[Biopython] Bio.Motif search_pwm

[Michiel de Hoon]

Hi everybody,

> On Wed, Aug 1, 2012 at 7:14 AM, Michiel de Hoon <mjldehoon at yahoo.com>
> wrote:
> > Hi everybody,
> >
> > I was using the search_pwm method in Bio.Motif (which
> btw is very useful, thanks Bartek) to search for motif
> instances on both strands of a sequence. If the motif starts
> at position and is located on the forward strand, this
> function returns +position; if it is located on the reverse
> strand, it returns -position. So for position==0, we cannot
> deduce from the sign whether the motif is located on the
> forward or on the backward strand.
> >
> > How about using Python-style negative indices to
> indicate the strand? For example, +20 means that the motif
> is located at [20:20+motif_length] on the forward strand,
> while -20 means that the motif is located at
> [-20:-20+motif_length].
> 
> Very nice idea! +1 from me

Done; see https://github.com/biopython/biopython/commit/d7b67b7192b211b6bd1e4ca6e42eee55c2bc34a8

Best,
-Michiel.