Support individual gapped sequences for pairwise alignment

[Ellmen]

Currently, the PairwiseAlignment class does not allow you to get the gapped sequences individually. This makes it hard to grab the sequences to, for instance, store them as a specified filetype.

There could be gapped_target() and gapped_query() functions that return these sequences. These functions could also be used when generating the formatted string. It would also be helpful to directly save a pairwise alignment as a fasta or something but that could wait for another ticket.

I'm happy to take a stab at this if you think it makes sense.

https://github.com/biopython/biopython/blob/master/Bio/Align/__init__.py

[mdehoon]

@Ellmen It makes sense; I am happy to look at your proposed code. Probably it makes most sense if gapped_target and gapped_query return a string instead of a Seq object. Also, we may merge the PairwiseAlignment and MultipleSeqAlignment classes at some point, so it may be better to have a single function or attribute that takes an index (0 or 1 for now) instead of target/query.

[Ellmen]

@mdehoon great, I'll try to get to that today. I like the idea of merging the pairwise and MSA classes 👍

[mdehoon]

@Ellmen I believe this issue has been fixed by #3565 (which is in Biopython release 1.79). Please reopen this issue if it hasn't been solved.