[Biopython] Bio.pairwise2

[Peter Cock]

I think what you were missing is alignment[0] and alignment[1] will
give the two sequences in a pairwise alignment from
Bio.Align.PairwiseAlignment - does that help?

Peter

On Tue, Mar 21, 2023 at 9:41 PM Vitoria Zanon <zanon.vih at gmail.com> wrote:
>
> Hello! I hope this email finds you well.
>
> My name is Vitoria and I'm currently using Biopython to develop a new multiple sequence alignment tool as my PhD project, specially the Bio.pairwise2 method, which is the main reason I'm writing this email: the deprecated warning told me I should talk to you about this.
>
> In my code, the pairwise2 method helps produce an alignment library which contains (n²-n)/2 pairwise alignments, being n the number of sequences in the input file. This library helps the COFFEE objective function (NOTREDAME et al., 1998) to evaluate the MSAs produced by the tool. I was using the Bio.Align.PairwiseAlignment method but I faced an issue with it: I couldn't get the aligned sequences from the PairwiseAlignment object as a Seq object, String or neither a SeqRecord object. The library should keep the name of the sequences, the sequences itself and the alignment score, but all I was able to do is to get the target/query sequences (unaligned) or the Align object itself, which wouldn't work for me. However with pairwise2 i was able to get the sequences and work with them as i planned to. I must admit the PairwiseAlignment has a more intuitive and useful class structure and I already thought about using it in other projects from our lab, but it doesn't work for this specific project in specific. I'm also sending a print from my code to illustrate the pairwise2 use.
>
> Therefore, I would like you to consider adding this feature in PairwiseAlignment or as a different method since you discontinued pairwise2. By now, my main objective is to finish the whole tool and test its results so I can get data about the performance of the new algorithm I'm proposing. After that I plan to make the tool available on the internet and I want to work with the latest releases from each library involved so it can work fine in any machine and improve its execution when the libraries themselves get improved.
>
> Thank you for reading!
>
> Sincerely yours,
> Vitoria
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