[Biopython-dev] Alignment object

[Peter]

On Tue, Mar 2, 2010 at 3:03 PM, Brad Chapman <chapmanb at 50mail.com> wrote:
> Peter and Kevin;
>
>> >> My code does not (yet) attempt to deal with next-gen sequencing
>> >> alignments,
> [...]
>> >> Perhaps until this is settled, it would be premature to merge my
>> >> alignment class to the trunk. After all, we may need to tweak the
>> >> alignment object class heirachy.
>
> My vote would be to merge what you've done in for handling
> standard multiple alignments, and then look at next-generation read
> representation as an analogous but separate problem. All of the
> SeqRecord objects which are useful for drilling in on multiple
> alignments are likely going to be memory hogs for any real world
> next gen work.

OK - that is what I was leaning towards.

What do you think about the fact I am introducing an "improved"
version of the existing Bio.Align.Generic.Alignment class under
Bio.Align.MultipleSeqAlignment?

That's actually several questions in one - should this be a new
object or just enhance the old one? I favour a new object here
because I want to *enforce* the fact that all the rows are the
same length, but I doubt people are using the flexibility of
the current alignment object in this way.

Next where should the new object live? I find the current use
of Bio.Align.Generic somewhat hidden away, thus my
suggestion of using Bio.Align directly.

Next, what should the new object be called? We could reuse
the old name of Alignment but it is a bit vague and would
cause confusion given the existing object is also called that.
I have used MultipleSeqAlignment but am open to suggestions
(e.g. MulSeqAlignment is shorter).

Peter