Set NCBI download
Closed this issue · 2 comments
Set the appropiate code to download one or many GenBank IDs provided
Use python package ncbi-genome-download
https://pypi.org/project/ncbi-genome-download/
I did something similar but not quite the same using: edirect
. See code examples in BacterialTyper:
https://github.com/HCGB-IGTP/BacterialTyper/blob/master/BacterialTyper/scripts/edirect_caller.py
Ideally, we should manage to do something that uses both packages and allows to retreive: the first 100 complete genomes, from Staphylococcus aures. See intention in:
https://github.com/HCGB-IGTP/BacterialTyper/blob/master/BacterialTyper/scripts/get_descendant.py
See details to get_descendant here:
https://github.com/kblin/ncbi-genome-download/blob/master/contrib/gimme_taxa.py