I want to use this to convert a bunch of identifiers but I need to know exactly which taxonomic rank is assigned to each taxonomy code. Shown below is an example of conversion that makes sense but I don't know what to label some of the taxonomy calls. The basic taxonomic ranks are: (domain, kingdom, phylum, class, order, family, genus, and species) https://en.wikipedia.org/wiki/Taxonomic_rank.
For most cases it will be easy, but in the case of having subspecies and strains for bacteria this can get confusing.
How do I get ete3 to specify what rank the lineage IDs correspond to in the taxonomic rank?
import ete3
import pandas as pd
ncbi = ete3.NCBITaxa()
taxon_id = 505
lineage = ncbi.get_lineage(taxon_id)
Se_lineage = pd.Series(ncbi.get_taxid_translator(lineage), name=taxon_id)
Se_lineage[lineage]
1 root
131567 cellular organisms
2 Bacteria
1224 Proteobacteria
28216 Betaproteobacteria
206351 Neisseriales
481 Neisseriaceae
32257 Kingella
505 Kingella oralis
Name: 505, dtype: object
Use ncbi.get_rank() to get a dictionary of {id:name} then do some basic transformations to get {name:taxonomy}