[Biopython] fasta-m10 al_start and al_end?

[Peter]

On Fri, Oct 23, 2009 at 11:00 PM, Anne Pajon <ap12 at sanger.ac.uk> wrote:
>
> Hi Peter,
>
> Thanks for your fast answer.
>
> I've already discovered the _annotations and I am prepared to update my
> code as soon as a better solution is provided.

Good.

> Concerning the al_start and al_end, I am looking for a solution very soon,
> as I am working on an annotation pipeline prototype in python. What would be
> your recommendation? Writing a parser myself, using another tool (but which
> one?), or helping storing this information in SeqRecord in biopython as it
> is almost there. Thanks to let me know.

I would rather not add them directly to the SeqRecord annotations
dictionary because that will make doing something meaningful with
slicing (the SeqRecord, or in future the Alignment) much harder. I
think the best way to handle these is in the Alignment object, but
this isn't really supported at the moment.

Are you happy to run a development version of Biopython, or at least
to update the file Bio/AlignIO/FastaIO.py? I'm thinking in the short
term we can record these bits of information as private properties of
the SeqRecord, i.e. _al_start and _al_end

Would that suit you for now?

Peter