Wei Shen

I'm still fixing it.

I got it. For the case of " a chain of taxids being merged" ``` // previous: A -> B // current : B -> C ``` Previously: // change...

I'm exhausted, leave it another day. > I think taxonkit's logic is as close as we can get to a "documentation" I don't get it.

Here's the way how I defined a merging event. ``` // tree is a hash table mapping a child taxid to its parent. // For GTDB taxonomy, genome assembly accessions...

No existing one, but you can create it by yourself following the [example](https://bioinf.shenwei.me/taxonkit/usage/#create-taxdump), using the binaries [here](https://github.com/shenwei356/taxonkit/issues/70#issuecomment-1326378899).

Taxa should be tab-separated, as shown in [Example 4](https://bioinf.shenwei.me/taxonkit/usage/#create-taxdump). 1. Prepare lineages $ echo -e "129138\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Pseudomonas amygdali" \ | sed 's/;/\t/g' \ | cut -f 2-8 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales...

If you need to map the Silver TaxIDs to the created ones. $ echo -e "129138\tBacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Pseudomonas amygdali" \ | sed 's/;/\t/g' \ | taxonkit create-taxdump -R "superkingdom,phylum,class,order,famil,genus,species" -O taxdump2 -A...

Sure, please follow the [usage and examples](https://bioinf.shenwei.me/taxonkit/usage/#lca).

It just maps custom IDs to TaxIDs of the taxa of the lowest rank, e.g. species. If you need to map to taxa of other ranks, like the genus Staphylococcus....

So, mapping only IDs to taxa of species rank is reasonable. Back to the previous concern, why did you want map IDs to the genus Staphylococcus? > For a particular...