[Biopython] Pairwise sequence aligner

[Peter Cock]

This looks interesting Michiel,

Could you turn this into a pull request to facilitate discussion on GitHub?
I'm sure Markus would be interested.

It looks like the new PairwiseAligner object is defined entirely in C code,
which something I am not overly familiar with (e.g. how easily can we
link this to the MultipleSeqAlignment class inheritance).

Peter

On Sun, Mar 11, 2018 at 2:37 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> Dear all,
>
> For my work I needed a fast pairwise sequence aligner with more fine-grained
> control over gap penalties.
> I have implemented a C extension to do this, which is available in this
> branch on github:
>
> https://github.com/mdehoon/biopython/tree/pairwise_aligner
>
> There is some rudimentary documentation in Doc/Tutorial/chapter_align.tex
> (under section 6.5).
> Examples can be found in Tests/test_pairwise_aligner.py.
>
> I think this aligner can be a replacement for pairwise2 aligner.
> In particular, it is more flexible and more Pythonic, using a
> PairwiseAligner object to store the alignment scoring scheme instead of
> interpreting the function name (as in pairwise2).
>
> Comments are welcome.
> Note that this aligner returns PairwiseAlignment objects; it may be better
> to integrate this with the existing MultipleSeqAlignment class in Bio/Align.
>
>
> Best,
> -Michiel
>
>
>
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