These changes introduce a more refined genome download functionality. It takes into account several edge cases when interacting with the NCBI API.
If available it should now prefer reference genomes over representative genomes. If these are not available the latest genome will be downloaded. In case of several available genomes, it is checked if the taxid is correct as well. This is necessary because it can happen that under a species name also other genomes are deposited (eg. Wolbachia endosymbiont genomes for insects...).
The output of genome download is now also more verbose.
These changes introduce a more refined genome download functionality. It takes into account several edge cases when interacting with the NCBI API. If available it should now prefer reference genomes over representative genomes. If these are not available the latest genome will be downloaded. In case of several available genomes, it is checked if the taxid is correct as well. This is necessary because it can happen that under a species name also other genomes are deposited (eg. Wolbachia endosymbiont genomes for insects...). The output of genome download is now also more verbose.