[BioRuby] BGZF support, was Re: Biopython 1.60 plans and beyond

[Raoul Bonnal]

Thanks Peter,
These are valuable hints.


On 22/05/12 13.07, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

> Hi all,
> 
> I've CC'd the BioRuby mailing list just to ensure you're aware of the
> potentially useful combination of MAF indexing and BGZF compression.
> We can continue this on the BioRuby list if more appropriate.
> 
> The start of this Biopython-dev thread is here:
> http://lists.open-bio.org/pipermail/biopython-dev/2012-April/009561.html
> 
> This might be a nice opportunity to combine the work of this year's OBF
> Google Summer of Code students - Clayton is doing MAF for BioRuby,
> and part of Artem's project could provide BGZF support for BioRuby.
> 
> On Fri, Apr 27, 2012 at 8:57 PM, Andrew Sczesnak
> <andrew.sczesnak at med.nyu.edu> wrote:
>> Peter,
>> 
>>> It should be easy enough to follow the BGZF changes to Bio/SeqIO/_index.py
>>> and I'm willing to do this myself for MAF (while going over your index
>>> work - something I want to do anyway). The only potential catch is
>>> avoiding offset arithmetic.
>> 
>> I have no problem with you doing this if you're willing. It would be great
>> to have some code review of MafIndex as well.
> 
> I'm not sure if Clayton will be able to comment on the Python code,
> but he should have some thoughts on the MAF indexing itself.
> 
> Regards,
> 
> Peter
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