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shenwei356 / taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
https://bioinf.shenwei.me/taxonkit
MIT License
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taxonkit reformat omits species for some species taxids #31

Closed Shellfishgene closed 4 years ago

Shellfishgene commented 4 years ago

Hi!

The following command does not output the species, I'm not sure why. Is this a bug or related to the taxonomy of this species in NCBI?

echo '272799' | taxonkit lineage --data-dir $BLASTDB | taxonkit --data-dir $BLASTDB reformat | csvtk -tH cut -f 1,3              
272799  Eukaryota;Chordata;Mammalia;Chiroptera;Vespertilionidae;Plecotus;

The full output of the taxon using

echo '272799' | taxonkit lineage --data-dir $BLASTDB

ends correctly with the species, Plecotus gaisleri. More example taxids where this happens: 2493713, 1629512, 602068

Thanks for all the nice programs!

shenwei356 commented 4 years ago

is 272799 species? check rank with taxonkit lineage -r

Shellfishgene commented 4 years ago

Ah, it's a subspecies, and there is no species. I didn't know that existed, does not make much sense to me. So it's just NCBI, thanks!