How to get Taxonomy and Taxon ID for an Accession number using Python?

Question

[pramirez]

Hi! I am writing a python script to obtain the taxonomic classification to the phylum level of some protein sequences. I currently have the NCBI accession numbers (see question Retrieving taxonomy from entrez search in biopython). I realized that I need the taxon ID to search it in the taxonomy database to obtain the information about the phylum. Do you know how to do this in Python?

Many thanks!

Answer 1

[GenoMax]

Using EntrezDirect (you will need to translate this to biopython):

Following answers will work for both of your questions.

$ esearch -db protein -query OGI11933 | elink -target taxonomy | efetch -format native -mode xml | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName,TaxId
superkingdom    Archaea 2157
clade   DPANN group     1783276
phylum  Candidatus Micrarchaeota        1801631

$ esearch -db protein -query OGI11933 | elink -target taxonomy | efetch -format native -mode xml | xtract -pattern Taxon -block "*/Taxon" -if Rank -equals "phylum" -element ScientificName
Candidatus Micrarchaeota

[pramirez]

Thank you!