[Biopython-dev] Bio.Motif update

[Michiel de Hoon]

Hi Peter,

--- On Mon, 2/4/13, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Rather than having two (very similar) chapters in the
> Tutorial for the old Bio.Motif and new Bio.motifs modules,
> I've downgraded the old chapter to just a section of
> the new chapter:
... 
> There is still a lot of redundant content - would you be
> able to shorten this?

I think it's OK if it is redundant. Anyway the chapter on the older Bio.Motif will be removed a few releases later.

> I think a summary of the differences be more useful,
> to help people convert from the old module to the new
> motifs module.

Maybe, but for me it doesn't have a high priority. It's easier to understand the new chapter on Bio.motifs.
 
> Also, what is the point of the Bio.motifs.create function?
> Is there a reason not to initialise a Motif object directly?

There are two ways to initialize a Motif: either to specify the alignment from which the motif is created, or directly from a position-weight matrix. This can be a bit confusing. To separate the two, the Bio.motifs.create function only initializes a Motif from an alignment; some of the motif parsers initialize a Motif from a position-weight matrix. 

Best,
-Michiel.