Johannes Werner

Maybe this can be solved in concurrence with https://github.com/ropensci/biomartr/issues/6#issuecomment-788771908 (`taxonkit`).

I assume you are referring to something like [here](https://rstudio.com/resources/cheatsheets/)? @HajkD Do you believe that this is still relevant? After all, the [documentation of `biomartr`](https://docs.ropensci.org/biomartr/articles/) is very comprehensive. It might still...

Maybe stupid question, but what information is available in `assembly_summary.txt` that is required? @taylorreiter If this is still an active project of yours ... why do you open a new...

I did not work with `taxize` yet, I got the idea also from the `ncbi-genome-download` package. They have a python script (which uses `ete3`) that gets the descending taxa based...

Possibly linked with https://github.com/ropensci/biomartr/issues/6#issuecomment-788771908

https://github.com/shenwei356/taxonkit/issues/41

From the referenced issue > I wrote [Python bindings for TaxonKit](https://github.com/bioforensics/pytaxonkit) recently, if you’d like to use that as a reference. I primarily used the `Popen` construct in Python’s `subprocess`...

If I can help in any way with the package, let me know. I like it a lot. :-)

Thank you, the current developer version solved that issue, well, partly at least. But it still does not download all genomes. After the third attempt, it aborts after `Circoviridae 17...

For the record, I only tested with viral genomes.