[Biopython-dev] Next release plans?
chapmanb at 50mail.com
Mon Jul 27 22:44:06 UTC 2009
> The FASTQ cross-validation is on going, as you may have
> gathered from the cross-project thread (now on open-bio-l)
> I did start testing against BioPerl SVN which uncovered
> some BioPerl problems, and a grey area of the format
> worth debate. See also:
> This is taking longer than I had expected, but think it will be
> worth the effort.
Glad you are tackling this -- fleshing out the incompatibilities is
tough work but will save a lot of headaches for people in the
> P.S. Anyone care to guess on how EMBOSS, BioPerl, and
> Biopython's FASTQ parsing stacks up in terms of run time?
We better be the fastest. Everyone knows that C code is bloated and
In terms of 1.51 and beyond, I've got two things:
- SQLite support: I'd love to push this in now for 1.51. If we have
a working version that people can test on, it'll encourage
adoption for the next BioSQL release.
- GFF parsing: The code is revamped to be more SeqIO like based on
the discussion you, Michiel and I had earlier, and the
documentation is in progress. I'll plan to get this in post-1.51
so people can work with it in git and find bugs.
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