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Suggestion for tutorial section on get_descendant_taxa()

Open W-L opened this issue 4 years ago • 1 comments

Hi, Not really an issue or a bug, just a small suggestion. I ran into a slightly confusing situation while trying to get all taxonomy ids for mammals.

mammals = ncbi.get_descendant_taxa(40674, collapse_subspecies=False)

Retrieved like this, Homo sapiens (9606) is not included. I guess this is because 9606 is an internal node in ncbi's taxonomy. Thus,

mammals = ncbi.get_descendant_taxa(40674, collapse_subspecies=False, intermediate_nodes=True)`

includes it. The tutorial section on getting descendant taxa does not have an explanation of intermediate_nodes at the moment, which might be worthwhile for situations like this. Or cases like the one in this related issue: #369

W-L avatar Apr 06 '20 12:04 W-L

I think intermediate_nodes should set to True by default. That's the real meaning of "descendant".

seahurt avatar Mar 15 '22 06:03 seahurt