[Biopython] Start positions for local pairwise alignments?

[Peter Cock]

On Fri, Sep 7, 2012 at 9:51 AM, Jan T Kim <jttkim at googlemail.com> wrote:
>
> Ok, thanks for clarifying. I think I understand, I wasn't sure whether to
> expect that information in the Seq, the SeqRecord or the MultipleAlignment
> objects.
>
> For what it's worth, it currently would seem most adequate to me
> if a (say) AlignedSeq subclass of Seq could provide a couple of
> optional additional instance variables, such as the start index
> of the aligned sequence within the input sequence.
>
> I'd envision this information to be optional in the sense that the
> instance variable would be None if the start position is not
> available, which would obviously be the case for some alignment
> formats (for most multiple alignments, in fact).
>

That's exactly what we hope to have in the next release, see:
http://lists.open-bio.org/pipermail/biopython-dev/2012-September/009930.html

Regards,

Peter