python - ete3: How to get taxonomic rank names from taxonomy id? -
i want use convert bunch of identifiers need know taxonomic rank assigned each taxonomy code. shown below example of conversion makes sense don't know label of taxonomy calls. basic taxonomic ranks are: (domain, kingdom, phylum, class, order, family, genus, , species) https://en.wikipedia.org/wiki/taxonomic_rank.
for cases easy, in case of having subspecies , strains bacteria can confusing.
how ete3 specify rank lineage ids correspond in taxonomic rank?
import ete3 import pandas 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()
dictionary of {id:name}
basic transformations {name:taxonomy}
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