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Hi, I run into some consistency issues while working with TaxIDs that have been merged on NCBI's end. Le's take 2074836 and 2588313 as an example of what I mean.
1/ When I run ncbi.get_lineage(), I get back 2074836's lineage in both cases: [1, 131567, 2759, 33154, 4751, 451864, 4890, 716545, 147538, 716546, 715989, 147550, 222544, 5139, 35718, 2382315, 2074836]
2/ When I run ncbi.get_taxid_translator(), I get back both TaxID's in results: {2074836: 'Arxotrichum gangligerum'} {2588313: 'Arxotrichum gangligerum'}
3/ Finally, when I run ncbi.get_rank(), I get back the proper result for 2074836 but an empty dict for 2588313. {2074836: 'species'} {}
So, depending on the function call, the results can lead to different conclusions - (1) indicates they are the same species, (2) indicates that they might be different strains of the same species (due to different IDs) and (3) that one of the IDs is completely invalid.
So, I was hoping for some clarity on that, and perhaps some streamlining too, in order to avoid the confusing results?
The text was updated successfully, but these errors were encountered:
Hi, I run into some consistency issues while working with TaxIDs that have been merged on NCBI's end. Le's take 2074836 and 2588313 as an example of what I mean.
1/ When I run
ncbi.get_lineage()
, I get back 2074836's lineage in both cases:[1, 131567, 2759, 33154, 4751, 451864, 4890, 716545, 147538, 716546, 715989, 147550, 222544, 5139, 35718, 2382315, 2074836]
2/ When I run
ncbi.get_taxid_translator()
, I get back both TaxID's in results:{2074836: 'Arxotrichum gangligerum'}
{2588313: 'Arxotrichum gangligerum'}
3/ Finally, when I run
ncbi.get_rank()
, I get back the proper result for 2074836 but an empty dict for 2588313.{2074836: 'species'}
{}
So, depending on the function call, the results can lead to different conclusions - (1) indicates they are the same species, (2) indicates that they might be different strains of the same species (due to different IDs) and (3) that one of the IDs is completely invalid.
So, I was hoping for some clarity on that, and perhaps some streamlining too, in order to avoid the confusing results?
The text was updated successfully, but these errors were encountered: