[Biopython] fasta-m10 al_start and al_end?

[Peter]

On Mon, Oct 26, 2009 at 10:04 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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

Make that _al_start and _al_end (to match the field names used in
the FASTA output). This change is in the repository now, which you
can grab via github.  See http://www.biopython.org/wiki/SourceCode

As with any "private" variables (leading underscore), they are not
really intended for public use, but should at least solve your
immediate requirement for now.

Peter