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More Recipes

Jun 24, 2014 at 3:22 PM
OK, Lawrence has just added another one - direct programmatic download of a gbk file from NCBI - and we have now three new students starting projects for the coming semester. So, we have some others related to mummer, gc content and similar matters which we will add over the coming days, but I'm sure there are others among you who might 'have a little list' of coding fragments that are currently missed...

Mark did a great job of kicking this off: one of the tricks is to build on these as pre-reqs or bookends (getting data in and out) for other recipes. Over time, we want the simple list not to be adequate. But for now - others that are crying out for discussion?

Some thoughts:
  • some more alignment examples with different aligners and settings
  • some canonical data selections which we then use in examples
  • some more parsing examples including obviously vcf
  • some newick based tree examples.
These are a few starting points, but we have students who need to get familiar with the libraries before they do proper projects, so we are going to use these as an 'orientation' exercise before the main course.

All suggestions welcome.