""" Script used to generate ncbi_subset_tax.json
NCBI taxonomy downloaded in 2019 July 1st.
"""
from taxonomy import Taxonomy
tax = Taxonomy.from_ncbi("nodes.dmp", "names.dmp")
new_tax = tax.prune(remove=['28384', '12908', '10239', '2', '2157'] +
[t for t in tax.children("2759") if t != "543769"])
with open("new_tax.json", "wb") as f:
f.write(new_tax.to_json(True))
def _create_tax(self):
return Taxonomy.from_ncbi("tests/data/ncbi_subset_tax.nodes.dmp",
"tests/data/ncbi_subset_tax.names.dmp")
