[Biopython-dev] Biopython 1.60 plans and beyond

Peter Cock p.j.a.cock at googlemail.com
Sat Feb 18 09:39:06 UTC 2012

Hi all,

Assuming we ship Biopython 1.59 soon (Feb 2012),
we should start thinking about what is ready to merge to
the trunk afterwards to be included in Biopython 1.60,
and what else is being worked on beyond that. This
might also help with GSoC project ideas.


Here are some things that I think are strong
candidates for 1.60 (not an exclusive list!)

MAF support (the multiple alignment format) for AlignIO,
including bespoke indexing (MAF specific).

BGZF support: Low level module like Python's gzip,
support in SeqIO for indexing BGZF compressed files,
and probably also indexing large MAF files too (I've
had some positive discussions off list about this).

Brad's GFF code. People are using this already,
so it probably is ready for inclusion (even if we do
need some fine tuning for SeqIO integration).

Official releases for Python 3 (even if we do call it
a beta status release). Maybe we can even do this
with Biopython 1.59? Most things are working (with
the exception of some C code and missing third
party dependencies), and my concerns about the
memory overhead of unicode strings should be
resolved with Python 3.3 (the parsing speed
overhead perhaps not).


Other work at various stages:

Ontologies, GO and OBO - several people are looking
at this stuff but is anything "ready" yet? I can't see
Chris Lasher's repository on github anymore.

VCF format? Variant Call Format - Tiago what's
you're impression of work in this area?

I know there are other things but I'm struggling
to recall them right now. If I've overlooked your
work it isn't malice but forgetfulness - please
reply with a status update.

So, what other cool things are you all working on,
and in particular what is ready or near-ready for
inclusion with Biopython this year?



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