[Biopython] fasta-m10 al_start and al_end?

[Peter]

On Mon, Oct 26, 2009 at 3:44 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> Hi Peter,
>
> Here's +1 for Python counting. That would match SeqFeature and the
> ProteinDomain class in Bio.Tree.PhyloXML.
>
> While we're on this topic -- I have some unpublished code for rendering an
> alignment object in HTML, with plans for colorization, conservation
> profiles, etc. I rolled my own alignment class since the one in
> Bio.Align.Generic didn't have the attributes (start, end, selected columns)
> for a particular file format I was parsing. It's not urgent, but at some
> point could you publish your plans for the Alignment classes so I (and
> probably others) can stay/become compatible?

My rough work in progress in on github - at the moment I'm still trying
things out, and don't assume anything is set in stone. If you want to
have a play with this code, feedback is very welcome - probably best
on the dev list rather than here. See:

http://github.com/peterjc/biopython/tree/seqrecords

(a lot of the alignment things I want to support, like slicing and adding
are very closely linked to doing the same operations to SeqRecords)

Peter