biocore/scikit-bio-cookbook — pull request #49 by wasade (2014-11-21 21:44:00+00:00)
Title: WIP: Workflow recipe

@gregcaporaso, can you comment on this when you have a chance? I'm still adding in text, a couple of methods for the `Workflow` itself, and a small block of code to drive the workflow.

The general flow is:

- define query methods against RNAcentral and NCBI
- show some examples of the queries
- construct a singular method for doing some processing of the sequence data (emphasizes complexity of the method)
- construct a `Workflow` for doing the same processing (emphasizes small light functions)
- Discuss downfalls to the `Workflow` (though it simplifies things, the reliance on common state requires care)

To do:

- [ ] define a common options `dict`
- [ ] finish the methods in the `Workflow`
- [ ] comment the NCBI query further
- [ ] add additional surrounding text on the cells
- [ ] briefly discuss code complexity
- [ ] discussion on pitfalls, etc