Hello, I just packaged xpore, which points to https://github.com/openvax/pyensembl to get various sorts of sequencing data, also complete genomes. I like that and address its packaging now. New packages are uploaded to PyPi, not release tagged, but, well, ... .
In my reading this is a way to get test data for various applications of ours in a reproducible way. Since this packages only the routines to retrieve the data, not the data itself, we cannot use that for package autotests. However, we can still use it for testing our workflows if our workflow-test-environment is allowed to have internet access, which I think it should have. On a sidenote - that group is producing a series of interesting packages for individualised cancer vaccination, see https://github.com/openvax . The idea behind that is that you sequence the MHC region of the patient's genome (which is difficult to sequence since very redundant, but you know where to look and the Nanopore is about to help, too) so you learn what kind of peptides (protein fragments) the immune system is most likely to detect/accept as foreign that cancer cells are characteristic for the cancer cells and then you immunize against these. Best, Steffen
