[Biopython-dev] Next release plans?

Peter biopython at maubp.freeserve.co.uk
Tue Jul 28 12:07:23 UTC 2009

On Mon, Jul 27, 2009 at 11:44 PM, Brad Chapman<chapmanb at 50mail.com> wrote:
> 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 future.


>> 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 slow.

I pretty sure that was tongue in check, but if you were being mean
you probably could describe some of the EMBOSS infrastructure
as bloat. In any case, I'm sure that EMBOSS can be made faster
now that speed matters here with next generation sequencing, see:

And I've got bad news for you then - currently EMBOSS seqret
is about twice as fast as CVS Biopython SeqIO (measuring parsing
versus writing is a bit tricky). However, I have a cunning plan:


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