[Biopython-dev] Next release plans?

Brad Chapman chapmanb at 50mail.com
Mon Jul 27 22:44:06 UTC 2009

Hi Peter;

> 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:
> http://lists.open-bio.org/pipermail/open-bio-l/2009-July/
> 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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