ete3 toolkit usage

[McVeigh, Richard (NIH/NLM/NCBI) [C]]

Hi
I am trying to use the ete3 toolkit to populate ncbi tax lineage from a pandas dataframe and ultimately add the lineage into the dataframe. I have a dataframe with thousands of taxid where I want to obtain the lineages.

I am trying

orgtable = pd.read_csv(data_table, sep='\t', index_col=None, low_memory=False, usecols=[2,3,7], header=None, skiprows=1, names=["orgname", "taxid", "accession"]) taxid = [] for index, row in orgtable.iterrows():
taxid = orgtable['taxid'].astype(int)
lineage = ncbi.get_lineage(taxid)
print(lineage)


but getting I get ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
It's clearly unhappy with lineage = ncbi.get_lineage(taxid)

Any idea what I am doing wrong?

Thank you
Rich

[Alexandros Pittis]

Hi Rich,

Few rows of the data_table would be helpful. The "get_lineage" function takes a single taxid (integer or string) as argument, you seem to be providing a pandas Series there. That should be it.

Alexandros

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[L Thiberio Rangel]

Hi Rich,

here is a short example of the code I use to do this kind of work: https://gist.github.com/lthiberiol/a3dae750d1b64135490097c0eb4da66f

L. Thibério Rangel, Ph.D.

Postdoctoral Associate
Department of Earth, Atmospheric & Planetary Sciences
Massachusetts Institute of Technology
77 Massachusetts Ave
Cambridge, MA 02139

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