[Biopython-dev] Next release plans?

[Peter]

On Thu, Jul 23, 2009 at 12:08 PM, Peter<biopython at maubp.freeserve.co.uk> wrote:
>
> The FASTQ checking is on going. I have updated our FASTQ
> code to map Solexa scores as I understood Peter Rice's
> description of the intended EMBOSS behaviour (this is for the
> corner case of very poor quality reads). However, due to a
> couple of minor bugs I found in EMBOSS 6.1.0 we'll either
> have to cross check against their CVS code, or hope they
> release EMBOSS 6.1.1 soon.
>
> Cross checking against MAQ would also be worthwhile, but
> while there are some patches about to fix a couple of MAQ
> FASTQ bugs and include Illumina to Sanger standard
> conversion, this isn't in their official repository yet.
>
> I guess I could cross check against BioPerl's new FASTQ
> support ...

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.

Peter

P.S. Anyone care to guess on how EMBOSS, BioPerl, and
Biopython's FASTQ parsing stacks up in terms of run time?