[Biopython] GSoC - BioPython and PyCogent Interoperability

[Peter]

On Thu, Apr 8, 2010 at 10:41 AM, Singer Ma <sma.hmc at gmail.com> wrote:
> I am a junior Computer Science major with heavy bioinformatic leanings
> at Harvey Mudd College. I know that it is very late for new summer of
> code applications, but I was wondering if you could have a look at my
> proposed schedule to give me some pointers and answer a few questions.
> I am also considering applying for the project involving adding more
> ways to use R through python, but I was unsure of which project had
> more users who wanted it completed.
>
> Questions:
> What does it mean by BioPython's acquired sequences? I can't seem to
> find out what or where information about "acquired sequences" is.
> Thus, I do not discuss anything about it in my current proposal.

http://www.biopython.org/wiki/Google_Summer_of_Code#Biopython_and_PyCogent_interoperability

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.

> Week 6 and 7: Adapt PyCogent to query genomics databases. Currently
> there is at least some support for PyCogent to query ENSEMBL. It seems
> like it would be useful to query other genomics databases such as
> Entrez of NCBI. Unfortunately, it seems like NCBI only has PERL
> queries into their MySQL database. ...

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.

Peter