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

Peter Cock p.j.a.cock at googlemail.com
Tue May 22 11:07:15 UTC 2012

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:

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.



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