[Biopython] bug with pairwise2 local alignments?

[Peter Cock]

On Thu, Sep 6, 2012 at 9:31 PM, Jocelyne <jocelyne at gmail.com> wrote:
> Hello:
> First, I'd like to say that I really appreciate the effort of the community
> to provide us with such a nice package.
> I found some odd scoring behavior with the pairwise2 local alignment (see 5
> below). I think these 2 alignments should have the same score.

Hmm. I'm not overly familiar with this bit of the code, but did
occur to me it might be something related to this open issue:

https://redmine.open-bio.org/issues/2776

I was able to repeat your pairwise2.align.localms example
and the score matrix example a Mac using the latest code
from github, and got the same answers. So (as I suspected)
this does not seem to be a platform specific issue.

Unfortunately the original author of this code (Jeff Chang)
isn't active with Biopython anymore - we can try emailing
him directly, but if you're willing to look into this in more
detail and can propose a fix, I'm happy to take a look at
merging it.

Peter