify/all_samples.tsv in the first column.

Extract to a file using the following:

cut -f1 all_samples.tsv | tail -n +3 > taxids.txt

Step 2 Run get_lineages.py

python get_lineages.py -o lineages.txt < taxids.txt

Your output file should be a tab-delimited list with standard taxonomic ranks + Baltimore class for all tax ids passed in.

To check and confirm, run grep 'Viruses' lineages.txt and ensure the Baltimore class is shown immediately after 'Viruses'.