[Biopython] GSoC - BioPython and PyCogent Interoperability

[Singer Ma]

> You mean "Connecting Biopython acquired sequences to PyCogent's
> alignment, phylogenetic tree preparation and tree visualization code."?
>
> I think Brad means using Biopython to load (parse) sequence data (e.g.
> with Bio.AlignIO), and then give this to PyCogent. i.e. Acquire data in
> the sense of get/load data.

Ah, so, its just the most straightforward use of the conversion tools
that would be made. Sorry, I thought I was missing something here.
Shouldn't be this be taken care of in the first use case of "Allow
round-trip conversion between biopython and pycogent core objects
(sequence, alignment, tree, etc.)."? Or does this require me to
determine how the interactions will be made?

>
> Are you are talking about the NCBI Entrez Utitlites (E-Utils)? Those are
> language neutral and we have Bio.Entrez to support them in Biopython.

Ah, I misread my information, so NCBI Entrez can already be queried.
What exactly do we need to get from ENSEMBL that isn't already
supported then?

Singer