[Biopython] How to only extract the best alignment without looping with Bio.Align

[Peter Cock]

Oh good. We can probably add a line to the new pairwise aligner docstring
saying that then - e.g.

"All the alignments returned will have the same score, but differ in the
number
of gaps, matches and mismatches, and are listed in an unspecified order."

Peter

On Wed, Aug 14, 2024 at 1:48 PM Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> All alignments returned by the PairwiseAligner have the same score, and
> they are all equally good. Same is true for the alignments returned by
> pairwise2.
> So you just pick one of the alignments randomly, e.g. the first one:
> alignment = alignments[0]
> and then get whatever information you want from that alignment. This is
> essentially the same as what you would get from pairwise2.
> Note that the alignments, although they all have the same score, can have
> different number of gaps, matches, mismatches, so your problem may not be
> well-defined.
>
> Best,
> -Michiel
>
> On Wednesday, August 14, 2024 at 08:36:39 PM GMT+9, Peter Cock <
> p.j.a.cock at googlemail.com> wrote:
>
>
> Hello Slowat,
>
> Are you clear that there can be multiple equally scoring "best" alignments?
> This means the details of how you sort or rank pairwise alignments is
> important (i.e. how to tie-break alignments of the same score) and the
> "best" alignment may differ with usage context.
>
> Looking at the code in the old pairwise2 module, using one_alignment_only
> simply returns the first alignment - it wasn't immediately obvious to me if
> that would automatically be one of the  top scoring alignments or not.
>
> As far as I could see, the new PairwiseAligner docstring doesn't explicitly
> comment on how the alignments returned are sorted either:
>
>
> https://github.com/biopython/biopython/blob/biopython-184/Bio/Align/__init__.py#L3759
>
> This does need clarification, hopefully Markus or Michiel can comment.
>
> Peter
>
> On Wed, Aug 14, 2024 at 11:46 AM Slowat <slowat0kela at gmail.com> wrote:
>
> Hello -
>
> May I ask. I want to align two sequences, and return, for the optimal
> alignment only, the score, number of identities, mismatches, gaps etc.
>
> I can see that this is possible by using the 'one_alignment_only=True'
> parameter in the pairwise2 module, however when I load the pairwise2
> module, I get the message that this module is deprecated.
>
> Using Bio.Align, I can see how you can obtain the .score for the best
> alignment, but not how to obtain the other information I require about the
> best alignment.
>
> I don't want to loop through all the possible alignments, as this would be
> prohibitively time-consuming for me. Also, since the .score of the best
> alignment can be returned, it makes me think that the best alignment should
> be saved somewhere and I should be able to see it (even to calculate the
> gaps, identities and mismatches myself).
>
> Could someone explain how to go about this, without using the deprecated
> pairwise2 module?
>
> Thanks
> Slowat
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