[Biopython] SIBsim4 alignment support

[Peter]

On Tue, May 4, 2010 at 3:22 PM, Martin Mokrejs
<mmokrejs at ribosome.natur.cuni.cz> wrote:
> Hi Peter,
>
>> How much of the data do you actually care about? Just the pairwise
>> alignment (two sequences)? Right now annotation support is limited
>
> If you give me just the two sequences without their coordinates in each
> chromosome and mRNA it would hep but is not "enough" for my
> _future_ work - see below.
> ;)
>
> ...
>
> Do you want to work on this project? ;-)

You will eventually want the coordinates... this is also something we'd
need to sort out for the FASTA m10 parser (and related examples
like the mooted BLAST pairwise alignment parser for Bio.AlignIO).
Right now neither the SeqRecord or alignment object support this.
I have no work related interest in SIBsim4 output, but this does touch
on several issues with alignment support which I am interested in.

Peter